Starting phenix.real_space_refine (version: dev) on Sun Dec 18 14:59:50 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxm_20521/12_2022/6pxm_20521.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxm_20521/12_2022/6pxm_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_20521/12_2022/6pxm_20521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxm_20521/12_2022/6pxm_20521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxm_20521/12_2022/6pxm_20521.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxm_20521/12_2022/6pxm_20521.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 17.13, per 1000 atoms: 0.52 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: 12.48 Conformation dependent library (CDL) restraints added in 4.9 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: 0.82 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: 9.64 Time building geometry restraints manager: 13.44 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 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. 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 10.480 Check model and map are aligned: 0.470 Convert atoms to be neutral: 0.280 Process input model: 76.350 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 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 % 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 *********************** 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 : 4.186 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 673 average time/residue: 1.9268 time to fit residues: 1470.4759 Evaluate side-chains 446 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 3.585 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1066 ------------------------------------------------------------------------------- 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: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 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 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 132 HIS S 7 ASN S 71 GLN S 132 HIS T 7 ASN T 71 GLN T 132 HIS V 7 ASN 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: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.018 33264 Z= 0.196 Angle : 0.488 4.835 44784 Z= 0.276 Chirality : 0.035 0.125 4920 Planarity : 0.004 0.030 5880 Dihedral : 4.294 16.815 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 : 0.69 % 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: 2.35 (0.13), residues: 4032 helix: 2.02 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.70 (0.24), residues: 696 *********************** 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 610 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 586 time to evaluate : 4.387 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 610 average time/residue: 1.6874 time to fit residues: 1188.8751 Evaluate side-chains 507 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 507 time to evaluate : 4.346 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7096 ------------------------------------------------------------------------------- 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: 9.9990 chunk 308 optimal weight: 7.9990 chunk 252 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 371 optimal weight: 8.9990 chunk 400 optimal weight: 1.9990 chunk 330 optimal weight: 1.9990 chunk 368 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 297 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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: 0.8851 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.018 33264 Z= 0.191 Angle : 0.468 4.534 44784 Z= 0.263 Chirality : 0.034 0.120 4920 Planarity : 0.003 0.027 5880 Dihedral : 4.206 16.120 4464 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer Outliers : 0.20 % 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: 4.16 (0.14), residues: 4032 helix: 3.36 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.64 (0.25), residues: 696 *********************** 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 522 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 515 time to evaluate : 4.500 Fit side-chains outliers start: 7 outliers final: 0 residues processed: 522 average time/residue: 1.8327 time to fit residues: 1097.5050 Evaluate side-chains 518 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 518 time to evaluate : 4.155 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6647 ------------------------------------------------------------------------------- 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: 10.0000 chunk 192 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 249 optimal weight: 10.0000 chunk 372 optimal weight: 8.9990 chunk 394 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 353 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.8859 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.020 33264 Z= 0.228 Angle : 0.488 4.345 44784 Z= 0.273 Chirality : 0.036 0.124 4920 Planarity : 0.003 0.027 5880 Dihedral : 4.286 16.263 4464 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.72 % 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: 4.57 (0.14), residues: 4032 helix: 3.66 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.60 (0.24), residues: 696 *********************** 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 570 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 545 time to evaluate : 4.323 Fit side-chains outliers start: 25 outliers final: 0 residues processed: 570 average time/residue: 1.9550 time to fit residues: 1272.7830 Evaluate side-chains 553 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 553 time to evaluate : 3.915 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 293 optimal weight: 8.9990 chunk 162 optimal weight: 0.9990 chunk 336 optimal weight: 7.9990 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: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 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 0.011 33264 Z= 0.115 Angle : 0.391 4.304 44784 Z= 0.224 Chirality : 0.032 0.111 4920 Planarity : 0.002 0.024 5880 Dihedral : 3.848 13.082 4464 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 0.03 % 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: 5.05 (0.14), residues: 4032 helix: 4.00 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.50 (0.24), residues: 696 *********************** 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 633 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 632 time to evaluate : 3.935 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 633 average time/residue: 1.9154 time to fit residues: 1377.0500 Evaluate side-chains 582 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 582 time to evaluate : 4.015 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 0.9980 chunk 355 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 231 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 394 optimal weight: 9.9990 chunk 327 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 GLN F 71 GLN G 71 GLN O 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1826 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= 0.227 Angle : 0.486 4.238 44784 Z= 0.272 Chirality : 0.036 0.125 4920 Planarity : 0.003 0.027 5880 Dihedral : 4.181 15.329 4464 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.09 % 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: 4.91 (0.14), residues: 4032 helix: 3.89 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.46 (0.24), residues: 696 *********************** 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 546 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 543 time to evaluate : 4.230 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 543 average time/residue: 1.8495 time to fit residues: 1153.2666 Evaluate side-chains 522 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 522 time to evaluate : 4.023 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 224 optimal weight: 0.2980 chunk 288 optimal weight: 6.9990 chunk 223 optimal weight: 7.9990 chunk 332 optimal weight: 0.8980 chunk 220 optimal weight: 0.9990 chunk 393 optimal weight: 6.9990 chunk 246 optimal weight: 0.1980 chunk 239 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 GLN F 71 GLN G 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.010 33264 Z= 0.104 Angle : 0.382 4.145 44784 Z= 0.220 Chirality : 0.031 0.110 4920 Planarity : 0.002 0.023 5880 Dihedral : 3.773 11.811 4464 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 0.29 % 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: 5.32 (0.14), residues: 4032 helix: 4.18 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.38 (0.24), residues: 696 *********************** 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 620 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 610 time to evaluate : 4.086 Fit side-chains outliers start: 10 outliers final: 0 residues processed: 620 average time/residue: 1.7527 time to fit residues: 1249.4537 Evaluate side-chains 594 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 594 time to evaluate : 3.736 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 234 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 250 optimal weight: 9.9990 chunk 267 optimal weight: 0.8980 chunk 194 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 309 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN C 71 GLN E 71 GLN F 71 GLN G 71 GLN Y 71 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.015 33264 Z= 0.160 Angle : 0.438 3.993 44784 Z= 0.248 Chirality : 0.033 0.117 4920 Planarity : 0.003 0.025 5880 Dihedral : 3.970 13.870 4464 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 0.09 % 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: 5.23 (0.14), residues: 4032 helix: 4.10 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.31 (0.24), residues: 696 *********************** 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 593 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 590 time to evaluate : 3.653 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 593 average time/residue: 2.0713 time to fit residues: 1386.6740 Evaluate side-chains 573 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 573 time to evaluate : 4.086 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 8.9990 chunk 376 optimal weight: 8.9990 chunk 343 optimal weight: 9.9990 chunk 366 optimal weight: 0.9990 chunk 220 optimal weight: 0.5980 chunk 159 optimal weight: 9.9990 chunk 287 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 331 optimal weight: 2.9990 chunk 346 optimal weight: 9.9990 chunk 365 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 GLN F 71 GLN G 71 GLN J 71 GLN K 71 GLN T 71 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 33264 Z= 0.213 Angle : 0.481 4.181 44784 Z= 0.269 Chirality : 0.035 0.122 4920 Planarity : 0.003 0.026 5880 Dihedral : 4.150 14.960 4464 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 0.09 % 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: 5.10 (0.14), residues: 4032 helix: 4.00 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.28 (0.24), residues: 696 *********************** 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 535 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 532 time to evaluate : 3.949 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 535 average time/residue: 1.8371 time to fit residues: 1124.8865 Evaluate side-chains 530 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 530 time to evaluate : 4.026 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 7.9990 chunk 387 optimal weight: 6.9990 chunk 236 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 269 optimal weight: 3.9990 chunk 406 optimal weight: 4.9990 chunk 374 optimal weight: 7.9990 chunk 323 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 GLN F 71 GLN Y 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 33264 Z= 0.349 Angle : 0.567 4.885 44784 Z= 0.314 Chirality : 0.040 0.131 4920 Planarity : 0.004 0.030 5880 Dihedral : 4.478 16.444 4464 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer Outliers : 0.09 % 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: 4.71 (0.13), residues: 4032 helix: 3.72 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.38 (0.24), residues: 696 ********************** 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 527 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 524 time to evaluate : 3.846 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 527 average time/residue: 1.8118 time to fit residues: 1093.3931 Evaluate side-chains 501 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 501 time to evaluate : 3.620 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 6.9990 chunk 344 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 324 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 332 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 GLN F 71 GLN G 71 GLN I 71 GLN L 71 GLN M 71 GLN P 71 GLN Q 71 GLN S 71 GLN W 71 GLN X 71 GLN Y 71 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.126774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.110218 restraints weight = 33560.299| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.33 r_work: 0.3241 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.014 33264 Z= 0.119 Angle : 0.406 4.222 44784 Z= 0.233 Chirality : 0.032 0.112 4920 Planarity : 0.002 0.024 5880 Dihedral : 3.906 12.884 4464 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 0.12 % 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: 5.26 (0.14), residues: 4032 helix: 4.12 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.27 (0.24), residues: 696 =============================================================================== Job complete usr+sys time: 16246.99 seconds wall clock time: 284 minutes 15.46 seconds (17055.46 seconds total)