Starting phenix.real_space_refine on Mon Mar 18 06:38:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3t_0825/03_2024/6l3t_0825_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3t_0825/03_2024/6l3t_0825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3t_0825/03_2024/6l3t_0825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3t_0825/03_2024/6l3t_0825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3t_0825/03_2024/6l3t_0825_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3t_0825/03_2024/6l3t_0825_trim_updated.pdb" } resolution = 2.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 6540 2.51 5 N 1638 2.21 5 O 1890 1.98 5 H 9588 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 12": "OE1" <-> "OE2" Residue "A ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A ARG 170": "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 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B ARG 170": "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 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C ARG 170": "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 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D ARG 170": "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 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 12": "OE1" <-> "OE2" Residue "E ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E ARG 170": "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 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 12": "OE1" <-> "OE2" Residue "F ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F ARG 170": "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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19722 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "B" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "C" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "D" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "E" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "F" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 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} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Time building chain proxies: 9.09, per 1000 atoms: 0.46 Number of scatterers: 19722 At special positions: 0 Unit cell: (112.391, 121.813, 93.547, 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 1890 8.00 N 1638 7.00 C 6540 6.00 H 9588 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 180 " distance=2.04 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=2.04 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=2.04 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=2.04 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: 15.42 Conformation dependent library (CDL) restraints added in 2.0 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: 2172 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 6 sheets defined 69.2% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 3.625A 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 103 Processing helix chain 'A' and resid 130 through 159 removed outlier: 3.606A pdb=" N LEU A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 213 removed outlier: 3.589A pdb=" N LEU A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 219 Processing helix chain 'B' and resid 3 through 13 removed outlier: 3.625A 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 103 Processing helix chain 'B' and resid 130 through 159 removed outlier: 3.606A pdb=" N LEU B 134 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 213 removed outlier: 3.589A pdb=" N LEU B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 219 Processing helix chain 'C' and resid 3 through 13 removed outlier: 3.626A 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 103 Processing helix chain 'C' and resid 130 through 159 removed outlier: 3.607A pdb=" N LEU C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 213 removed outlier: 3.589A pdb=" N LEU C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 219 Processing helix chain 'D' and resid 3 through 13 removed outlier: 3.625A 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 103 Processing helix chain 'D' and resid 130 through 159 removed outlier: 3.607A pdb=" N LEU D 134 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP D 135 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 213 removed outlier: 3.589A pdb=" N LEU D 213 " --> pdb=" O GLU D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 219 Processing helix chain 'E' and resid 3 through 13 removed outlier: 3.625A 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 103 Processing helix chain 'E' and resid 130 through 159 removed outlier: 3.607A pdb=" N LEU E 134 " --> pdb=" O SER E 130 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 213 removed outlier: 3.590A pdb=" N LEU E 213 " --> pdb=" O GLU E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 219 Processing helix chain 'F' and resid 3 through 13 removed outlier: 3.626A 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 103 Processing helix chain 'F' and resid 130 through 159 removed outlier: 3.608A pdb=" N LEU F 134 " --> pdb=" O SER F 130 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP F 135 " --> pdb=" O LEU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 213 removed outlier: 3.590A pdb=" N LEU F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 219 Processing sheet with id= A, first strand: chain 'A' and resid 51 through 53 Processing sheet with id= B, first strand: chain 'B' and resid 51 through 53 Processing sheet with id= C, first strand: chain 'C' and resid 51 through 53 Processing sheet with id= D, first strand: chain 'D' and resid 51 through 53 Processing sheet with id= E, first strand: chain 'E' and resid 51 through 53 Processing sheet with id= F, first strand: chain 'F' and resid 51 through 53 612 hydrogen bonds defined for protein. 1818 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: 6.45 Time building geometry restraints manager: 16.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9576 1.03 - 1.23: 27 1.23 - 1.43: 4377 1.43 - 1.62: 5748 1.62 - 1.82: 84 Bond restraints: 19812 Sorted by residual: bond pdb=" CCJ LMN C 301 " pdb=" OBV LMN C 301 " ideal model delta sigma weight residual 1.378 1.466 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CCJ LMN E 301 " pdb=" OBV LMN E 301 " ideal model delta sigma weight residual 1.378 1.465 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" CCJ LMN F 301 " pdb=" OBV LMN F 301 " ideal model delta sigma weight residual 1.378 1.465 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" CCJ LMN D 301 " pdb=" OBV LMN D 301 " ideal model delta sigma weight residual 1.378 1.465 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" CCJ LMN A 301 " pdb=" OBV LMN A 301 " ideal model delta sigma weight residual 1.378 1.465 -0.087 2.00e-02 2.50e+03 1.89e+01 ... (remaining 19807 not shown) Histogram of bond angle deviations from ideal: 101.71 - 108.92: 9475 108.92 - 116.12: 15027 116.12 - 123.33: 9150 123.33 - 130.54: 1826 130.54 - 137.74: 72 Bond angle restraints: 35550 Sorted by residual: angle pdb=" C GLU E 172 " pdb=" N PRO E 173 " pdb=" CA PRO E 173 " ideal model delta sigma weight residual 127.00 137.74 -10.74 2.40e+00 1.74e-01 2.00e+01 angle pdb=" C GLU F 172 " pdb=" N PRO F 173 " pdb=" CA PRO F 173 " ideal model delta sigma weight residual 127.00 137.73 -10.73 2.40e+00 1.74e-01 2.00e+01 angle pdb=" C GLU C 172 " pdb=" N PRO C 173 " pdb=" CA PRO C 173 " ideal model delta sigma weight residual 127.00 137.73 -10.73 2.40e+00 1.74e-01 2.00e+01 angle pdb=" C GLU A 172 " pdb=" N PRO A 173 " pdb=" CA PRO A 173 " ideal model delta sigma weight residual 127.00 137.71 -10.71 2.40e+00 1.74e-01 1.99e+01 angle pdb=" C GLU D 172 " pdb=" N PRO D 173 " pdb=" CA PRO D 173 " ideal model delta sigma weight residual 127.00 137.69 -10.69 2.40e+00 1.74e-01 1.98e+01 ... (remaining 35545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.02: 8824 19.02 - 38.04: 618 38.04 - 57.06: 308 57.06 - 76.07: 96 76.07 - 95.09: 48 Dihedral angle restraints: 9894 sinusoidal: 5592 harmonic: 4302 Sorted by residual: dihedral pdb=" CAZ LMN D 301 " pdb=" CBB LMN D 301 " pdb=" CBD LMN D 301 " pdb=" CBF LMN D 301 " ideal model delta sinusoidal sigma weight residual 180.29 85.20 95.09 1 3.00e+01 1.11e-03 1.16e+01 dihedral pdb=" CAZ LMN A 301 " pdb=" CBB LMN A 301 " pdb=" CBD LMN A 301 " pdb=" CBF LMN A 301 " ideal model delta sinusoidal sigma weight residual 180.29 85.23 95.06 1 3.00e+01 1.11e-03 1.16e+01 dihedral pdb=" CAZ LMN C 301 " pdb=" CBB LMN C 301 " pdb=" CBD LMN C 301 " pdb=" CBF LMN C 301 " ideal model delta sinusoidal sigma weight residual 180.29 85.24 95.05 1 3.00e+01 1.11e-03 1.16e+01 ... (remaining 9891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1213 0.046 - 0.092: 277 0.092 - 0.138: 66 0.138 - 0.184: 16 0.184 - 0.230: 6 Chirality restraints: 1578 Sorted by residual: chirality pdb=" CCV LMN A 301 " pdb=" CCR LMN A 301 " pdb=" CCT LMN A 301 " pdb=" OAU LMN A 301 " both_signs ideal model delta sigma weight residual False 2.28 2.51 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CCV LMN B 301 " pdb=" CCR LMN B 301 " pdb=" CCT LMN B 301 " pdb=" OAU LMN B 301 " both_signs ideal model delta sigma weight residual False 2.28 2.51 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CCV LMN F 301 " pdb=" CCR LMN F 301 " pdb=" CCT LMN F 301 " pdb=" OAU LMN F 301 " both_signs ideal model delta sigma weight residual False 2.28 2.51 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1575 not shown) Planarity restraints: 2784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 171 " -0.060 9.50e-02 1.11e+02 2.31e-02 3.41e+00 pdb=" NE ARG C 171 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG C 171 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG C 171 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 171 " -0.024 2.00e-02 2.50e+03 pdb="HH11 ARG C 171 " -0.008 2.00e-02 2.50e+03 pdb="HH12 ARG C 171 " 0.005 2.00e-02 2.50e+03 pdb="HH21 ARG C 171 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG C 171 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 171 " -0.060 9.50e-02 1.11e+02 2.30e-02 3.39e+00 pdb=" NE ARG D 171 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG D 171 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG D 171 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 171 " -0.024 2.00e-02 2.50e+03 pdb="HH11 ARG D 171 " -0.009 2.00e-02 2.50e+03 pdb="HH12 ARG D 171 " 0.005 2.00e-02 2.50e+03 pdb="HH21 ARG D 171 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG D 171 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 171 " 0.059 9.50e-02 1.11e+02 2.27e-02 3.35e+00 pdb=" NE ARG A 171 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 171 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG A 171 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 171 " 0.025 2.00e-02 2.50e+03 pdb="HH11 ARG A 171 " 0.008 2.00e-02 2.50e+03 pdb="HH12 ARG A 171 " -0.005 2.00e-02 2.50e+03 pdb="HH21 ARG A 171 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 171 " -0.010 2.00e-02 2.50e+03 ... (remaining 2781 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 3949 2.31 - 2.88: 40034 2.88 - 3.45: 46735 3.45 - 4.03: 65786 4.03 - 4.60: 98158 Nonbonded interactions: 254662 Sorted by model distance: nonbonded pdb=" HE2 HIS F 54 " pdb=" OD1 ASN F 181 " model vdw 1.734 1.850 nonbonded pdb=" HE2 HIS B 54 " pdb=" OD1 ASN B 181 " model vdw 1.734 1.850 nonbonded pdb=" HE2 HIS E 54 " pdb=" OD1 ASN E 181 " model vdw 1.734 1.850 nonbonded pdb=" HE2 HIS D 54 " pdb=" OD1 ASN D 181 " model vdw 1.734 1.850 nonbonded pdb=" HE2 HIS C 54 " pdb=" OD1 ASN C 181 " model vdw 1.734 1.850 ... (remaining 254657 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.300 Extract box with map and model: 7.830 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 62.740 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.088 10224 Z= 0.648 Angle : 1.071 10.744 13872 Z= 0.475 Chirality : 0.047 0.230 1578 Planarity : 0.006 0.038 1650 Dihedral : 18.398 95.092 4194 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.61 % Allowed : 4.82 % Favored : 91.57 % 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: -3.24 (0.20), residues: 1182 helix: -1.92 (0.14), residues: 870 sheet: -0.67 (0.58), residues: 60 loop : -2.55 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 103 HIS 0.005 0.002 HIS B 69 PHE 0.018 0.002 PHE F 31 TYR 0.007 0.002 TYR B 44 ARG 0.020 0.002 ARG C 171 *********************** 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 205 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 169 time to evaluate : 1.529 Fit side-chains REVERT: A 132 ARG cc_start: 0.7484 (mtp85) cc_final: 0.6866 (tpm170) REVERT: A 220 ARG cc_start: 0.3992 (OUTLIER) cc_final: 0.3482 (pmt100) REVERT: B 4 ARG cc_start: 0.7095 (tpt-90) cc_final: 0.6868 (tmm-80) REVERT: B 132 ARG cc_start: 0.7547 (mtp85) cc_final: 0.6882 (tpm170) REVERT: B 220 ARG cc_start: 0.3965 (OUTLIER) cc_final: 0.3574 (ptt-90) REVERT: C 132 ARG cc_start: 0.7480 (mtp85) cc_final: 0.6905 (tpm170) REVERT: C 171 ARG cc_start: 0.6788 (mmm-85) cc_final: 0.6438 (ttt180) REVERT: C 220 ARG cc_start: 0.4026 (OUTLIER) cc_final: 0.3533 (pmt100) REVERT: D 132 ARG cc_start: 0.7458 (mtp85) cc_final: 0.6845 (tpm170) REVERT: D 220 ARG cc_start: 0.4035 (OUTLIER) cc_final: 0.3680 (ptt-90) REVERT: E 4 ARG cc_start: 0.7072 (tpt-90) cc_final: 0.6842 (tmm-80) REVERT: E 132 ARG cc_start: 0.7548 (mtp85) cc_final: 0.6870 (tpm170) REVERT: E 220 ARG cc_start: 0.4016 (OUTLIER) cc_final: 0.3590 (ptt-90) REVERT: F 132 ARG cc_start: 0.7471 (mtp85) cc_final: 0.6870 (tpm170) REVERT: F 220 ARG cc_start: 0.4009 (OUTLIER) cc_final: 0.3602 (pmt100) outliers start: 36 outliers final: 9 residues processed: 191 average time/residue: 3.5668 time to fit residues: 716.5270 Evaluate side-chains 155 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 104 GLU 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: 1.9990 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 GLN F 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10224 Z= 0.188 Angle : 0.688 7.405 13872 Z= 0.341 Chirality : 0.037 0.121 1578 Planarity : 0.005 0.039 1650 Dihedral : 13.886 89.630 2124 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.81 % Allowed : 9.24 % Favored : 88.96 % 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: 0.58 (0.25), residues: 1182 helix: 1.16 (0.17), residues: 900 sheet: -0.44 (0.57), residues: 60 loop : -2.53 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 101 HIS 0.002 0.001 HIS A 54 PHE 0.014 0.002 PHE E 94 TYR 0.009 0.002 TYR D 97 ARG 0.002 0.000 ARG A 4 *********************** 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 150 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.478 Fit side-chains revert: symmetry clash REVERT: B 4 ARG cc_start: 0.6443 (tpt-90) cc_final: 0.6186 (tmm-80) REVERT: B 132 ARG cc_start: 0.7123 (mtp85) cc_final: 0.6333 (tpt170) REVERT: E 4 ARG cc_start: 0.6490 (tpt-90) cc_final: 0.6220 (tmm-80) REVERT: E 132 ARG cc_start: 0.7133 (mtp85) cc_final: 0.6330 (tpt170) REVERT: F 4 ARG cc_start: 0.6340 (tpp80) cc_final: 0.6086 (tmm-80) outliers start: 18 outliers final: 7 residues processed: 144 average time/residue: 3.5799 time to fit residues: 542.0986 Evaluate side-chains 138 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 4 ARG Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain F residue 104 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10224 Z= 0.154 Angle : 0.543 4.259 13872 Z= 0.272 Chirality : 0.033 0.102 1578 Planarity : 0.004 0.028 1650 Dihedral : 11.136 73.938 2094 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 2.11 % Allowed : 10.24 % Favored : 87.65 % 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: 1.93 (0.25), residues: 1182 helix: 2.20 (0.18), residues: 882 sheet: 0.14 (0.56), residues: 60 loop : -2.10 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 101 HIS 0.005 0.001 HIS B 102 PHE 0.013 0.001 PHE D 31 TYR 0.009 0.001 TYR A 156 ARG 0.003 0.000 ARG A 4 *********************** 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 154 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 4 ARG cc_start: 0.6555 (tpt-90) cc_final: 0.6327 (tmm-80) outliers start: 21 outliers final: 14 residues processed: 149 average time/residue: 3.4559 time to fit residues: 543.5347 Evaluate side-chains 145 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 4 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 104 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10224 Z= 0.211 Angle : 0.611 4.092 13872 Z= 0.307 Chirality : 0.036 0.110 1578 Planarity : 0.005 0.029 1650 Dihedral : 10.926 67.584 2094 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.41 % Allowed : 10.64 % Favored : 86.95 % 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: 2.08 (0.25), residues: 1182 helix: 2.31 (0.17), residues: 888 sheet: 0.53 (0.57), residues: 60 loop : -2.26 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 101 HIS 0.003 0.001 HIS F 98 PHE 0.015 0.002 PHE D 31 TYR 0.013 0.002 TYR D 97 ARG 0.003 0.000 ARG F 4 *********************** 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 162 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.325 Fit side-chains REVERT: A 220 ARG cc_start: 0.3828 (OUTLIER) cc_final: 0.3385 (pmt100) REVERT: B 220 ARG cc_start: 0.3878 (OUTLIER) cc_final: 0.3373 (pmt100) REVERT: C 220 ARG cc_start: 0.3875 (OUTLIER) cc_final: 0.3431 (pmt100) REVERT: D 4 ARG cc_start: 0.6374 (OUTLIER) cc_final: 0.5766 (ttm-80) REVERT: D 104 GLU cc_start: 0.5359 (OUTLIER) cc_final: 0.4982 (mm-30) REVERT: D 220 ARG cc_start: 0.3860 (OUTLIER) cc_final: 0.3369 (pmt100) REVERT: E 220 ARG cc_start: 0.3841 (OUTLIER) cc_final: 0.3386 (pmt100) REVERT: F 220 ARG cc_start: 0.3891 (OUTLIER) cc_final: 0.3462 (pmt100) outliers start: 24 outliers final: 11 residues processed: 158 average time/residue: 3.6364 time to fit residues: 604.4838 Evaluate side-chains 156 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 4 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 104 GLU 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: 0.0980 chunk 1 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10224 Z= 0.155 Angle : 0.527 4.276 13872 Z= 0.269 Chirality : 0.034 0.101 1578 Planarity : 0.004 0.027 1650 Dihedral : 10.113 75.969 2094 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.21 % Allowed : 11.35 % Favored : 86.45 % 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: 2.54 (0.25), residues: 1182 helix: 2.60 (0.17), residues: 888 sheet: 0.92 (0.60), residues: 60 loop : -2.00 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 101 HIS 0.003 0.001 HIS B 102 PHE 0.010 0.001 PHE B 51 TYR 0.010 0.001 TYR B 156 ARG 0.002 0.000 ARG A 4 *********************** 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 162 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 140 time to evaluate : 1.493 Fit side-chains outliers start: 22 outliers final: 8 residues processed: 161 average time/residue: 3.3398 time to fit residues: 568.8101 Evaluate side-chains 147 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 104 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 116 optimal weight: 0.3980 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.8467 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10224 Z= 0.153 Angle : 0.515 3.966 13872 Z= 0.260 Chirality : 0.033 0.100 1578 Planarity : 0.004 0.026 1650 Dihedral : 9.348 82.418 2082 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.81 % Allowed : 11.04 % Favored : 87.15 % 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: 2.84 (0.25), residues: 1182 helix: 2.85 (0.17), residues: 888 sheet: 1.23 (0.63), residues: 60 loop : -2.11 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 101 HIS 0.004 0.001 HIS E 102 PHE 0.010 0.001 PHE C 31 TYR 0.010 0.001 TYR B 156 ARG 0.002 0.000 ARG F 4 *********************** 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 155 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 1.444 Fit side-chains REVERT: C 104 GLU cc_start: 0.5522 (OUTLIER) cc_final: 0.5004 (mp0) REVERT: D 220 ARG cc_start: 0.3766 (OUTLIER) cc_final: 0.3320 (pmt100) REVERT: F 104 GLU cc_start: 0.5404 (OUTLIER) cc_final: 0.5071 (mp0) outliers start: 18 outliers final: 6 residues processed: 155 average time/residue: 3.2125 time to fit residues: 526.4037 Evaluate side-chains 148 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 139 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 104 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.8529 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10224 Z= 0.281 Angle : 0.653 4.378 13872 Z= 0.328 Chirality : 0.039 0.116 1578 Planarity : 0.005 0.029 1650 Dihedral : 10.224 82.373 2082 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 1.61 % Allowed : 11.75 % Favored : 86.65 % 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: 2.38 (0.25), residues: 1182 helix: 2.50 (0.17), residues: 894 sheet: 1.07 (0.62), residues: 60 loop : -2.30 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 103 HIS 0.004 0.001 HIS C 98 PHE 0.016 0.002 PHE F 31 TYR 0.016 0.003 TYR A 97 ARG 0.003 0.000 ARG C 75 *********************** 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 153 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 1.548 Fit side-chains REVERT: A 220 ARG cc_start: 0.3780 (OUTLIER) cc_final: 0.3302 (pmt100) REVERT: B 220 ARG cc_start: 0.3810 (OUTLIER) cc_final: 0.3336 (pmt100) REVERT: C 104 GLU cc_start: 0.5677 (OUTLIER) cc_final: 0.5300 (mp0) REVERT: C 220 ARG cc_start: 0.3860 (OUTLIER) cc_final: 0.3498 (pmt100) REVERT: D 220 ARG cc_start: 0.3796 (OUTLIER) cc_final: 0.3351 (pmt100) REVERT: E 220 ARG cc_start: 0.3841 (OUTLIER) cc_final: 0.3352 (pmt100) REVERT: F 104 GLU cc_start: 0.5540 (OUTLIER) cc_final: 0.5023 (mp0) REVERT: F 220 ARG cc_start: 0.3936 (OUTLIER) cc_final: 0.3515 (pmt100) outliers start: 16 outliers final: 6 residues processed: 151 average time/residue: 3.5171 time to fit residues: 559.9393 Evaluate side-chains 149 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 104 GLU 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: 2.9990 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 90 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.8486 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10224 Z= 0.162 Angle : 0.534 5.098 13872 Z= 0.272 Chirality : 0.034 0.100 1578 Planarity : 0.004 0.028 1650 Dihedral : 10.148 88.034 2082 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.51 % Allowed : 12.35 % Favored : 86.14 % 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: 2.71 (0.25), residues: 1182 helix: 2.76 (0.17), residues: 888 sheet: 1.15 (0.63), residues: 60 loop : -2.12 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 103 HIS 0.003 0.001 HIS E 102 PHE 0.011 0.001 PHE B 51 TYR 0.010 0.001 TYR B 156 ARG 0.001 0.000 ARG E 8 *********************** 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 153 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 1.439 Fit side-chains REVERT: A 220 ARG cc_start: 0.3756 (OUTLIER) cc_final: 0.3269 (pmt100) REVERT: B 220 ARG cc_start: 0.3779 (OUTLIER) cc_final: 0.3309 (pmt100) REVERT: E 220 ARG cc_start: 0.3818 (OUTLIER) cc_final: 0.3327 (pmt100) REVERT: F 104 GLU cc_start: 0.5527 (OUTLIER) cc_final: 0.4945 (mp0) outliers start: 15 outliers final: 7 residues processed: 153 average time/residue: 3.3616 time to fit residues: 543.3302 Evaluate side-chains 149 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 104 GLU 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: 0.9980 chunk 107 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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: 0.8506 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10224 Z= 0.206 Angle : 0.576 4.627 13872 Z= 0.291 Chirality : 0.036 0.106 1578 Planarity : 0.004 0.028 1650 Dihedral : 10.605 89.136 2079 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.41 % Allowed : 12.55 % Favored : 86.04 % 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: 2.56 (0.25), residues: 1182 helix: 2.66 (0.17), residues: 894 sheet: 1.15 (0.62), residues: 60 loop : -2.37 (0.35), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 103 HIS 0.003 0.001 HIS B 98 PHE 0.014 0.002 PHE B 51 TYR 0.013 0.002 TYR D 97 ARG 0.002 0.000 ARG F 4 *********************** 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 153 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 1.738 Fit side-chains REVERT: A 220 ARG cc_start: 0.3749 (OUTLIER) cc_final: 0.3233 (pmt100) REVERT: B 220 ARG cc_start: 0.3803 (OUTLIER) cc_final: 0.3301 (pmt100) REVERT: C 220 ARG cc_start: 0.3828 (OUTLIER) cc_final: 0.3429 (pmt100) REVERT: D 220 ARG cc_start: 0.3754 (OUTLIER) cc_final: 0.3287 (pmt100) REVERT: E 220 ARG cc_start: 0.3800 (OUTLIER) cc_final: 0.3319 (pmt100) REVERT: F 104 GLU cc_start: 0.5566 (OUTLIER) cc_final: 0.5067 (mp0) REVERT: F 220 ARG cc_start: 0.3857 (OUTLIER) cc_final: 0.3528 (pmt100) outliers start: 14 outliers final: 7 residues processed: 153 average time/residue: 3.4555 time to fit residues: 557.9565 Evaluate side-chains 153 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 104 GLU 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: 0.4980 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 95 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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: 0.8498 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10224 Z= 0.186 Angle : 0.548 4.799 13872 Z= 0.280 Chirality : 0.035 0.102 1578 Planarity : 0.004 0.027 1650 Dihedral : 9.871 86.527 2079 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 1.41 % Allowed : 12.55 % Favored : 86.04 % 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: 2.68 (0.25), residues: 1182 helix: 2.74 (0.17), residues: 888 sheet: 1.18 (0.63), residues: 60 loop : -2.19 (0.35), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 103 HIS 0.003 0.001 HIS B 98 PHE 0.012 0.002 PHE E 51 TYR 0.011 0.002 TYR A 156 ARG 0.001 0.000 ARG C 15 ********************** 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 154 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 1.473 Fit side-chains REVERT: A 220 ARG cc_start: 0.3763 (OUTLIER) cc_final: 0.3251 (pmt100) REVERT: B 220 ARG cc_start: 0.3779 (OUTLIER) cc_final: 0.3289 (pmt100) REVERT: E 220 ARG cc_start: 0.3800 (OUTLIER) cc_final: 0.3303 (pmt100) REVERT: F 104 GLU cc_start: 0.5540 (OUTLIER) cc_final: 0.5256 (mp0) REVERT: F 220 ARG cc_start: 0.3894 (OUTLIER) cc_final: 0.3544 (pmt100) outliers start: 14 outliers final: 7 residues processed: 154 average time/residue: 3.3213 time to fit residues: 540.3106 Evaluate side-chains 152 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 104 GLU 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 87 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.147032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.104648 restraints weight = 22869.916| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.24 r_work: 0.2853 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10224 Z= 0.201 Angle : 0.570 4.652 13872 Z= 0.289 Chirality : 0.035 0.106 1578 Planarity : 0.004 0.028 1650 Dihedral : 9.594 89.690 2079 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.51 % Allowed : 12.35 % Favored : 86.14 % 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: 2.57 (0.25), residues: 1182 helix: 2.68 (0.17), residues: 894 sheet: 1.14 (0.62), residues: 60 loop : -2.45 (0.34), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 103 HIS 0.003 0.001 HIS E 98 PHE 0.013 0.002 PHE B 51 TYR 0.012 0.002 TYR D 97 ARG 0.002 0.000 ARG F 4 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9234.03 seconds wall clock time: 160 minutes 43.83 seconds (9643.83 seconds total)