Starting phenix.real_space_refine on Mon Mar 18 04:27:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3v_0827/03_2024/6l3v_0827_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3v_0827/03_2024/6l3v_0827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3v_0827/03_2024/6l3v_0827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3v_0827/03_2024/6l3v_0827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3v_0827/03_2024/6l3v_0827_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3v_0827/03_2024/6l3v_0827_trim_updated.pdb" } resolution = 2.63 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= 0.001 sd= 0.276 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: 5 Type Number sf(0) Gaussians S 66 5.16 5 C 6516 2.51 5 N 1620 2.21 5 O 1686 1.98 5 H 9528 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 209": "OE1" <-> "OE2" Residue "F ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19416 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3167 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "B" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3167 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "C" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3167 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "D" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3167 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "E" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3167 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "F" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3167 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.84, per 1000 atoms: 0.46 Number of scatterers: 19416 At special positions: 0 Unit cell: (114.779, 121.683, 94.067, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 O 1686 8.00 N 1620 7.00 C 6516 6.00 H 9528 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 180 " distance=2.04 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 180 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 169 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 180 " distance=2.04 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 169 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 180 " distance=2.04 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 174 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 169 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 12.89 Conformation dependent library (CDL) restraints added in 1.5 seconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 6 sheets defined 70.6% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 4.207A pdb=" N ALA A 11 " --> pdb=" O ARG A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 22 No H-bonds generated for 'chain 'A' and resid 19 through 22' Processing helix chain 'A' and resid 24 through 44 Proline residue: A 41 - end of helix Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 73 through 84 Processing helix chain 'A' and resid 86 through 106 removed outlier: 3.684A pdb=" N HIS A 102 " --> pdb=" O HIS A 98 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU A 104 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU A 105 " --> pdb=" O TRP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 158 removed outlier: 3.808A pdb=" N LEU A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 213 removed outlier: 3.612A pdb=" N LEU A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'B' and resid 3 through 13 removed outlier: 4.207A pdb=" N ALA B 11 " --> pdb=" O ARG B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 22 No H-bonds generated for 'chain 'B' and resid 19 through 22' Processing helix chain 'B' and resid 24 through 44 Proline residue: B 41 - end of helix Processing helix chain 'B' and resid 60 through 68 Processing helix chain 'B' and resid 73 through 84 Processing helix chain 'B' and resid 86 through 106 removed outlier: 3.685A pdb=" N HIS B 102 " --> pdb=" O HIS B 98 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU B 105 " --> pdb=" O TRP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 158 removed outlier: 3.808A pdb=" N LEU B 134 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA B 136 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 213 removed outlier: 3.613A pdb=" N LEU B 210 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 220 Processing helix chain 'C' and resid 3 through 13 removed outlier: 4.207A pdb=" N ALA C 11 " --> pdb=" O ARG C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 22 No H-bonds generated for 'chain 'C' and resid 19 through 22' Processing helix chain 'C' and resid 24 through 44 Proline residue: C 41 - end of helix Processing helix chain 'C' and resid 60 through 68 Processing helix chain 'C' and resid 73 through 84 Processing helix chain 'C' and resid 86 through 106 removed outlier: 3.685A pdb=" N HIS C 102 " --> pdb=" O HIS C 98 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU C 104 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU C 105 " --> pdb=" O TRP C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 158 removed outlier: 3.807A pdb=" N LEU C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 213 removed outlier: 3.612A pdb=" N LEU C 210 " --> pdb=" O THR C 206 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 220 Processing helix chain 'D' and resid 3 through 13 removed outlier: 4.207A pdb=" N ALA D 11 " --> pdb=" O ARG D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 22 No H-bonds generated for 'chain 'D' and resid 19 through 22' Processing helix chain 'D' and resid 24 through 44 Proline residue: D 41 - end of helix Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 73 through 84 Processing helix chain 'D' and resid 86 through 106 removed outlier: 3.685A pdb=" N HIS D 102 " --> pdb=" O HIS D 98 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU D 105 " --> pdb=" O TRP D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 158 removed outlier: 3.808A pdb=" N LEU D 134 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP D 135 " --> pdb=" O LEU D 131 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA D 136 " --> pdb=" O ARG D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 213 removed outlier: 3.613A pdb=" N LEU D 210 " --> pdb=" O THR D 206 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU D 213 " --> pdb=" O GLU D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 220 Processing helix chain 'E' and resid 3 through 13 removed outlier: 4.207A pdb=" N ALA E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 22 No H-bonds generated for 'chain 'E' and resid 19 through 22' Processing helix chain 'E' and resid 24 through 44 Proline residue: E 41 - end of helix Processing helix chain 'E' and resid 60 through 68 Processing helix chain 'E' and resid 73 through 84 Processing helix chain 'E' and resid 86 through 106 removed outlier: 3.685A pdb=" N HIS E 102 " --> pdb=" O HIS E 98 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU E 104 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU E 105 " --> pdb=" O TRP E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 158 removed outlier: 3.808A pdb=" N LEU E 134 " --> pdb=" O SER E 130 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA E 136 " --> pdb=" O ARG E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 213 removed outlier: 3.613A pdb=" N LEU E 210 " --> pdb=" O THR E 206 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU E 213 " --> pdb=" O GLU E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 220 Processing helix chain 'F' and resid 3 through 13 removed outlier: 4.207A pdb=" N ALA F 11 " --> pdb=" O ARG F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 22 No H-bonds generated for 'chain 'F' and resid 19 through 22' Processing helix chain 'F' and resid 24 through 44 Proline residue: F 41 - end of helix Processing helix chain 'F' and resid 60 through 68 Processing helix chain 'F' and resid 73 through 84 Processing helix chain 'F' and resid 86 through 106 removed outlier: 3.685A pdb=" N HIS F 102 " --> pdb=" O HIS F 98 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU F 104 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU F 105 " --> pdb=" O TRP F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 158 removed outlier: 3.807A pdb=" N LEU F 134 " --> pdb=" O SER F 130 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP F 135 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA F 136 " --> pdb=" O ARG F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 213 removed outlier: 3.612A pdb=" N LEU F 210 " --> pdb=" O THR F 206 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 220 Processing sheet with id= A, first strand: chain 'A' and resid 51 through 53 removed outlier: 3.530A pdb=" N ILE A 178 " --> pdb=" O CYS A 169 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS A 169 " --> pdb=" O ILE A 178 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 51 through 53 removed outlier: 3.530A pdb=" N ILE B 178 " --> pdb=" O CYS B 169 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS B 169 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 51 through 53 removed outlier: 3.530A pdb=" N ILE C 178 " --> pdb=" O CYS C 169 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS C 169 " --> pdb=" O ILE C 178 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 51 through 53 removed outlier: 3.530A pdb=" N ILE D 178 " --> pdb=" O CYS D 169 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS D 169 " --> pdb=" O ILE D 178 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 51 through 53 removed outlier: 3.530A pdb=" N ILE E 178 " --> pdb=" O CYS E 169 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS E 169 " --> pdb=" O ILE E 178 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 51 through 53 removed outlier: 3.530A pdb=" N ILE F 178 " --> pdb=" O CYS F 169 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS F 169 " --> pdb=" O ILE F 178 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1764 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: 6.74 Time building geometry restraints manager: 13.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9516 1.03 - 1.23: 22 1.23 - 1.42: 4350 1.42 - 1.62: 5738 1.62 - 1.82: 84 Bond restraints: 19710 Sorted by residual: bond pdb=" CBS LMN F 301 " pdb=" CCM LMN F 301 " ideal model delta sigma weight residual 1.529 1.617 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" CBS LMN B 301 " pdb=" CCM LMN B 301 " ideal model delta sigma weight residual 1.529 1.617 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" CBS LMN A 301 " pdb=" CCM LMN A 301 " ideal model delta sigma weight residual 1.529 1.617 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CBS LMN C 301 " pdb=" CCM LMN C 301 " ideal model delta sigma weight residual 1.529 1.617 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CBS LMN E 301 " pdb=" CCM LMN E 301 " ideal model delta sigma weight residual 1.529 1.617 -0.088 2.00e-02 2.50e+03 1.92e+01 ... (remaining 19705 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.07: 981 107.07 - 113.80: 21995 113.80 - 120.53: 7094 120.53 - 127.27: 5131 127.27 - 134.00: 169 Bond angle restraints: 35370 Sorted by residual: angle pdb=" CA ARG A 220 " pdb=" CB ARG A 220 " pdb=" CG ARG A 220 " ideal model delta sigma weight residual 114.10 120.12 -6.02 2.00e+00 2.50e-01 9.05e+00 angle pdb=" CA ARG C 220 " pdb=" CB ARG C 220 " pdb=" CG ARG C 220 " ideal model delta sigma weight residual 114.10 120.05 -5.95 2.00e+00 2.50e-01 8.86e+00 angle pdb=" CA ARG B 220 " pdb=" CB ARG B 220 " pdb=" CG ARG B 220 " ideal model delta sigma weight residual 114.10 120.05 -5.95 2.00e+00 2.50e-01 8.86e+00 angle pdb=" CA ARG D 220 " pdb=" CB ARG D 220 " pdb=" CG ARG D 220 " ideal model delta sigma weight residual 114.10 120.05 -5.95 2.00e+00 2.50e-01 8.85e+00 angle pdb=" CA ARG F 220 " pdb=" CB ARG F 220 " pdb=" CG ARG F 220 " ideal model delta sigma weight residual 114.10 120.05 -5.95 2.00e+00 2.50e-01 8.84e+00 ... (remaining 35365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.14: 8850 24.14 - 48.27: 612 48.27 - 72.41: 252 72.41 - 96.55: 60 96.55 - 120.68: 78 Dihedral angle restraints: 9852 sinusoidal: 5562 harmonic: 4290 Sorted by residual: dihedral pdb=" OAU LMN A 301 " pdb=" CCR LMN A 301 " pdb=" CCV LMN A 301 " pdb=" OBY LMN A 301 " ideal model delta sinusoidal sigma weight residual 182.69 62.01 120.68 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" OAU LMN E 301 " pdb=" CCR LMN E 301 " pdb=" CCV LMN E 301 " pdb=" OBY LMN E 301 " ideal model delta sinusoidal sigma weight residual 182.69 62.04 120.65 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" OAU LMN C 301 " pdb=" CCR LMN C 301 " pdb=" CCV LMN C 301 " pdb=" OBY LMN C 301 " ideal model delta sinusoidal sigma weight residual 182.69 62.05 120.64 1 3.00e+01 1.11e-03 1.61e+01 ... (remaining 9849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1272 0.044 - 0.087: 198 0.087 - 0.131: 75 0.131 - 0.174: 9 0.174 - 0.218: 18 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CCQ LMN C 301 " pdb=" CCF LMN C 301 " pdb=" CCH LMN C 301 " pdb=" OCB LMN C 301 " both_signs ideal model delta sigma weight residual False -2.61 -2.39 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CCQ LMN A 301 " pdb=" CCF LMN A 301 " pdb=" CCH LMN A 301 " pdb=" OCB LMN A 301 " both_signs ideal model delta sigma weight residual False -2.61 -2.39 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CCQ LMN D 301 " pdb=" CCF LMN D 301 " pdb=" CCH LMN D 301 " pdb=" OCB LMN D 301 " both_signs ideal model delta sigma weight residual False -2.61 -2.39 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1569 not shown) Planarity restraints: 2778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 18 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO F 19 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO F 19 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 19 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 18 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO C 19 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 19 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 19 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 18 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO B 19 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 19 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 19 " 0.023 5.00e-02 4.00e+02 ... (remaining 2775 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 3151 2.30 - 2.88: 40234 2.88 - 3.45: 43556 3.45 - 4.03: 61066 4.03 - 4.60: 94281 Nonbonded interactions: 242288 Sorted by model distance: nonbonded pdb=" O CYS B 202 " pdb=" HG1 THR B 206 " model vdw 1.725 1.850 nonbonded pdb=" O CYS D 202 " pdb=" HG1 THR D 206 " model vdw 1.726 1.850 nonbonded pdb=" O CYS E 202 " pdb=" HG1 THR E 206 " model vdw 1.726 1.850 nonbonded pdb=" O CYS F 202 " pdb=" HG1 THR F 206 " model vdw 1.727 1.850 nonbonded pdb=" O CYS C 202 " pdb=" HG1 THR C 206 " model vdw 1.728 1.850 ... (remaining 242283 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.280 Extract box with map and model: 8.260 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 58.170 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 : 0.009 0.088 10182 Z= 0.582 Angle : 0.925 7.353 13818 Z= 0.402 Chirality : 0.043 0.218 1572 Planarity : 0.006 0.042 1644 Dihedral : 24.543 120.682 4164 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 5.45 % Allowed : 3.03 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -5.00 (0.16), residues: 1182 helix: -3.18 (0.11), residues: 858 sheet: -1.56 (0.56), residues: 60 loop : -3.20 (0.29), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 103 HIS 0.006 0.001 HIS E 69 PHE 0.010 0.001 PHE C 31 TYR 0.006 0.001 TYR F 137 ARG 0.006 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 149 time to evaluate : 1.481 Fit side-chains REVERT: A 8 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7252 (ttp-170) REVERT: A 47 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7828 (mt-10) REVERT: A 132 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6180 (tpm170) REVERT: A 135 TRP cc_start: 0.7789 (m-10) cc_final: 0.7270 (m100) REVERT: A 220 ARG cc_start: 0.4292 (OUTLIER) cc_final: 0.3600 (mtt-85) REVERT: B 4 ARG cc_start: 0.6383 (ttt-90) cc_final: 0.6115 (ttp-110) REVERT: B 8 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7395 (ttp80) REVERT: B 132 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6333 (tpm170) REVERT: B 135 TRP cc_start: 0.7696 (m-10) cc_final: 0.7190 (m100) REVERT: B 220 ARG cc_start: 0.3899 (OUTLIER) cc_final: 0.3371 (mtt90) REVERT: C 4 ARG cc_start: 0.6414 (ttt-90) cc_final: 0.6206 (ttp-110) REVERT: C 8 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7285 (ttp-170) REVERT: C 12 GLU cc_start: 0.7878 (tp30) cc_final: 0.7642 (tp30) REVERT: C 132 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6130 (tpm170) REVERT: C 135 TRP cc_start: 0.7808 (m-10) cc_final: 0.7275 (m100) REVERT: C 220 ARG cc_start: 0.4204 (OUTLIER) cc_final: 0.3534 (mtt-85) REVERT: D 8 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7315 (ttp-170) REVERT: D 132 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6073 (tpm170) REVERT: D 135 TRP cc_start: 0.7764 (m-10) cc_final: 0.7273 (m100) REVERT: D 220 ARG cc_start: 0.4344 (OUTLIER) cc_final: 0.3549 (mtt-85) REVERT: E 8 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7372 (ttp80) REVERT: E 47 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7823 (mt-10) REVERT: E 132 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6230 (tpt170) REVERT: E 135 TRP cc_start: 0.7691 (m-10) cc_final: 0.7217 (m100) REVERT: E 187 GLU cc_start: 0.8344 (tt0) cc_final: 0.8108 (tt0) REVERT: E 220 ARG cc_start: 0.3850 (OUTLIER) cc_final: 0.3345 (mtt-85) REVERT: F 4 ARG cc_start: 0.6311 (ttt-90) cc_final: 0.6006 (ttp-110) REVERT: F 8 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7368 (ttp80) REVERT: F 47 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7928 (mt-10) REVERT: F 132 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.6463 (tpm170) REVERT: F 135 TRP cc_start: 0.7650 (m-10) cc_final: 0.7131 (m100) REVERT: F 220 ARG cc_start: 0.4060 (OUTLIER) cc_final: 0.3549 (mtt90) outliers start: 54 outliers final: 4 residues processed: 184 average time/residue: 4.1013 time to fit residues: 788.3411 Evaluate side-chains 142 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 CYS Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 2 CYS Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 2 CYS Chi-restraints excluded: chain D residue 8 ARG Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 132 ARG Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 2 CYS Chi-restraints excluded: chain F residue 8 ARG Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 220 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 10182 Z= 0.271 Angle : 0.816 9.536 13818 Z= 0.385 Chirality : 0.044 0.214 1572 Planarity : 0.006 0.037 1644 Dihedral : 21.265 93.093 2146 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 3.13 % Allowed : 7.98 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.64 (0.22), residues: 1182 helix: 0.50 (0.16), residues: 858 sheet: -1.27 (0.56), residues: 60 loop : -3.17 (0.29), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 103 HIS 0.003 0.001 HIS C 54 PHE 0.011 0.002 PHE F 94 TYR 0.009 0.002 TYR F 159 ARG 0.004 0.001 ARG E 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 1.533 Fit side-chains revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6929 (ttp-170) REVERT: A 132 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6994 (ttt-90) REVERT: A 220 ARG cc_start: 0.4556 (OUTLIER) cc_final: 0.3719 (mtt-85) REVERT: B 8 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6757 (ttp-170) REVERT: B 132 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6179 (tpm170) REVERT: B 220 ARG cc_start: 0.4325 (OUTLIER) cc_final: 0.3457 (mtt-85) REVERT: C 8 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6821 (ttp-170) REVERT: C 132 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.5964 (tpm170) REVERT: C 220 ARG cc_start: 0.4290 (OUTLIER) cc_final: 0.3468 (mtt-85) REVERT: D 8 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6931 (ttp-170) REVERT: D 132 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6107 (tpm170) REVERT: D 220 ARG cc_start: 0.4610 (OUTLIER) cc_final: 0.3671 (mtt-85) REVERT: E 8 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6833 (ttp80) REVERT: E 47 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7832 (mt-10) REVERT: E 132 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6150 (tpm170) REVERT: E 220 ARG cc_start: 0.4366 (OUTLIER) cc_final: 0.3531 (mtt-85) REVERT: F 4 ARG cc_start: 0.5663 (ttt-90) cc_final: 0.5449 (ttp80) REVERT: F 8 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6802 (ttp-170) REVERT: F 47 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7848 (mt-10) REVERT: F 132 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6329 (tpm170) REVERT: F 220 ARG cc_start: 0.4189 (OUTLIER) cc_final: 0.3486 (mtt-85) outliers start: 31 outliers final: 10 residues processed: 147 average time/residue: 3.8169 time to fit residues: 588.3333 Evaluate side-chains 143 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 115 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 CYS Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 2 CYS Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 2 CYS Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 2 CYS Chi-restraints excluded: chain D residue 8 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 132 ARG Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 2 CYS Chi-restraints excluded: chain F residue 8 ARG Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 220 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10182 Z= 0.269 Angle : 0.704 8.118 13818 Z= 0.326 Chirality : 0.046 0.363 1572 Planarity : 0.006 0.037 1644 Dihedral : 16.961 90.908 2146 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 4.04 % Allowed : 7.68 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.48 (0.24), residues: 1182 helix: 1.43 (0.18), residues: 858 sheet: -0.82 (0.57), residues: 60 loop : -3.25 (0.29), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 101 HIS 0.003 0.001 HIS C 54 PHE 0.011 0.002 PHE C 94 TYR 0.010 0.002 TYR E 156 ARG 0.002 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6962 (ttp-170) REVERT: A 101 TRP cc_start: 0.6839 (m-10) cc_final: 0.6563 (m100) REVERT: A 132 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6081 (tpm170) REVERT: A 220 ARG cc_start: 0.4666 (OUTLIER) cc_final: 0.3676 (mtt-85) REVERT: B 8 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6787 (ttp-170) REVERT: B 101 TRP cc_start: 0.6902 (m-10) cc_final: 0.6685 (m-10) REVERT: B 132 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6173 (tpm170) REVERT: B 220 ARG cc_start: 0.4444 (OUTLIER) cc_final: 0.3501 (mtt-85) REVERT: C 8 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6802 (ttp-170) REVERT: C 132 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6116 (tpm170) REVERT: C 220 ARG cc_start: 0.4375 (OUTLIER) cc_final: 0.3543 (mtt-85) REVERT: D 8 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6923 (ttp-170) REVERT: D 101 TRP cc_start: 0.7008 (m-10) cc_final: 0.6703 (m-10) REVERT: D 132 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6179 (tpm170) REVERT: D 220 ARG cc_start: 0.4678 (OUTLIER) cc_final: 0.3669 (mtt-85) REVERT: E 8 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6742 (ttp-170) REVERT: E 101 TRP cc_start: 0.7038 (m-10) cc_final: 0.6822 (m-10) REVERT: E 132 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6129 (tpm170) REVERT: E 220 ARG cc_start: 0.4386 (OUTLIER) cc_final: 0.3487 (mtt-85) REVERT: F 8 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6831 (ttp-170) REVERT: F 47 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7866 (mt-10) REVERT: F 132 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6223 (tpm170) REVERT: F 220 ARG cc_start: 0.4251 (OUTLIER) cc_final: 0.3590 (mtt-85) outliers start: 40 outliers final: 7 residues processed: 149 average time/residue: 3.6492 time to fit residues: 571.5673 Evaluate side-chains 138 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 8 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 132 ARG Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 8 ARG Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 220 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 10182 Z= 0.239 Angle : 0.657 5.737 13818 Z= 0.306 Chirality : 0.042 0.318 1572 Planarity : 0.005 0.037 1644 Dihedral : 15.639 94.016 2142 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 3.33 % Allowed : 9.19 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.04 (0.25), residues: 1182 helix: 1.85 (0.18), residues: 864 sheet: -0.29 (0.59), residues: 60 loop : -3.30 (0.29), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 77 HIS 0.001 0.000 HIS D 54 PHE 0.010 0.002 PHE F 51 TYR 0.011 0.002 TYR B 156 ARG 0.004 0.000 ARG E 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 119 time to evaluate : 1.416 Fit side-chains revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6882 (ttp-170) REVERT: A 101 TRP cc_start: 0.7009 (m-10) cc_final: 0.6554 (m-10) REVERT: A 132 ARG cc_start: 0.7337 (ttt-90) cc_final: 0.6175 (tpm170) REVERT: A 220 ARG cc_start: 0.4650 (OUTLIER) cc_final: 0.3588 (mtt-85) REVERT: B 8 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6666 (ttp-170) REVERT: B 101 TRP cc_start: 0.6901 (m-10) cc_final: 0.6634 (m-10) REVERT: B 132 ARG cc_start: 0.7388 (ttt-90) cc_final: 0.6190 (tpt170) REVERT: B 220 ARG cc_start: 0.4483 (OUTLIER) cc_final: 0.3464 (mtt-85) REVERT: C 6 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.6956 (mp) REVERT: C 8 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6722 (ttp-170) REVERT: C 101 TRP cc_start: 0.6879 (m-10) cc_final: 0.6579 (m100) REVERT: C 132 ARG cc_start: 0.7292 (ttt-90) cc_final: 0.6156 (tpm170) REVERT: C 220 ARG cc_start: 0.4272 (OUTLIER) cc_final: 0.3410 (mtt-85) REVERT: D 8 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6801 (ttp-170) REVERT: D 101 TRP cc_start: 0.7032 (m-10) cc_final: 0.6588 (m-10) REVERT: D 132 ARG cc_start: 0.7438 (ttt-90) cc_final: 0.6225 (tpm170) REVERT: D 220 ARG cc_start: 0.4664 (OUTLIER) cc_final: 0.3525 (mtt-85) REVERT: E 8 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6651 (ttp-170) REVERT: E 101 TRP cc_start: 0.7003 (m-10) cc_final: 0.6751 (m-10) REVERT: E 132 ARG cc_start: 0.7377 (ttt-90) cc_final: 0.6176 (tpt170) REVERT: E 220 ARG cc_start: 0.4542 (OUTLIER) cc_final: 0.3530 (mtt-85) REVERT: F 8 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6836 (ttp-170) REVERT: F 47 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7856 (mt-10) REVERT: F 101 TRP cc_start: 0.6895 (m-10) cc_final: 0.6551 (m100) REVERT: F 132 ARG cc_start: 0.7307 (ttt-90) cc_final: 0.6217 (tpm170) REVERT: F 220 ARG cc_start: 0.4338 (OUTLIER) cc_final: 0.3583 (mtt-85) outliers start: 33 outliers final: 9 residues processed: 143 average time/residue: 3.8274 time to fit residues: 573.9002 Evaluate side-chains 137 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 2 CYS Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 8 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 8 ARG Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 220 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.9990 chunk 65 optimal weight: 0.0270 chunk 1 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10182 Z= 0.145 Angle : 0.554 4.680 13818 Z= 0.260 Chirality : 0.035 0.213 1572 Planarity : 0.005 0.033 1644 Dihedral : 14.655 98.902 2118 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.83 % Allowed : 10.00 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.26), residues: 1182 helix: 2.19 (0.18), residues: 900 sheet: 0.63 (0.69), residues: 60 loop : -3.28 (0.31), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP F 101 HIS 0.002 0.000 HIS C 69 PHE 0.009 0.001 PHE B 31 TYR 0.008 0.001 TYR B 156 ARG 0.003 0.000 ARG C 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 1.502 Fit side-chains revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6726 (ttp-170) REVERT: A 16 ARG cc_start: 0.7874 (ptp90) cc_final: 0.7606 (mtm110) REVERT: A 101 TRP cc_start: 0.6879 (m-10) cc_final: 0.6370 (m-10) REVERT: A 132 ARG cc_start: 0.7299 (ttt-90) cc_final: 0.6103 (tpm170) REVERT: A 220 ARG cc_start: 0.4593 (OUTLIER) cc_final: 0.4184 (ttm110) REVERT: B 6 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7055 (mp) REVERT: B 8 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.6656 (ttp-170) REVERT: B 101 TRP cc_start: 0.6848 (m-10) cc_final: 0.6492 (m-10) REVERT: B 132 ARG cc_start: 0.7363 (ttt-90) cc_final: 0.6153 (tpt170) REVERT: B 220 ARG cc_start: 0.4431 (OUTLIER) cc_final: 0.3400 (mtt-85) REVERT: C 4 ARG cc_start: 0.5974 (ttt-90) cc_final: 0.5773 (ttp-110) REVERT: C 6 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.6997 (mp) REVERT: C 8 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6740 (ttp-170) REVERT: C 101 TRP cc_start: 0.6768 (m-10) cc_final: 0.6550 (m100) REVERT: C 132 ARG cc_start: 0.7248 (ttt-90) cc_final: 0.6132 (tpm170) REVERT: C 220 ARG cc_start: 0.4526 (OUTLIER) cc_final: 0.3570 (mtt-85) REVERT: D 8 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6735 (ttp-170) REVERT: D 101 TRP cc_start: 0.6917 (m-10) cc_final: 0.6399 (m-10) REVERT: D 132 ARG cc_start: 0.7350 (ttt-90) cc_final: 0.6172 (tpm170) REVERT: D 220 ARG cc_start: 0.4677 (OUTLIER) cc_final: 0.4203 (ttm110) REVERT: E 8 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6600 (ttp-170) REVERT: E 101 TRP cc_start: 0.6816 (m-10) cc_final: 0.6472 (m-10) REVERT: E 132 ARG cc_start: 0.7337 (ttt-90) cc_final: 0.6143 (tpm170) REVERT: E 220 ARG cc_start: 0.4537 (OUTLIER) cc_final: 0.3579 (mtt-85) REVERT: F 6 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7115 (mp) REVERT: F 8 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6751 (ttp-170) REVERT: F 16 ARG cc_start: 0.7717 (ptp90) cc_final: 0.7412 (mtm110) REVERT: F 47 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7775 (mt-10) REVERT: F 101 TRP cc_start: 0.6737 (m-10) cc_final: 0.6502 (m100) REVERT: F 132 ARG cc_start: 0.7284 (ttt-90) cc_final: 0.6225 (tpm170) REVERT: F 220 ARG cc_start: 0.4420 (OUTLIER) cc_final: 0.3659 (mtt-85) outliers start: 28 outliers final: 8 residues processed: 138 average time/residue: 3.8714 time to fit residues: 559.5764 Evaluate side-chains 141 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 8 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 140 GLN Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 8 ARG Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 220 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10182 Z= 0.237 Angle : 0.604 5.120 13818 Z= 0.286 Chirality : 0.037 0.180 1572 Planarity : 0.005 0.036 1644 Dihedral : 14.855 99.099 2118 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.13 % Allowed : 9.90 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.62 (0.25), residues: 1182 helix: 2.09 (0.18), residues: 906 sheet: 0.73 (0.66), residues: 60 loop : -3.52 (0.31), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 77 HIS 0.001 0.001 HIS D 157 PHE 0.009 0.002 PHE A 51 TYR 0.015 0.002 TYR B 156 ARG 0.002 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6807 (ttp-170) REVERT: A 16 ARG cc_start: 0.7833 (ptp90) cc_final: 0.7603 (mtm110) REVERT: A 101 TRP cc_start: 0.6941 (m-10) cc_final: 0.6446 (m-10) REVERT: A 132 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6214 (tpm170) REVERT: A 220 ARG cc_start: 0.4572 (OUTLIER) cc_final: 0.4150 (ttm110) REVERT: B 8 ARG cc_start: 0.7064 (OUTLIER) cc_final: 0.6581 (ttp-170) REVERT: B 101 TRP cc_start: 0.6933 (m-10) cc_final: 0.6622 (m-10) REVERT: B 132 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6214 (tpt170) REVERT: B 220 ARG cc_start: 0.4566 (OUTLIER) cc_final: 0.3456 (mtt-85) REVERT: C 4 ARG cc_start: 0.6090 (ttt-90) cc_final: 0.5866 (ttp-110) REVERT: C 6 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7020 (mp) REVERT: C 8 ARG cc_start: 0.7147 (ttt-90) cc_final: 0.6707 (ttp-170) REVERT: C 101 TRP cc_start: 0.6832 (m-10) cc_final: 0.6534 (m100) REVERT: C 132 ARG cc_start: 0.7389 (ttt-90) cc_final: 0.6223 (tpm170) REVERT: C 220 ARG cc_start: 0.4494 (OUTLIER) cc_final: 0.3526 (mtt-85) REVERT: D 8 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6798 (ttp-170) REVERT: D 101 TRP cc_start: 0.6964 (m-10) cc_final: 0.6452 (m-10) REVERT: D 132 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6262 (tpm170) REVERT: D 220 ARG cc_start: 0.4550 (OUTLIER) cc_final: 0.4183 (ttm110) REVERT: E 6 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7191 (mp) REVERT: E 8 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6596 (ttp-170) REVERT: E 101 TRP cc_start: 0.6956 (m-10) cc_final: 0.6650 (m-10) REVERT: E 132 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6163 (tpt170) REVERT: E 220 ARG cc_start: 0.4487 (OUTLIER) cc_final: 0.3499 (mtt-85) REVERT: F 6 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7046 (mp) REVERT: F 8 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6736 (ttp-170) REVERT: F 16 ARG cc_start: 0.7743 (ptp90) cc_final: 0.7495 (mtm110) REVERT: F 47 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7782 (mt-10) REVERT: F 101 TRP cc_start: 0.6789 (m-10) cc_final: 0.6518 (m100) REVERT: F 132 ARG cc_start: 0.7312 (ttt-90) cc_final: 0.6220 (tpm170) REVERT: F 220 ARG cc_start: 0.4362 (OUTLIER) cc_final: 0.3649 (mtt-85) outliers start: 31 outliers final: 11 residues processed: 138 average time/residue: 4.0033 time to fit residues: 577.6438 Evaluate side-chains 146 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 8 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 132 ARG Chi-restraints excluded: chain E residue 140 GLN Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 8 ARG Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 220 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10182 Z= 0.297 Angle : 0.626 5.463 13818 Z= 0.299 Chirality : 0.038 0.170 1572 Planarity : 0.006 0.038 1644 Dihedral : 14.891 93.483 2114 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.54 % Allowed : 9.70 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.25), residues: 1182 helix: 2.00 (0.18), residues: 906 sheet: 0.90 (0.66), residues: 60 loop : -3.53 (0.31), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 77 HIS 0.002 0.001 HIS F 98 PHE 0.011 0.002 PHE A 51 TYR 0.013 0.002 TYR E 156 ARG 0.003 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 123 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6814 (ttp-170) REVERT: A 16 ARG cc_start: 0.7820 (ptp90) cc_final: 0.7196 (ptp-110) REVERT: A 101 TRP cc_start: 0.6956 (m-10) cc_final: 0.6461 (m-10) REVERT: A 132 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6302 (tpm170) REVERT: A 220 ARG cc_start: 0.4532 (OUTLIER) cc_final: 0.4176 (ttm110) REVERT: B 8 ARG cc_start: 0.7085 (ttt-90) cc_final: 0.6599 (ttp-170) REVERT: B 101 TRP cc_start: 0.6907 (m-10) cc_final: 0.6601 (m-10) REVERT: B 132 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6293 (tpt170) REVERT: B 135 TRP cc_start: 0.7234 (m-10) cc_final: 0.6775 (m100) REVERT: B 220 ARG cc_start: 0.4493 (OUTLIER) cc_final: 0.3470 (mtt-85) REVERT: C 4 ARG cc_start: 0.6177 (ttt-90) cc_final: 0.5769 (ttp-110) REVERT: C 6 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7048 (mp) REVERT: C 8 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6702 (ttp-170) REVERT: C 101 TRP cc_start: 0.6837 (m-10) cc_final: 0.6537 (m-10) REVERT: C 132 ARG cc_start: 0.7426 (ttt-90) cc_final: 0.6233 (tpm170) REVERT: C 135 TRP cc_start: 0.7207 (m-10) cc_final: 0.6710 (m100) REVERT: C 220 ARG cc_start: 0.4511 (OUTLIER) cc_final: 0.3555 (mtt-85) REVERT: D 8 ARG cc_start: 0.7231 (ttt-90) cc_final: 0.6788 (ttp-170) REVERT: D 101 TRP cc_start: 0.6972 (m-10) cc_final: 0.6466 (m-10) REVERT: D 132 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6330 (tpm170) REVERT: D 220 ARG cc_start: 0.4700 (OUTLIER) cc_final: 0.4297 (ttm110) REVERT: E 8 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6604 (ttp-170) REVERT: E 101 TRP cc_start: 0.6956 (m-10) cc_final: 0.6671 (m-10) REVERT: E 132 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6388 (tpt170) REVERT: E 135 TRP cc_start: 0.7208 (m-10) cc_final: 0.6769 (m100) REVERT: E 220 ARG cc_start: 0.4445 (OUTLIER) cc_final: 0.3558 (mtt-85) REVERT: F 6 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7018 (mp) REVERT: F 8 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6736 (ttp-170) REVERT: F 16 ARG cc_start: 0.7756 (ptp90) cc_final: 0.7524 (mtm110) REVERT: F 47 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7819 (mt-10) REVERT: F 132 ARG cc_start: 0.7467 (ttt-90) cc_final: 0.6342 (tpm170) REVERT: F 135 TRP cc_start: 0.7278 (m-10) cc_final: 0.6749 (m100) REVERT: F 220 ARG cc_start: 0.4446 (OUTLIER) cc_final: 0.3588 (mtt-85) outliers start: 35 outliers final: 13 residues processed: 145 average time/residue: 3.9281 time to fit residues: 596.2715 Evaluate side-chains 150 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 2 CYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 132 ARG Chi-restraints excluded: chain E residue 140 GLN Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 8 ARG Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 220 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10182 Z= 0.196 Angle : 0.575 5.139 13818 Z= 0.275 Chirality : 0.035 0.143 1572 Planarity : 0.005 0.037 1644 Dihedral : 14.505 94.671 2106 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 3.43 % Allowed : 10.40 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.77 (0.26), residues: 1182 helix: 2.18 (0.18), residues: 906 sheet: 1.15 (0.71), residues: 60 loop : -3.51 (0.31), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 101 HIS 0.001 0.000 HIS C 69 PHE 0.009 0.001 PHE F 51 TYR 0.011 0.002 TYR B 156 ARG 0.002 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7181 (ttt-90) cc_final: 0.6728 (ttp-170) REVERT: A 16 ARG cc_start: 0.7824 (ptp90) cc_final: 0.7149 (ptp-110) REVERT: A 101 TRP cc_start: 0.6971 (m-10) cc_final: 0.6462 (m-10) REVERT: A 132 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6256 (tpm170) REVERT: A 220 ARG cc_start: 0.4569 (OUTLIER) cc_final: 0.4219 (ttm110) REVERT: B 8 ARG cc_start: 0.7037 (ttt-90) cc_final: 0.6593 (ttp-170) REVERT: B 101 TRP cc_start: 0.6830 (m-10) cc_final: 0.6508 (m-10) REVERT: B 132 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6248 (tpt170) REVERT: B 135 TRP cc_start: 0.7089 (m-10) cc_final: 0.6633 (m100) REVERT: B 220 ARG cc_start: 0.4524 (OUTLIER) cc_final: 0.3464 (mtt-85) REVERT: C 4 ARG cc_start: 0.6130 (ttt-90) cc_final: 0.5782 (ttp-110) REVERT: C 6 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7024 (mp) REVERT: C 8 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6718 (ttp-170) REVERT: C 132 ARG cc_start: 0.7396 (ttt-90) cc_final: 0.6242 (tpm170) REVERT: C 220 ARG cc_start: 0.4523 (OUTLIER) cc_final: 0.4218 (ttm110) REVERT: D 8 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6731 (ttp-170) REVERT: D 101 TRP cc_start: 0.6957 (m-10) cc_final: 0.6441 (m-10) REVERT: D 132 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6286 (tpm170) REVERT: D 220 ARG cc_start: 0.4660 (OUTLIER) cc_final: 0.4277 (ttm110) REVERT: E 8 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6668 (ttp-170) REVERT: E 101 TRP cc_start: 0.6854 (m-10) cc_final: 0.6521 (m-10) REVERT: E 132 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6249 (tpt170) REVERT: E 135 TRP cc_start: 0.7074 (m-10) cc_final: 0.6631 (m100) REVERT: E 220 ARG cc_start: 0.4486 (OUTLIER) cc_final: 0.3559 (mtt-85) REVERT: F 6 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6999 (mp) REVERT: F 8 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6682 (ttp-170) REVERT: F 47 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7760 (mt-10) REVERT: F 132 ARG cc_start: 0.7462 (ttt-90) cc_final: 0.6303 (tpm170) REVERT: F 220 ARG cc_start: 0.4458 (OUTLIER) cc_final: 0.3570 (mtt-85) outliers start: 34 outliers final: 12 residues processed: 145 average time/residue: 3.8887 time to fit residues: 591.0998 Evaluate side-chains 148 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 2 CYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 8 ARG Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 132 ARG Chi-restraints excluded: chain E residue 140 GLN Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 8 ARG Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 220 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10182 Z= 0.198 Angle : 0.563 5.259 13818 Z= 0.269 Chirality : 0.035 0.137 1572 Planarity : 0.006 0.079 1644 Dihedral : 14.197 94.163 2102 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.83 % Allowed : 11.11 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.92 (0.26), residues: 1182 helix: 2.28 (0.18), residues: 906 sheet: 1.34 (0.73), residues: 60 loop : -3.48 (0.31), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 101 HIS 0.001 0.000 HIS C 69 PHE 0.009 0.001 PHE C 51 TYR 0.012 0.002 TYR E 156 ARG 0.014 0.000 ARG F 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7166 (ttt-90) cc_final: 0.6750 (ttp-170) REVERT: A 16 ARG cc_start: 0.7898 (ptp90) cc_final: 0.7162 (ptp-110) REVERT: A 132 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6261 (tpm170) REVERT: A 220 ARG cc_start: 0.4654 (OUTLIER) cc_final: 0.4299 (ttm110) REVERT: B 8 ARG cc_start: 0.7062 (ttt-90) cc_final: 0.6624 (ttp-170) REVERT: B 101 TRP cc_start: 0.6778 (m-10) cc_final: 0.6435 (m-10) REVERT: B 132 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6259 (tpt170) REVERT: B 220 ARG cc_start: 0.4590 (OUTLIER) cc_final: 0.3546 (mtt-85) REVERT: C 4 ARG cc_start: 0.6132 (ttt-90) cc_final: 0.5809 (ttp-110) REVERT: C 8 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6692 (ttp-170) REVERT: C 132 ARG cc_start: 0.7406 (ttt-90) cc_final: 0.6253 (tpm170) REVERT: C 220 ARG cc_start: 0.4508 (OUTLIER) cc_final: 0.4201 (ttm110) REVERT: D 8 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6748 (ttp-170) REVERT: D 132 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6268 (tpm170) REVERT: D 220 ARG cc_start: 0.4760 (OUTLIER) cc_final: 0.4384 (ttm110) REVERT: E 8 ARG cc_start: 0.7007 (ttt-90) cc_final: 0.6647 (ttp-170) REVERT: E 101 TRP cc_start: 0.6835 (m-10) cc_final: 0.6478 (m-10) REVERT: E 132 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6248 (tpt170) REVERT: E 220 ARG cc_start: 0.4482 (OUTLIER) cc_final: 0.3519 (mtt90) REVERT: F 8 ARG cc_start: 0.7112 (ttt-90) cc_final: 0.6650 (ttp-170) REVERT: F 16 ARG cc_start: 0.7347 (mtm110) cc_final: 0.6873 (ptp-110) REVERT: F 47 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7760 (mt-10) REVERT: F 132 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6284 (tpm170) REVERT: F 220 ARG cc_start: 0.4413 (OUTLIER) cc_final: 0.3516 (mtt-85) outliers start: 28 outliers final: 12 residues processed: 139 average time/residue: 3.9891 time to fit residues: 580.5153 Evaluate side-chains 143 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 2 CYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 8 ARG Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 132 ARG Chi-restraints excluded: chain E residue 140 GLN Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 220 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.0980 chunk 79 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10182 Z= 0.197 Angle : 0.563 5.309 13818 Z= 0.270 Chirality : 0.034 0.137 1572 Planarity : 0.005 0.042 1644 Dihedral : 13.850 93.854 2094 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.73 % Allowed : 11.62 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.98 (0.26), residues: 1182 helix: 2.32 (0.18), residues: 906 sheet: 1.42 (0.73), residues: 60 loop : -3.45 (0.31), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 77 HIS 0.001 0.000 HIS C 69 PHE 0.010 0.001 PHE A 31 TYR 0.012 0.002 TYR B 156 ARG 0.008 0.000 ARG F 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7161 (ttt-90) cc_final: 0.6744 (ttp-170) REVERT: A 16 ARG cc_start: 0.7921 (ptp90) cc_final: 0.7161 (ptp-110) REVERT: A 132 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6234 (tpm170) REVERT: A 220 ARG cc_start: 0.4644 (OUTLIER) cc_final: 0.4325 (ttm110) REVERT: B 8 ARG cc_start: 0.7039 (ttt-90) cc_final: 0.6590 (ttp-170) REVERT: B 101 TRP cc_start: 0.6809 (m-10) cc_final: 0.6440 (m-10) REVERT: B 132 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6271 (tpt170) REVERT: B 220 ARG cc_start: 0.4605 (OUTLIER) cc_final: 0.3541 (mtt-85) REVERT: C 4 ARG cc_start: 0.6135 (ttt-90) cc_final: 0.5822 (ttp-110) REVERT: C 8 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6647 (ttp-170) REVERT: C 132 ARG cc_start: 0.7417 (ttt-90) cc_final: 0.6259 (tpm170) REVERT: C 220 ARG cc_start: 0.4463 (OUTLIER) cc_final: 0.4202 (ttm110) REVERT: D 8 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6747 (ttp-170) REVERT: D 132 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6275 (tpm170) REVERT: D 220 ARG cc_start: 0.4697 (OUTLIER) cc_final: 0.4345 (ttm110) REVERT: E 8 ARG cc_start: 0.6983 (ttt-90) cc_final: 0.6637 (ttp-170) REVERT: E 101 TRP cc_start: 0.6850 (m-10) cc_final: 0.6514 (m-10) REVERT: E 132 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6252 (tpt170) REVERT: E 220 ARG cc_start: 0.4466 (OUTLIER) cc_final: 0.3540 (mtt90) REVERT: F 8 ARG cc_start: 0.7095 (ttt-90) cc_final: 0.6633 (ttp-170) REVERT: F 16 ARG cc_start: 0.7518 (mtm110) cc_final: 0.6883 (ptp-110) REVERT: F 47 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7768 (mt-10) REVERT: F 132 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6305 (tpm170) outliers start: 27 outliers final: 12 residues processed: 139 average time/residue: 3.9507 time to fit residues: 574.7131 Evaluate side-chains 143 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 2 CYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 8 ARG Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 132 ARG Chi-restraints excluded: chain E residue 140 GLN Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 132 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.145687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.105595 restraints weight = 29706.818| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.85 r_work: 0.3054 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10182 Z= 0.141 Angle : 0.521 5.126 13818 Z= 0.250 Chirality : 0.032 0.112 1572 Planarity : 0.005 0.072 1644 Dihedral : 13.385 95.281 2090 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.32 % Allowed : 12.02 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.26), residues: 1182 helix: 2.58 (0.18), residues: 900 sheet: 1.57 (0.75), residues: 60 loop : -3.11 (0.32), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.000 TRP B 103 HIS 0.001 0.000 HIS C 69 PHE 0.007 0.001 PHE C 51 TYR 0.009 0.001 TYR E 156 ARG 0.011 0.000 ARG F 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8910.92 seconds wall clock time: 155 minutes 8.66 seconds (9308.66 seconds total)