Starting phenix.real_space_refine on Fri Mar 22 07:34:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxm_20521/03_2024/6pxm_20521.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxm_20521/03_2024/6pxm_20521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxm_20521/03_2024/6pxm_20521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxm_20521/03_2024/6pxm_20521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxm_20521/03_2024/6pxm_20521.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxm_20521/03_2024/6pxm_20521.pdb" } resolution = 2.1 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= 0.174 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 20640 2.51 5 N 5736 2.21 5 O 6240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 11": "OE1" <-> "OE2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B ASP 127": "OD1" <-> "OD2" Residue "B ASP 135": "OD1" <-> "OD2" Residue "A GLU 11": "OE1" <-> "OE2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A GLU 53": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "C GLU 11": "OE1" <-> "OE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C ASP 127": "OD1" <-> "OD2" Residue "C ASP 135": "OD1" <-> "OD2" Residue "D GLU 11": "OE1" <-> "OE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D GLU 53": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D ASP 127": "OD1" <-> "OD2" Residue "D ASP 135": "OD1" <-> "OD2" Residue "E GLU 11": "OE1" <-> "OE2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E GLU 53": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "E ASP 127": "OD1" <-> "OD2" Residue "E ASP 135": "OD1" <-> "OD2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F GLU 45": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F ASP 127": "OD1" <-> "OD2" Residue "F ASP 135": "OD1" <-> "OD2" Residue "G GLU 11": "OE1" <-> "OE2" Residue "G GLU 45": "OE1" <-> "OE2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 88": "OE1" <-> "OE2" Residue "G ASP 127": "OD1" <-> "OD2" Residue "G ASP 135": "OD1" <-> "OD2" Residue "H GLU 11": "OE1" <-> "OE2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "H ASP 127": "OD1" <-> "OD2" Residue "H ASP 135": "OD1" <-> "OD2" Residue "I GLU 11": "OE1" <-> "OE2" Residue "I GLU 45": "OE1" <-> "OE2" Residue "I GLU 53": "OE1" <-> "OE2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "I GLU 60": "OE1" <-> "OE2" Residue "I GLU 88": "OE1" <-> "OE2" Residue "I ASP 127": "OD1" <-> "OD2" Residue "I ASP 135": "OD1" <-> "OD2" Residue "J GLU 11": "OE1" <-> "OE2" Residue "J GLU 45": "OE1" <-> "OE2" Residue "J GLU 53": "OE1" <-> "OE2" Residue "J GLU 57": "OE1" <-> "OE2" Residue "J GLU 60": "OE1" <-> "OE2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J ASP 127": "OD1" <-> "OD2" Residue "J ASP 135": "OD1" <-> "OD2" Residue "K GLU 11": "OE1" <-> "OE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K GLU 53": "OE1" <-> "OE2" Residue "K GLU 57": "OE1" <-> "OE2" Residue "K GLU 60": "OE1" <-> "OE2" Residue "K GLU 88": "OE1" <-> "OE2" Residue "K ASP 127": "OD1" <-> "OD2" Residue "K ASP 135": "OD1" <-> "OD2" Residue "L GLU 11": "OE1" <-> "OE2" Residue "L GLU 45": "OE1" <-> "OE2" Residue "L GLU 53": "OE1" <-> "OE2" Residue "L GLU 57": "OE1" <-> "OE2" Residue "L GLU 60": "OE1" <-> "OE2" Residue "L GLU 88": "OE1" <-> "OE2" Residue "L ASP 127": "OD1" <-> "OD2" Residue "L ASP 135": "OD1" <-> "OD2" Residue "M GLU 11": "OE1" <-> "OE2" Residue "M GLU 45": "OE1" <-> "OE2" Residue "M GLU 53": "OE1" <-> "OE2" Residue "M GLU 57": "OE1" <-> "OE2" Residue "M GLU 60": "OE1" <-> "OE2" Residue "M GLU 88": "OE1" <-> "OE2" Residue "M ASP 127": "OD1" <-> "OD2" Residue "M ASP 135": "OD1" <-> "OD2" Residue "N GLU 11": "OE1" <-> "OE2" Residue "N GLU 45": "OE1" <-> "OE2" Residue "N GLU 53": "OE1" <-> "OE2" Residue "N GLU 57": "OE1" <-> "OE2" Residue "N GLU 60": "OE1" <-> "OE2" Residue "N GLU 88": "OE1" <-> "OE2" Residue "N ASP 127": "OD1" <-> "OD2" Residue "N ASP 135": "OD1" <-> "OD2" Residue "O GLU 11": "OE1" <-> "OE2" Residue "O GLU 45": "OE1" <-> "OE2" Residue "O GLU 53": "OE1" <-> "OE2" Residue "O GLU 57": "OE1" <-> "OE2" Residue "O GLU 60": "OE1" <-> "OE2" Residue "O GLU 88": "OE1" <-> "OE2" Residue "O ASP 127": "OD1" <-> "OD2" Residue "O ASP 135": "OD1" <-> "OD2" Residue "P GLU 11": "OE1" <-> "OE2" Residue "P GLU 45": "OE1" <-> "OE2" Residue "P GLU 53": "OE1" <-> "OE2" Residue "P GLU 57": "OE1" <-> "OE2" Residue "P GLU 60": "OE1" <-> "OE2" Residue "P GLU 88": "OE1" <-> "OE2" Residue "P ASP 127": "OD1" <-> "OD2" Residue "P ASP 135": "OD1" <-> "OD2" Residue "Q GLU 11": "OE1" <-> "OE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q GLU 53": "OE1" <-> "OE2" Residue "Q GLU 57": "OE1" <-> "OE2" Residue "Q GLU 60": "OE1" <-> "OE2" Residue "Q GLU 88": "OE1" <-> "OE2" Residue "Q ASP 127": "OD1" <-> "OD2" Residue "Q ASP 135": "OD1" <-> "OD2" Residue "R GLU 11": "OE1" <-> "OE2" Residue "R GLU 45": "OE1" <-> "OE2" Residue "R GLU 53": "OE1" <-> "OE2" Residue "R GLU 57": "OE1" <-> "OE2" Residue "R GLU 60": "OE1" <-> "OE2" Residue "R GLU 88": "OE1" <-> "OE2" Residue "R ASP 127": "OD1" <-> "OD2" Residue "R ASP 135": "OD1" <-> "OD2" Residue "S GLU 11": "OE1" <-> "OE2" Residue "S GLU 45": "OE1" <-> "OE2" Residue "S GLU 53": "OE1" <-> "OE2" Residue "S GLU 57": "OE1" <-> "OE2" Residue "S GLU 60": "OE1" <-> "OE2" Residue "S GLU 88": "OE1" <-> "OE2" Residue "S ASP 127": "OD1" <-> "OD2" Residue "S ASP 135": "OD1" <-> "OD2" Residue "T GLU 11": "OE1" <-> "OE2" Residue "T GLU 45": "OE1" <-> "OE2" Residue "T GLU 53": "OE1" <-> "OE2" Residue "T GLU 57": "OE1" <-> "OE2" Residue "T GLU 60": "OE1" <-> "OE2" Residue "T GLU 88": "OE1" <-> "OE2" Residue "T ASP 127": "OD1" <-> "OD2" Residue "T ASP 135": "OD1" <-> "OD2" Residue "V GLU 11": "OE1" <-> "OE2" Residue "V GLU 45": "OE1" <-> "OE2" Residue "V GLU 53": "OE1" <-> "OE2" Residue "V GLU 57": "OE1" <-> "OE2" Residue "V GLU 60": "OE1" <-> "OE2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "V ASP 127": "OD1" <-> "OD2" Residue "V ASP 135": "OD1" <-> "OD2" Residue "W GLU 11": "OE1" <-> "OE2" Residue "W GLU 45": "OE1" <-> "OE2" Residue "W GLU 53": "OE1" <-> "OE2" Residue "W GLU 57": "OE1" <-> "OE2" Residue "W GLU 60": "OE1" <-> "OE2" Residue "W GLU 88": "OE1" <-> "OE2" Residue "W ASP 127": "OD1" <-> "OD2" Residue "W ASP 135": "OD1" <-> "OD2" Residue "X GLU 11": "OE1" <-> "OE2" Residue "X GLU 45": "OE1" <-> "OE2" Residue "X GLU 53": "OE1" <-> "OE2" Residue "X GLU 57": "OE1" <-> "OE2" Residue "X GLU 60": "OE1" <-> "OE2" Residue "X GLU 88": "OE1" <-> "OE2" Residue "X ASP 127": "OD1" <-> "OD2" Residue "X ASP 135": "OD1" <-> "OD2" Residue "Y GLU 11": "OE1" <-> "OE2" Residue "Y GLU 45": "OE1" <-> "OE2" Residue "Y GLU 53": "OE1" <-> "OE2" Residue "Y GLU 57": "OE1" <-> "OE2" Residue "Y GLU 60": "OE1" <-> "OE2" Residue "Y GLU 88": "OE1" <-> "OE2" Residue "Y ASP 127": "OD1" <-> "OD2" Residue "Y ASP 135": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32736 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "A" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "C" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "D" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "E" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "F" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "G" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "H" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "I" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "J" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "K" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "L" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "M" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "N" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "O" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "P" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "Q" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "R" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "S" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "T" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "V" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "W" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "X" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "Y" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Time building chain proxies: 16.07, per 1000 atoms: 0.49 Number of scatterers: 32736 At special positions: 0 Unit cell: (133.952, 133.952, 133.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 6240 8.00 N 5736 7.00 C 20640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 11.60 Conformation dependent library (CDL) restraints added in 6.3 seconds 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7632 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 80.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'B' and resid 9 through 37 Processing helix chain 'B' and resid 44 through 72 Processing helix chain 'B' and resid 91 through 120 Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 133 through 155 Processing helix chain 'B' and resid 158 through 170 Processing helix chain 'A' and resid 9 through 37 Processing helix chain 'A' and resid 44 through 72 Processing helix chain 'A' and resid 91 through 120 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 133 through 155 Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'C' and resid 9 through 37 Processing helix chain 'C' and resid 44 through 72 Processing helix chain 'C' and resid 91 through 120 Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 133 through 155 Processing helix chain 'C' and resid 158 through 170 Processing helix chain 'D' and resid 9 through 37 Processing helix chain 'D' and resid 44 through 72 Processing helix chain 'D' and resid 91 through 120 Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 133 through 155 Processing helix chain 'D' and resid 158 through 170 Processing helix chain 'E' and resid 9 through 37 Processing helix chain 'E' and resid 44 through 72 Processing helix chain 'E' and resid 91 through 120 Processing helix chain 'E' and resid 122 through 133 Processing helix chain 'E' and resid 133 through 155 Processing helix chain 'E' and resid 158 through 170 Processing helix chain 'F' and resid 9 through 37 Processing helix chain 'F' and resid 44 through 72 Processing helix chain 'F' and resid 91 through 120 Processing helix chain 'F' and resid 122 through 133 Processing helix chain 'F' and resid 133 through 155 Processing helix chain 'F' and resid 158 through 170 Processing helix chain 'G' and resid 9 through 37 Processing helix chain 'G' and resid 44 through 72 Processing helix chain 'G' and resid 91 through 120 Processing helix chain 'G' and resid 122 through 133 Processing helix chain 'G' and resid 133 through 155 Processing helix chain 'G' and resid 158 through 170 Processing helix chain 'H' and resid 9 through 37 Processing helix chain 'H' and resid 44 through 72 Processing helix chain 'H' and resid 91 through 120 Processing helix chain 'H' and resid 122 through 133 Processing helix chain 'H' and resid 133 through 155 Processing helix chain 'H' and resid 158 through 170 Processing helix chain 'I' and resid 9 through 37 Processing helix chain 'I' and resid 44 through 72 Processing helix chain 'I' and resid 91 through 120 Processing helix chain 'I' and resid 122 through 133 Processing helix chain 'I' and resid 133 through 155 Processing helix chain 'I' and resid 158 through 170 Processing helix chain 'J' and resid 9 through 37 Processing helix chain 'J' and resid 44 through 72 Processing helix chain 'J' and resid 91 through 120 Processing helix chain 'J' and resid 122 through 133 Processing helix chain 'J' and resid 133 through 155 Processing helix chain 'J' and resid 158 through 170 Processing helix chain 'K' and resid 9 through 37 Processing helix chain 'K' and resid 44 through 72 Processing helix chain 'K' and resid 91 through 120 Processing helix chain 'K' and resid 122 through 133 Processing helix chain 'K' and resid 133 through 155 Processing helix chain 'K' and resid 158 through 170 Processing helix chain 'L' and resid 9 through 37 Processing helix chain 'L' and resid 44 through 72 Processing helix chain 'L' and resid 91 through 120 Processing helix chain 'L' and resid 122 through 133 Processing helix chain 'L' and resid 133 through 155 Processing helix chain 'L' and resid 158 through 170 Processing helix chain 'M' and resid 9 through 37 Processing helix chain 'M' and resid 44 through 72 Processing helix chain 'M' and resid 91 through 120 Processing helix chain 'M' and resid 122 through 133 Processing helix chain 'M' and resid 133 through 155 Processing helix chain 'M' and resid 158 through 170 Processing helix chain 'N' and resid 9 through 37 Processing helix chain 'N' and resid 44 through 72 Processing helix chain 'N' and resid 91 through 120 Processing helix chain 'N' and resid 122 through 133 Processing helix chain 'N' and resid 133 through 155 Processing helix chain 'N' and resid 158 through 170 Processing helix chain 'O' and resid 9 through 37 Processing helix chain 'O' and resid 44 through 72 Processing helix chain 'O' and resid 91 through 120 Processing helix chain 'O' and resid 122 through 133 Processing helix chain 'O' and resid 133 through 155 Processing helix chain 'O' and resid 158 through 170 Processing helix chain 'P' and resid 9 through 37 Processing helix chain 'P' and resid 44 through 72 Processing helix chain 'P' and resid 91 through 120 Processing helix chain 'P' and resid 122 through 133 Processing helix chain 'P' and resid 133 through 155 Processing helix chain 'P' and resid 158 through 170 Processing helix chain 'Q' and resid 9 through 37 Processing helix chain 'Q' and resid 44 through 72 Processing helix chain 'Q' and resid 91 through 120 Processing helix chain 'Q' and resid 122 through 133 Processing helix chain 'Q' and resid 133 through 155 Processing helix chain 'Q' and resid 158 through 170 Processing helix chain 'R' and resid 9 through 37 Processing helix chain 'R' and resid 44 through 72 Processing helix chain 'R' and resid 91 through 120 Processing helix chain 'R' and resid 122 through 133 Processing helix chain 'R' and resid 133 through 155 Processing helix chain 'R' and resid 158 through 170 Processing helix chain 'S' and resid 9 through 37 Processing helix chain 'S' and resid 44 through 72 Processing helix chain 'S' and resid 91 through 120 Processing helix chain 'S' and resid 122 through 133 Processing helix chain 'S' and resid 133 through 155 Processing helix chain 'S' and resid 158 through 170 Processing helix chain 'T' and resid 9 through 37 Processing helix chain 'T' and resid 44 through 72 Processing helix chain 'T' and resid 91 through 120 Processing helix chain 'T' and resid 122 through 133 Processing helix chain 'T' and resid 133 through 155 Processing helix chain 'T' and resid 158 through 170 Processing helix chain 'V' and resid 9 through 37 Processing helix chain 'V' and resid 44 through 72 Processing helix chain 'V' and resid 91 through 120 Processing helix chain 'V' and resid 122 through 133 Processing helix chain 'V' and resid 133 through 155 Processing helix chain 'V' and resid 158 through 170 Processing helix chain 'W' and resid 9 through 37 Processing helix chain 'W' and resid 44 through 72 Processing helix chain 'W' and resid 91 through 120 Processing helix chain 'W' and resid 122 through 133 Processing helix chain 'W' and resid 133 through 155 Processing helix chain 'W' and resid 158 through 170 Processing helix chain 'X' and resid 9 through 37 Processing helix chain 'X' and resid 44 through 72 Processing helix chain 'X' and resid 91 through 120 Processing helix chain 'X' and resid 122 through 133 Processing helix chain 'X' and resid 133 through 155 Processing helix chain 'X' and resid 158 through 170 Processing helix chain 'Y' and resid 9 through 37 Processing helix chain 'Y' and resid 44 through 72 Processing helix chain 'Y' and resid 91 through 120 Processing helix chain 'Y' and resid 122 through 133 Processing helix chain 'Y' and resid 133 through 155 Processing helix chain 'Y' and resid 158 through 170 2688 hydrogen bonds defined for protein. 8064 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: 9.85 Time building geometry restraints manager: 12.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 5736 1.28 - 1.41: 8339 1.41 - 1.55: 18997 1.55 - 1.68: 0 1.68 - 1.81: 192 Bond restraints: 33264 Sorted by residual: bond pdb=" C ALA L 26 " pdb=" O ALA L 26 " ideal model delta sigma weight residual 1.236 1.147 0.089 1.15e-02 7.56e+03 6.06e+01 bond pdb=" C ALA O 26 " pdb=" O ALA O 26 " ideal model delta sigma weight residual 1.236 1.148 0.089 1.15e-02 7.56e+03 5.95e+01 bond pdb=" C ALA B 26 " pdb=" O ALA B 26 " ideal model delta sigma weight residual 1.237 1.146 0.090 1.17e-02 7.31e+03 5.95e+01 bond pdb=" C ALA Y 26 " pdb=" O ALA Y 26 " ideal model delta sigma weight residual 1.237 1.147 0.090 1.17e-02 7.31e+03 5.88e+01 bond pdb=" C ALA T 26 " pdb=" O ALA T 26 " ideal model delta sigma weight residual 1.237 1.147 0.090 1.17e-02 7.31e+03 5.85e+01 ... (remaining 33259 not shown) Histogram of bond angle deviations from ideal: 98.33 - 105.45: 192 105.45 - 112.58: 16625 112.58 - 119.71: 11632 119.71 - 126.83: 16095 126.83 - 133.96: 240 Bond angle restraints: 44784 Sorted by residual: angle pdb=" CA ALA D 26 " pdb=" C ALA D 26 " pdb=" O ALA D 26 " ideal model delta sigma weight residual 120.55 116.69 3.86 1.06e+00 8.90e-01 1.33e+01 angle pdb=" CA ALA G 26 " pdb=" C ALA G 26 " pdb=" O ALA G 26 " ideal model delta sigma weight residual 120.82 117.03 3.79 1.05e+00 9.07e-01 1.31e+01 angle pdb=" CA ALA O 26 " pdb=" C ALA O 26 " pdb=" O ALA O 26 " ideal model delta sigma weight residual 120.82 117.03 3.79 1.05e+00 9.07e-01 1.30e+01 angle pdb=" CA ALA L 26 " pdb=" C ALA L 26 " pdb=" O ALA L 26 " ideal model delta sigma weight residual 120.82 117.05 3.77 1.05e+00 9.07e-01 1.29e+01 angle pdb=" CA ALA S 26 " pdb=" C ALA S 26 " pdb=" O ALA S 26 " ideal model delta sigma weight residual 120.55 116.77 3.78 1.06e+00 8.90e-01 1.27e+01 ... (remaining 44779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 17712 17.65 - 35.30: 1806 35.30 - 52.95: 378 52.95 - 70.61: 120 70.61 - 88.26: 48 Dihedral angle restraints: 20064 sinusoidal: 8232 harmonic: 11832 Sorted by residual: dihedral pdb=" CA VAL I 42 " pdb=" C VAL I 42 " pdb=" N ALA I 43 " pdb=" CA ALA I 43 " ideal model delta harmonic sigma weight residual 180.00 161.21 18.79 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA VAL Y 42 " pdb=" C VAL Y 42 " pdb=" N ALA Y 43 " pdb=" CA ALA Y 43 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA VAL T 42 " pdb=" C VAL T 42 " pdb=" N ALA T 43 " pdb=" CA ALA T 43 " ideal model delta harmonic sigma weight residual 180.00 161.23 18.77 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 20061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2623 0.032 - 0.064: 1656 0.064 - 0.095: 468 0.095 - 0.127: 149 0.127 - 0.159: 24 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CG LEU Q 24 " pdb=" CB LEU Q 24 " pdb=" CD1 LEU Q 24 " pdb=" CD2 LEU Q 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CG LEU F 24 " pdb=" CB LEU F 24 " pdb=" CD1 LEU F 24 " pdb=" CD2 LEU F 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CG LEU L 24 " pdb=" CB LEU L 24 " pdb=" CD1 LEU L 24 " pdb=" CD2 LEU L 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.26e-01 ... (remaining 4917 not shown) Planarity restraints: 5880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS X 83 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO X 84 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO X 84 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO X 84 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS I 83 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO I 84 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO I 84 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 84 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS T 83 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO T 84 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO T 84 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO T 84 " -0.021 5.00e-02 4.00e+02 ... (remaining 5877 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 11474 2.89 - 3.40: 31684 3.40 - 3.90: 61179 3.90 - 4.40: 68991 4.40 - 4.90: 112181 Nonbonded interactions: 285509 Sorted by model distance: nonbonded pdb=" OH TYR V 8 " pdb=" OE1 GLN V 69 " model vdw 2.392 2.440 nonbonded pdb=" OH TYR N 8 " pdb=" OE1 GLN N 69 " model vdw 2.392 2.440 nonbonded pdb=" OH TYR D 8 " pdb=" OE1 GLN D 69 " model vdw 2.392 2.440 nonbonded pdb=" OH TYR Y 8 " pdb=" OE1 GLN Y 69 " model vdw 2.392 2.440 nonbonded pdb=" OH TYR L 8 " pdb=" OE1 GLN L 69 " model vdw 2.392 2.440 ... (remaining 285504 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 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: 0.020 Extract box with map and model: 9.190 Check model and map are aligned: 0.500 Set scattering table: 0.290 Process input model: 79.230 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.390 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:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 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 : 0.008 0.090 33264 Z= 0.522 Angle : 0.706 3.904 44784 Z= 0.428 Chirality : 0.044 0.159 4920 Planarity : 0.004 0.037 5880 Dihedral : 16.033 88.256 12432 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.44 (0.09), residues: 4032 helix: -2.24 (0.06), residues: 3312 sheet: None (None), residues: 0 loop : -1.12 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 89 HIS 0.005 0.001 HIS O 124 PHE 0.018 0.003 PHE M 37 TYR 0.012 0.002 TYR B 28 ARG 0.008 0.001 ARG V 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 673 time to evaluate : 3.842 Fit side-chains REVERT: A 135 ASP cc_start: 0.8285 (t70) cc_final: 0.8049 (t0) REVERT: C 135 ASP cc_start: 0.8281 (t70) cc_final: 0.8053 (t0) REVERT: E 135 ASP cc_start: 0.8282 (t70) cc_final: 0.8056 (t0) REVERT: G 135 ASP cc_start: 0.8273 (t70) cc_final: 0.8048 (t0) REVERT: J 135 ASP cc_start: 0.8278 (t70) cc_final: 0.8044 (t0) REVERT: M 135 ASP cc_start: 0.8286 (t70) cc_final: 0.8053 (t0) REVERT: N 135 ASP cc_start: 0.8277 (t70) cc_final: 0.8052 (t0) REVERT: P 135 ASP cc_start: 0.8281 (t70) cc_final: 0.8055 (t0) REVERT: R 135 ASP cc_start: 0.8288 (t70) cc_final: 0.8066 (t0) REVERT: V 135 ASP cc_start: 0.8279 (t70) cc_final: 0.8062 (t0) REVERT: W 135 ASP cc_start: 0.8280 (t70) cc_final: 0.8046 (t0) outliers start: 0 outliers final: 0 residues processed: 673 average time/residue: 2.1150 time to fit residues: 1599.0821 Evaluate side-chains 436 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 436 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 10.0000 chunk 309 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 165 optimal weight: 6.9990 chunk 319 optimal weight: 0.8980 chunk 123 optimal weight: 0.2980 chunk 194 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 370 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 ASN B 71 GLN B 132 HIS A 7 ASN A 71 GLN A 132 HIS C 7 ASN C 71 GLN C 132 HIS D 71 GLN D 132 HIS E 7 ASN E 71 GLN E 132 HIS F 71 GLN F 132 HIS G 7 ASN G 71 GLN G 132 HIS H 7 ASN H 132 HIS I 7 ASN I 71 GLN I 132 HIS J 7 ASN J 71 GLN J 132 HIS K 7 ASN K 71 GLN K 132 HIS L 7 ASN L 71 GLN L 132 HIS M 71 GLN M 132 HIS N 7 ASN N 71 GLN N 132 HIS O 71 GLN O 132 HIS P 7 ASN P 71 GLN P 132 HIS Q 7 ASN Q 71 GLN Q 132 HIS R 7 ASN R 71 GLN R 132 HIS S 7 ASN S 71 GLN S 132 HIS T 7 ASN T 71 GLN T 132 HIS V 7 ASN V 71 GLN V 132 HIS W 7 ASN W 71 GLN W 132 HIS X 7 ASN X 71 GLN X 132 HIS Y 7 ASN Y 71 GLN Y 132 HIS Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 33264 Z= 0.186 Angle : 0.481 4.734 44784 Z= 0.273 Chirality : 0.034 0.125 4920 Planarity : 0.004 0.030 5880 Dihedral : 4.281 16.617 4464 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.72 % Allowed : 7.44 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.34 (0.13), residues: 4032 helix: 2.01 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.69 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 89 HIS 0.003 0.001 HIS K 49 PHE 0.014 0.002 PHE R 37 TYR 0.008 0.001 TYR R 28 ARG 0.001 0.000 ARG Q 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 577 time to evaluate : 4.428 Fit side-chains outliers start: 25 outliers final: 0 residues processed: 602 average time/residue: 1.8600 time to fit residues: 1277.0258 Evaluate side-chains 522 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 522 time to evaluate : 3.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 308 optimal weight: 7.9990 chunk 252 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 371 optimal weight: 8.9990 chunk 400 optimal weight: 2.9990 chunk 330 optimal weight: 4.9990 chunk 368 optimal weight: 6.9990 chunk 126 optimal weight: 0.0980 chunk 297 optimal weight: 5.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- 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: 0.8597 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 33264 Z= 0.241 Angle : 0.505 4.416 44784 Z= 0.281 Chirality : 0.036 0.128 4920 Planarity : 0.003 0.028 5880 Dihedral : 4.340 16.812 4464 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.17 % Allowed : 9.52 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.03 (0.13), residues: 4032 helix: 3.26 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.63 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 89 HIS 0.003 0.001 HIS K 124 PHE 0.016 0.003 PHE F 37 TYR 0.008 0.001 TYR Q 28 ARG 0.002 0.000 ARG L 153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 547 time to evaluate : 4.143 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 553 average time/residue: 1.9631 time to fit residues: 1232.2120 Evaluate side-chains 509 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 509 time to evaluate : 4.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 2.9990 chunk 279 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 249 optimal weight: 6.9990 chunk 372 optimal weight: 9.9990 chunk 394 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 353 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN A 71 GLN C 71 GLN Q 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 33264 Z= 0.169 Angle : 0.446 4.220 44784 Z= 0.252 Chirality : 0.034 0.117 4920 Planarity : 0.003 0.026 5880 Dihedral : 4.112 15.452 4464 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.87 % Allowed : 8.13 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.65 (0.14), residues: 4032 helix: 3.71 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.56 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 89 HIS 0.003 0.001 HIS J 124 PHE 0.014 0.002 PHE S 37 TYR 0.006 0.001 TYR C 28 ARG 0.001 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 544 time to evaluate : 4.159 Fit side-chains REVERT: B 69 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8430 (tp-100) REVERT: A 69 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8432 (tp-100) REVERT: C 69 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8363 (tp-100) REVERT: D 69 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8425 (tp-100) REVERT: E 69 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8425 (tp-100) REVERT: F 69 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8429 (tp-100) REVERT: G 69 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8371 (tp-100) REVERT: H 69 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8425 (tp-100) REVERT: I 25 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8101 (tmt170) REVERT: I 69 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8372 (tp-100) REVERT: J 69 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8365 (tp-100) REVERT: K 25 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8102 (tmt170) REVERT: K 69 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8430 (tp-100) REVERT: L 25 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8107 (tmt170) REVERT: L 69 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8371 (tp-100) REVERT: M 69 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8433 (tp-100) REVERT: N 69 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8433 (tp-100) REVERT: O 25 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8108 (tmt170) REVERT: O 69 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8370 (tp-100) REVERT: P 69 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8368 (tp-100) REVERT: Q 25 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8103 (tmt170) REVERT: Q 69 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8434 (tp-100) REVERT: R 69 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8429 (tp-100) REVERT: S 69 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8431 (tp-100) REVERT: T 69 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8368 (tp-100) REVERT: V 69 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8433 (tp-100) REVERT: W 25 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8104 (tmt170) REVERT: W 69 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8423 (tp-100) REVERT: X 69 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8368 (tp-100) REVERT: Y 69 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8375 (tp-100) outliers start: 30 outliers final: 0 residues processed: 574 average time/residue: 2.0955 time to fit residues: 1354.3009 Evaluate side-chains 534 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 504 time to evaluate : 4.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain G residue 69 GLN Chi-restraints excluded: chain H residue 69 GLN Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain J residue 69 GLN Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 69 GLN Chi-restraints excluded: chain L residue 25 ARG Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain M residue 69 GLN Chi-restraints excluded: chain N residue 69 GLN Chi-restraints excluded: chain O residue 25 ARG Chi-restraints excluded: chain O residue 69 GLN Chi-restraints excluded: chain P residue 69 GLN Chi-restraints excluded: chain Q residue 25 ARG Chi-restraints excluded: chain Q residue 69 GLN Chi-restraints excluded: chain R residue 69 GLN Chi-restraints excluded: chain S residue 69 GLN Chi-restraints excluded: chain T residue 69 GLN Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain W residue 25 ARG Chi-restraints excluded: chain W residue 69 GLN Chi-restraints excluded: chain X residue 69 GLN Chi-restraints excluded: chain Y residue 69 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 0.9980 chunk 223 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 336 optimal weight: 0.0370 chunk 272 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 chunk 353 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- 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: 0.8522 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 33264 Z= 0.105 Angle : 0.379 4.036 44784 Z= 0.218 Chirality : 0.031 0.110 4920 Planarity : 0.002 0.024 5880 Dihedral : 3.748 12.321 4464 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.87 % Allowed : 9.00 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 5.18 (0.14), residues: 4032 helix: 4.10 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.48 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP S 89 HIS 0.005 0.001 HIS B 49 PHE 0.015 0.002 PHE B 50 TYR 0.003 0.001 TYR Y 23 ARG 0.001 0.000 ARG F 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 676 time to evaluate : 4.020 Fit side-chains REVERT: I 25 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8096 (tmt170) REVERT: K 25 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8099 (tmt170) REVERT: L 25 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8101 (tmt170) REVERT: O 25 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8090 (tmt170) REVERT: Q 25 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8092 (tmt170) REVERT: W 25 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8092 (tmt170) outliers start: 30 outliers final: 0 residues processed: 706 average time/residue: 2.0720 time to fit residues: 1646.3545 Evaluate side-chains 589 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 583 time to evaluate : 4.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain L residue 25 ARG Chi-restraints excluded: chain O residue 25 ARG Chi-restraints excluded: chain Q residue 25 ARG Chi-restraints excluded: chain W residue 25 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 8.9990 chunk 355 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 231 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 394 optimal weight: 9.9990 chunk 327 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN A 69 GLN C 69 GLN D 69 GLN D 71 GLN E 69 GLN E 71 GLN F 69 GLN F 71 GLN G 69 GLN H 69 GLN I 69 GLN J 69 GLN K 69 GLN L 69 GLN M 69 GLN N 69 GLN O 69 GLN P 69 GLN Q 69 GLN R 69 GLN S 69 GLN T 69 GLN V 69 GLN W 69 GLN X 69 GLN Y 69 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 33264 Z= 0.359 Angle : 0.566 4.907 44784 Z= 0.313 Chirality : 0.041 0.139 4920 Planarity : 0.004 0.030 5880 Dihedral : 4.398 16.307 4464 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.95 % Allowed : 9.58 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.74 (0.13), residues: 4032 helix: 3.76 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.48 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 89 HIS 0.007 0.002 HIS H 49 PHE 0.018 0.003 PHE B 37 TYR 0.007 0.002 TYR B 30 ARG 0.003 0.001 ARG G 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 544 time to evaluate : 3.825 Fit side-chains REVERT: B 69 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8469 (tp-100) REVERT: A 69 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8472 (tp-100) REVERT: D 69 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8497 (tp-100) REVERT: E 69 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8499 (tp-100) REVERT: F 69 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8494 (tp-100) REVERT: G 69 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8472 (tp-100) REVERT: H 69 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8437 (tp-100) REVERT: I 69 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8471 (tp-100) REVERT: K 69 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8438 (tp-100) REVERT: L 69 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8483 (tp-100) REVERT: M 69 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8442 (tp-100) REVERT: N 69 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8442 (tp-100) REVERT: O 69 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8482 (tp-100) REVERT: Q 69 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8472 (tp-100) REVERT: R 69 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8436 (tp-100) REVERT: S 69 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8438 (tp-100) REVERT: V 69 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8443 (tp-100) REVERT: Y 69 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8485 (tp-100) outliers start: 33 outliers final: 0 residues processed: 574 average time/residue: 2.0215 time to fit residues: 1310.9624 Evaluate side-chains 529 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 511 time to evaluate : 3.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain G residue 69 GLN Chi-restraints excluded: chain H residue 69 GLN Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain K residue 69 GLN Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain M residue 69 GLN Chi-restraints excluded: chain N residue 69 GLN Chi-restraints excluded: chain O residue 69 GLN Chi-restraints excluded: chain Q residue 69 GLN Chi-restraints excluded: chain R residue 69 GLN Chi-restraints excluded: chain S residue 69 GLN Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain Y residue 69 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 288 optimal weight: 0.8980 chunk 223 optimal weight: 0.9990 chunk 332 optimal weight: 0.6980 chunk 220 optimal weight: 4.9990 chunk 393 optimal weight: 6.9990 chunk 246 optimal weight: 7.9990 chunk 239 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN A 69 GLN C 69 GLN D 69 GLN D 71 GLN E 69 GLN E 71 GLN F 69 GLN F 71 GLN G 69 GLN H 69 GLN I 69 GLN J 69 GLN K 69 GLN L 69 GLN M 69 GLN N 69 GLN O 69 GLN P 69 GLN Q 69 GLN R 69 GLN S 69 GLN T 69 GLN V 69 GLN W 69 GLN X 69 GLN Y 69 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 33264 Z= 0.129 Angle : 0.424 4.045 44784 Z= 0.242 Chirality : 0.032 0.114 4920 Planarity : 0.002 0.024 5880 Dihedral : 3.957 13.389 4464 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.07 % Allowed : 9.46 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 5.19 (0.13), residues: 4032 helix: 4.08 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.34 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 89 HIS 0.003 0.001 HIS F 49 PHE 0.013 0.002 PHE E 50 TYR 0.004 0.001 TYR K 23 ARG 0.002 0.000 ARG F 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 589 time to evaluate : 4.223 Fit side-chains REVERT: B 153 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7349 (ptp90) REVERT: A 153 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7346 (ptp90) REVERT: H 153 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7354 (ptp90) REVERT: I 25 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8086 (tmt170) REVERT: K 25 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8081 (tmt170) REVERT: L 25 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8084 (tmt170) REVERT: L 135 ASP cc_start: 0.8066 (t70) cc_final: 0.7865 (t0) REVERT: M 135 ASP cc_start: 0.8068 (t70) cc_final: 0.7866 (t0) REVERT: O 25 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8082 (tmt170) REVERT: P 135 ASP cc_start: 0.8070 (t70) cc_final: 0.7870 (t0) REVERT: Q 25 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8080 (tmt170) REVERT: Q 153 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7345 (ptp90) REVERT: W 25 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8080 (tmt170) REVERT: W 135 ASP cc_start: 0.8065 (t70) cc_final: 0.7865 (t0) outliers start: 37 outliers final: 0 residues processed: 624 average time/residue: 1.9424 time to fit residues: 1374.9687 Evaluate side-chains 600 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 590 time to evaluate : 3.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain L residue 25 ARG Chi-restraints excluded: chain O residue 25 ARG Chi-restraints excluded: chain Q residue 25 ARG Chi-restraints excluded: chain Q residue 153 ARG Chi-restraints excluded: chain W residue 25 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 2.9990 chunk 157 optimal weight: 0.4980 chunk 234 optimal weight: 0.6980 chunk 118 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 250 optimal weight: 10.0000 chunk 267 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 309 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN E 71 GLN F 71 GLN J 71 GLN N 71 GLN P 71 GLN S 71 GLN W 71 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 33264 Z= 0.130 Angle : 0.414 3.918 44784 Z= 0.236 Chirality : 0.032 0.111 4920 Planarity : 0.002 0.024 5880 Dihedral : 3.882 12.983 4464 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.90 % Allowed : 9.81 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 5.30 (0.14), residues: 4032 helix: 4.16 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.33 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 89 HIS 0.002 0.001 HIS E 49 PHE 0.012 0.002 PHE B 37 TYR 0.004 0.001 TYR G 23 ARG 0.002 0.000 ARG X 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 590 time to evaluate : 3.889 Fit side-chains REVERT: B 69 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8283 (tp-100) REVERT: B 153 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7367 (ptp90) REVERT: A 69 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8281 (tp-100) REVERT: A 153 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7364 (ptp90) REVERT: C 153 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7370 (ptp90) REVERT: D 69 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8404 (tp-100) REVERT: E 69 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8403 (tp-100) REVERT: F 69 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8405 (tp-100) REVERT: G 69 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8323 (tp-100) REVERT: H 69 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8345 (tp-100) REVERT: H 153 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7373 (ptp90) REVERT: I 69 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8322 (tp-100) REVERT: J 153 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7369 (ptp90) REVERT: K 69 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8309 (tp-100) REVERT: L 69 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8320 (tp-100) REVERT: L 153 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7368 (ptp90) REVERT: M 69 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8310 (tp-100) REVERT: N 69 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8312 (tp-100) REVERT: O 69 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8317 (tp-100) REVERT: Q 69 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8281 (tp-100) REVERT: Q 153 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7363 (ptp90) REVERT: R 69 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8310 (tp-100) REVERT: S 69 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8309 (tp-100) REVERT: T 153 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7368 (ptp90) REVERT: V 69 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8310 (tp-100) REVERT: X 153 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7366 (ptp90) REVERT: Y 69 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8321 (tp-100) REVERT: Y 153 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7368 (ptp90) outliers start: 31 outliers final: 0 residues processed: 621 average time/residue: 2.0277 time to fit residues: 1422.8284 Evaluate side-chains 633 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 605 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain G residue 69 GLN Chi-restraints excluded: chain H residue 69 GLN Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain J residue 153 ARG Chi-restraints excluded: chain K residue 69 GLN Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 153 ARG Chi-restraints excluded: chain M residue 69 GLN Chi-restraints excluded: chain N residue 69 GLN Chi-restraints excluded: chain O residue 69 GLN Chi-restraints excluded: chain Q residue 69 GLN Chi-restraints excluded: chain Q residue 153 ARG Chi-restraints excluded: chain R residue 69 GLN Chi-restraints excluded: chain S residue 69 GLN Chi-restraints excluded: chain T residue 153 ARG Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain X residue 153 ARG Chi-restraints excluded: chain Y residue 69 GLN Chi-restraints excluded: chain Y residue 153 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 7.9990 chunk 376 optimal weight: 8.9990 chunk 343 optimal weight: 0.7980 chunk 366 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 287 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 331 optimal weight: 0.0060 chunk 346 optimal weight: 9.9990 chunk 365 optimal weight: 0.0870 overall best weight: 1.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN E 71 GLN F 71 GLN G 71 GLN I 71 GLN K 71 GLN L 71 GLN M 71 GLN O 71 GLN R 71 GLN T 71 GLN V 71 GLN X 71 GLN Y 71 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 33264 Z= 0.138 Angle : 0.424 3.865 44784 Z= 0.241 Chirality : 0.033 0.112 4920 Planarity : 0.002 0.024 5880 Dihedral : 3.936 13.353 4464 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.56 % Allowed : 10.07 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 5.27 (0.14), residues: 4032 helix: 4.13 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.28 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 89 HIS 0.002 0.001 HIS B 124 PHE 0.013 0.002 PHE B 37 TYR 0.005 0.001 TYR L 23 ARG 0.002 0.000 ARG F 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 622 time to evaluate : 4.463 Fit side-chains REVERT: B 69 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8328 (tp-100) REVERT: B 153 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7338 (ptp90) REVERT: A 69 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8327 (tp-100) REVERT: A 153 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7336 (ptp90) REVERT: C 69 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8321 (tp-100) REVERT: C 153 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7338 (ptp90) REVERT: D 69 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8422 (tp-100) REVERT: E 69 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8420 (tp-100) REVERT: F 69 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8424 (tp-100) REVERT: G 69 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8332 (tp-100) REVERT: G 153 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7336 (ptp90) REVERT: H 69 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8324 (tp-100) REVERT: H 153 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.7345 (ptp90) REVERT: I 25 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8099 (tmt170) REVERT: I 69 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8333 (tp-100) REVERT: I 153 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.7343 (ptp90) REVERT: J 69 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8292 (tp-100) REVERT: J 153 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7354 (ptp90) REVERT: K 25 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8099 (tmt170) REVERT: K 69 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8333 (tp-100) REVERT: K 153 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.7353 (ptp90) REVERT: L 25 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8097 (tmt170) REVERT: L 69 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8277 (tp-100) REVERT: L 153 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7338 (ptp90) REVERT: M 69 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8334 (tp-100) REVERT: M 153 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7371 (ptp90) REVERT: N 69 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8333 (tp-100) REVERT: N 152 GLN cc_start: 0.8587 (mt0) cc_final: 0.8282 (mt0) REVERT: N 153 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7365 (ptp90) REVERT: O 25 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8098 (tmt170) REVERT: O 69 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8278 (tp-100) REVERT: O 153 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7350 (ptp90) REVERT: P 69 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8351 (tp-100) REVERT: P 153 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7368 (ptp90) REVERT: Q 25 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8095 (tmt170) REVERT: Q 69 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8327 (tp-100) REVERT: Q 153 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7336 (ptp90) REVERT: R 69 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8333 (tp-100) REVERT: R 153 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7347 (ptp90) REVERT: S 69 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8330 (tp-100) REVERT: S 152 GLN cc_start: 0.8588 (mt0) cc_final: 0.8284 (mt0) REVERT: S 153 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7362 (ptp90) REVERT: T 69 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8350 (tp-100) REVERT: T 153 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7355 (ptp90) REVERT: V 69 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8334 (tp-100) REVERT: V 153 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7344 (ptp90) REVERT: W 25 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8098 (tmt170) REVERT: W 69 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8289 (tp-100) REVERT: W 153 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7368 (ptp90) REVERT: X 69 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8347 (tp-100) REVERT: X 153 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7353 (ptp90) REVERT: Y 69 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8278 (tp-100) REVERT: Y 153 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7337 (ptp90) outliers start: 54 outliers final: 0 residues processed: 676 average time/residue: 2.2441 time to fit residues: 1693.8812 Evaluate side-chains 630 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 579 time to evaluate : 3.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain G residue 69 GLN Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain H residue 69 GLN Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 153 ARG Chi-restraints excluded: chain J residue 69 GLN Chi-restraints excluded: chain J residue 153 ARG Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 69 GLN Chi-restraints excluded: chain K residue 153 ARG Chi-restraints excluded: chain L residue 25 ARG Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 153 ARG Chi-restraints excluded: chain M residue 69 GLN Chi-restraints excluded: chain M residue 153 ARG Chi-restraints excluded: chain N residue 69 GLN Chi-restraints excluded: chain N residue 153 ARG Chi-restraints excluded: chain O residue 25 ARG Chi-restraints excluded: chain O residue 69 GLN Chi-restraints excluded: chain O residue 153 ARG Chi-restraints excluded: chain P residue 69 GLN Chi-restraints excluded: chain P residue 153 ARG Chi-restraints excluded: chain Q residue 25 ARG Chi-restraints excluded: chain Q residue 69 GLN Chi-restraints excluded: chain Q residue 153 ARG Chi-restraints excluded: chain R residue 69 GLN Chi-restraints excluded: chain R residue 153 ARG Chi-restraints excluded: chain S residue 69 GLN Chi-restraints excluded: chain S residue 153 ARG Chi-restraints excluded: chain T residue 69 GLN Chi-restraints excluded: chain T residue 153 ARG Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain V residue 153 ARG Chi-restraints excluded: chain W residue 25 ARG Chi-restraints excluded: chain W residue 69 GLN Chi-restraints excluded: chain W residue 153 ARG Chi-restraints excluded: chain X residue 69 GLN Chi-restraints excluded: chain X residue 153 ARG Chi-restraints excluded: chain Y residue 69 GLN Chi-restraints excluded: chain Y residue 153 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 9.9990 chunk 387 optimal weight: 1.9990 chunk 236 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 269 optimal weight: 5.9990 chunk 406 optimal weight: 10.0000 chunk 374 optimal weight: 7.9990 chunk 323 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 250 optimal weight: 9.9990 chunk 198 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN E 71 GLN F 71 GLN N 71 GLN P 71 GLN S 71 GLN W 71 GLN Y 71 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 33264 Z= 0.300 Angle : 0.541 4.720 44784 Z= 0.300 Chirality : 0.039 0.132 4920 Planarity : 0.004 0.029 5880 Dihedral : 4.376 15.806 4464 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.07 % Allowed : 10.73 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.92 (0.14), residues: 4032 helix: 3.86 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.29 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 89 HIS 0.004 0.002 HIS E 124 PHE 0.017 0.003 PHE J 37 TYR 0.007 0.002 TYR O 30 ARG 0.002 0.001 ARG P 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 547 time to evaluate : 4.293 Fit side-chains REVERT: B 69 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8479 (tp-100) REVERT: A 69 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8481 (tp-100) REVERT: C 153 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7296 (ptp90) REVERT: D 69 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8506 (tp-100) REVERT: E 69 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8506 (tp-100) REVERT: F 69 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8510 (tp-100) REVERT: G 69 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8434 (tp-100) REVERT: H 69 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8476 (tp-100) REVERT: I 25 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8144 (tmt170) REVERT: I 69 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8435 (tp-100) REVERT: J 153 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7290 (ptp90) REVERT: K 25 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8144 (tmt170) REVERT: K 69 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8495 (tp-100) REVERT: L 25 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8142 (tmt170) REVERT: L 69 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8434 (tp-100) REVERT: M 69 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8499 (tp-100) REVERT: N 69 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8484 (tp-100) REVERT: O 25 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8141 (tmt170) REVERT: O 69 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8434 (tp-100) REVERT: O 153 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.7296 (ptp90) REVERT: Q 25 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8143 (tmt170) REVERT: Q 69 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8482 (tp-100) REVERT: R 69 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8496 (tp-100) REVERT: S 69 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8482 (tp-100) REVERT: V 69 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8498 (tp-100) REVERT: V 153 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.7300 (ptp90) REVERT: W 25 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8143 (tmt170) REVERT: Y 69 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8435 (tp-100) outliers start: 37 outliers final: 0 residues processed: 584 average time/residue: 2.1379 time to fit residues: 1410.8932 Evaluate side-chains 571 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 543 time to evaluate : 4.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain G residue 69 GLN Chi-restraints excluded: chain H residue 69 GLN Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain J residue 153 ARG Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 69 GLN Chi-restraints excluded: chain L residue 25 ARG Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain M residue 69 GLN Chi-restraints excluded: chain N residue 69 GLN Chi-restraints excluded: chain O residue 25 ARG Chi-restraints excluded: chain O residue 69 GLN Chi-restraints excluded: chain O residue 153 ARG Chi-restraints excluded: chain Q residue 25 ARG Chi-restraints excluded: chain Q residue 69 GLN Chi-restraints excluded: chain R residue 69 GLN Chi-restraints excluded: chain S residue 69 GLN Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain V residue 153 ARG Chi-restraints excluded: chain W residue 25 ARG Chi-restraints excluded: chain Y residue 69 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 4.9990 chunk 344 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 298 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 324 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 332 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN E 71 GLN F 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.111952 restraints weight = 33577.134| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.34 r_work: 0.3256 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 33264 Z= 0.118 Angle : 0.404 4.005 44784 Z= 0.232 Chirality : 0.032 0.111 4920 Planarity : 0.002 0.024 5880 Dihedral : 3.858 12.308 4464 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.72 % Allowed : 11.08 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 5.29 (0.14), residues: 4032 helix: 4.14 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.25 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 89 HIS 0.002 0.001 HIS G 49 PHE 0.012 0.002 PHE B 50 TYR 0.004 0.001 TYR G 23 ARG 0.002 0.000 ARG E 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18069.24 seconds wall clock time: 316 minutes 21.10 seconds (18981.10 seconds total)