Starting phenix.real_space_refine (version: dev) on Tue Feb 21 08:14:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd5_10149/02_2023/6sd5_10149.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd5_10149/02_2023/6sd5_10149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd5_10149/02_2023/6sd5_10149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd5_10149/02_2023/6sd5_10149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd5_10149/02_2023/6sd5_10149.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd5_10149/02_2023/6sd5_10149.pdb" } resolution = 3.1 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= 0.001 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 Process input model Symmetric amino acids flipped Residue "A ARG 134": "NH1" <-> "NH2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "F ARG 134": "NH1" <-> "NH2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F ARG 154": "NH1" <-> "NH2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "G ARG 134": "NH1" <-> "NH2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G ARG 154": "NH1" <-> "NH2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "I ARG 134": "NH1" <-> "NH2" Residue "I GLU 139": "OE1" <-> "OE2" Residue "I ARG 154": "NH1" <-> "NH2" Residue "I GLU 188": "OE1" <-> "OE2" Residue "J ARG 134": "NH1" <-> "NH2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J ARG 154": "NH1" <-> "NH2" Residue "J GLU 188": "OE1" <-> "OE2" Residue "L ARG 134": "NH1" <-> "NH2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "L ARG 154": "NH1" <-> "NH2" Residue "L GLU 188": "OE1" <-> "OE2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "M GLU 139": "OE1" <-> "OE2" Residue "M ARG 154": "NH1" <-> "NH2" Residue "M GLU 188": "OE1" <-> "OE2" Residue "O ARG 134": "NH1" <-> "NH2" Residue "O GLU 139": "OE1" <-> "OE2" Residue "O ARG 154": "NH1" <-> "NH2" Residue "O GLU 188": "OE1" <-> "OE2" Residue "P ARG 134": "NH1" <-> "NH2" Residue "P GLU 139": "OE1" <-> "OE2" Residue "P ARG 154": "NH1" <-> "NH2" Residue "P GLU 188": "OE1" <-> "OE2" Residue "R ARG 134": "NH1" <-> "NH2" Residue "R GLU 139": "OE1" <-> "OE2" Residue "R ARG 154": "NH1" <-> "NH2" Residue "R GLU 188": "OE1" <-> "OE2" Residue "T ARG 134": "NH1" <-> "NH2" Residue "T GLU 139": "OE1" <-> "OE2" Residue "T ARG 154": "NH1" <-> "NH2" Residue "T GLU 188": "OE1" <-> "OE2" Residue "U ARG 134": "NH1" <-> "NH2" Residue "U GLU 139": "OE1" <-> "OE2" Residue "U ARG 154": "NH1" <-> "NH2" Residue "U GLU 188": "OE1" <-> "OE2" Residue "W ARG 134": "NH1" <-> "NH2" Residue "W GLU 139": "OE1" <-> "OE2" Residue "W ARG 154": "NH1" <-> "NH2" Residue "W GLU 188": "OE1" <-> "OE2" Residue "X ARG 134": "NH1" <-> "NH2" Residue "X GLU 139": "OE1" <-> "OE2" Residue "X ARG 154": "NH1" <-> "NH2" Residue "X GLU 188": "OE1" <-> "OE2" Residue "Z ARG 134": "NH1" <-> "NH2" Residue "Z GLU 139": "OE1" <-> "OE2" Residue "Z ARG 154": "NH1" <-> "NH2" Residue "Z GLU 188": "OE1" <-> "OE2" Residue "a ARG 134": "NH1" <-> "NH2" Residue "a GLU 139": "OE1" <-> "OE2" Residue "a ARG 154": "NH1" <-> "NH2" Residue "a GLU 188": "OE1" <-> "OE2" Residue "c ARG 134": "NH1" <-> "NH2" Residue "c GLU 139": "OE1" <-> "OE2" Residue "c ARG 154": "NH1" <-> "NH2" Residue "c GLU 188": "OE1" <-> "OE2" Residue "d ARG 134": "NH1" <-> "NH2" Residue "d GLU 139": "OE1" <-> "OE2" Residue "d ARG 154": "NH1" <-> "NH2" Residue "d GLU 188": "OE1" <-> "OE2" Residue "f ARG 134": "NH1" <-> "NH2" Residue "f GLU 139": "OE1" <-> "OE2" Residue "f ARG 154": "NH1" <-> "NH2" Residue "f GLU 188": "OE1" <-> "OE2" Residue "g ARG 134": "NH1" <-> "NH2" Residue "g GLU 139": "OE1" <-> "OE2" Residue "g ARG 154": "NH1" <-> "NH2" Residue "g GLU 188": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 14212 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "C" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "D" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "G" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "I" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "J" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "L" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "M" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "O" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "P" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "R" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "T" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "U" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "W" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "X" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "Z" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "a" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "c" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "d" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "f" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "g" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Time building chain proxies: 7.94, per 1000 atoms: 0.56 Number of scatterers: 14212 At special positions: 0 Unit cell: (171.798, 170.154, 41.1, 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 22 16.00 O 2816 8.00 N 2530 7.00 C 8844 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: 5.54 Conformation dependent library (CDL) restraints added in 2.1 seconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3564 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 44 sheets defined 38.6% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 194 " --> pdb=" O GLN A 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 198 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 132 Processing helix chain 'C' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER C 192 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 194 " --> pdb=" O GLN C 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR D 146 " --> pdb=" O ARG D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER D 192 " --> pdb=" O GLU D 188 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 193 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 194 " --> pdb=" O GLN D 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL D 198 " --> pdb=" O VAL D 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 132 Processing helix chain 'F' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR F 146 " --> pdb=" O ARG F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER F 192 " --> pdb=" O GLU F 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA F 193 " --> pdb=" O GLY F 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL F 194 " --> pdb=" O GLN F 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL F 198 " --> pdb=" O VAL F 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 132 Processing helix chain 'G' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR G 146 " --> pdb=" O ARG G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 200 removed outlier: 4.400A pdb=" N SER G 192 " --> pdb=" O GLU G 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA G 193 " --> pdb=" O GLY G 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL G 194 " --> pdb=" O GLN G 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL G 198 " --> pdb=" O VAL G 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 132 Processing helix chain 'I' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR I 146 " --> pdb=" O ARG I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER I 192 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA I 193 " --> pdb=" O GLY I 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL I 194 " --> pdb=" O GLN I 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL I 198 " --> pdb=" O VAL I 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 132 Processing helix chain 'J' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR J 146 " --> pdb=" O ARG J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER J 192 " --> pdb=" O GLU J 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA J 193 " --> pdb=" O GLY J 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL J 194 " --> pdb=" O GLN J 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 132 Processing helix chain 'L' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER L 192 " --> pdb=" O GLU L 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA L 193 " --> pdb=" O GLY L 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL L 194 " --> pdb=" O GLN L 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL L 198 " --> pdb=" O VAL L 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 132 Processing helix chain 'M' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR M 146 " --> pdb=" O ARG M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER M 192 " --> pdb=" O GLU M 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA M 193 " --> pdb=" O GLY M 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL M 194 " --> pdb=" O GLN M 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL M 198 " --> pdb=" O VAL M 194 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 132 Processing helix chain 'O' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR O 146 " --> pdb=" O ARG O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER O 192 " --> pdb=" O GLU O 188 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA O 193 " --> pdb=" O GLY O 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL O 194 " --> pdb=" O GLN O 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL O 198 " --> pdb=" O VAL O 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 132 Processing helix chain 'P' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR P 146 " --> pdb=" O ARG P 142 " (cutoff:3.500A) Processing helix chain 'P' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER P 192 " --> pdb=" O GLU P 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA P 193 " --> pdb=" O GLY P 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL P 194 " --> pdb=" O GLN P 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL P 198 " --> pdb=" O VAL P 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 132 Processing helix chain 'R' and resid 132 through 146 removed outlier: 3.634A pdb=" N THR R 146 " --> pdb=" O ARG R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER R 192 " --> pdb=" O GLU R 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA R 193 " --> pdb=" O GLY R 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL R 194 " --> pdb=" O GLN R 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL R 198 " --> pdb=" O VAL R 194 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 132 Processing helix chain 'T' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR T 146 " --> pdb=" O ARG T 142 " (cutoff:3.500A) Processing helix chain 'T' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER T 192 " --> pdb=" O GLU T 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA T 193 " --> pdb=" O GLY T 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL T 194 " --> pdb=" O GLN T 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL T 198 " --> pdb=" O VAL T 194 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 132 Processing helix chain 'U' and resid 132 through 146 removed outlier: 3.634A pdb=" N THR U 146 " --> pdb=" O ARG U 142 " (cutoff:3.500A) Processing helix chain 'U' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER U 192 " --> pdb=" O GLU U 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA U 193 " --> pdb=" O GLY U 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL U 194 " --> pdb=" O GLN U 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL U 198 " --> pdb=" O VAL U 194 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 132 Processing helix chain 'W' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR W 146 " --> pdb=" O ARG W 142 " (cutoff:3.500A) Processing helix chain 'W' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA W 193 " --> pdb=" O GLY W 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL W 194 " --> pdb=" O GLN W 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL W 198 " --> pdb=" O VAL W 194 " (cutoff:3.500A) Processing helix chain 'X' and resid 127 through 132 Processing helix chain 'X' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR X 146 " --> pdb=" O ARG X 142 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER X 192 " --> pdb=" O GLU X 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA X 193 " --> pdb=" O GLY X 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL X 194 " --> pdb=" O GLN X 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL X 198 " --> pdb=" O VAL X 194 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 132 Processing helix chain 'Z' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR Z 146 " --> pdb=" O ARG Z 142 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER Z 192 " --> pdb=" O GLU Z 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA Z 193 " --> pdb=" O GLY Z 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL Z 194 " --> pdb=" O GLN Z 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL Z 198 " --> pdb=" O VAL Z 194 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 132 Processing helix chain 'a' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR a 146 " --> pdb=" O ARG a 142 " (cutoff:3.500A) Processing helix chain 'a' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER a 192 " --> pdb=" O GLU a 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA a 193 " --> pdb=" O GLY a 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL a 194 " --> pdb=" O GLN a 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL a 198 " --> pdb=" O VAL a 194 " (cutoff:3.500A) Processing helix chain 'c' and resid 127 through 132 Processing helix chain 'c' and resid 132 through 146 removed outlier: 3.632A pdb=" N THR c 146 " --> pdb=" O ARG c 142 " (cutoff:3.500A) Processing helix chain 'c' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER c 192 " --> pdb=" O GLU c 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA c 193 " --> pdb=" O GLY c 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL c 194 " --> pdb=" O GLN c 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL c 198 " --> pdb=" O VAL c 194 " (cutoff:3.500A) Processing helix chain 'd' and resid 127 through 132 Processing helix chain 'd' and resid 132 through 146 removed outlier: 3.634A pdb=" N THR d 146 " --> pdb=" O ARG d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER d 192 " --> pdb=" O GLU d 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA d 193 " --> pdb=" O GLY d 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL d 194 " --> pdb=" O GLN d 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL d 198 " --> pdb=" O VAL d 194 " (cutoff:3.500A) Processing helix chain 'f' and resid 127 through 132 Processing helix chain 'f' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR f 146 " --> pdb=" O ARG f 142 " (cutoff:3.500A) Processing helix chain 'f' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER f 192 " --> pdb=" O GLU f 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA f 193 " --> pdb=" O GLY f 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL f 194 " --> pdb=" O GLN f 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL f 198 " --> pdb=" O VAL f 194 " (cutoff:3.500A) Processing helix chain 'g' and resid 127 through 132 Processing helix chain 'g' and resid 132 through 146 removed outlier: 3.634A pdb=" N THR g 146 " --> pdb=" O ARG g 142 " (cutoff:3.500A) Processing helix chain 'g' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER g 192 " --> pdb=" O GLU g 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA g 193 " --> pdb=" O GLY g 189 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL g 194 " --> pdb=" O GLN g 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL g 198 " --> pdb=" O VAL g 194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR A 179 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS A 156 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR C 179 " --> pdb=" O LYS C 151 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS C 156 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR D 179 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS D 156 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR F 179 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS F 156 " --> pdb=" O SER F 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR G 179 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS G 156 " --> pdb=" O SER G 175 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR I 179 " --> pdb=" O LYS I 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS I 156 " --> pdb=" O SER I 175 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR J 179 " --> pdb=" O LYS J 151 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS J 156 " --> pdb=" O SER J 175 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR L 179 " --> pdb=" O LYS L 151 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 156 through 157 removed outlier: 3.546A pdb=" N HIS L 156 " --> pdb=" O SER L 175 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR M 179 " --> pdb=" O LYS M 151 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS M 156 " --> pdb=" O SER M 175 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR O 179 " --> pdb=" O LYS O 151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS O 156 " --> pdb=" O SER O 175 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'P' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR P 179 " --> pdb=" O LYS P 151 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS P 156 " --> pdb=" O SER P 175 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR R 179 " --> pdb=" O LYS R 151 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'R' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS R 156 " --> pdb=" O SER R 175 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR T 179 " --> pdb=" O LYS T 151 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS T 156 " --> pdb=" O SER T 175 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR U 179 " --> pdb=" O LYS U 151 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'U' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS U 156 " --> pdb=" O SER U 175 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'W' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR W 179 " --> pdb=" O LYS W 151 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'W' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS W 156 " --> pdb=" O SER W 175 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR X 179 " --> pdb=" O LYS X 151 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'X' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS X 156 " --> pdb=" O SER X 175 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Z' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR Z 179 " --> pdb=" O LYS Z 151 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Z' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS Z 156 " --> pdb=" O SER Z 175 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'a' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR a 179 " --> pdb=" O LYS a 151 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'a' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS a 156 " --> pdb=" O SER a 175 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'c' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR c 179 " --> pdb=" O LYS c 151 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'c' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS c 156 " --> pdb=" O SER c 175 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR d 179 " --> pdb=" O LYS d 151 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS d 156 " --> pdb=" O SER d 175 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'f' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR f 179 " --> pdb=" O LYS f 151 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'f' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS f 156 " --> pdb=" O SER f 175 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'g' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR g 179 " --> pdb=" O LYS g 151 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'g' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS g 156 " --> pdb=" O SER g 175 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1386 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: 4.08 Time building geometry restraints manager: 6.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4928 1.34 - 1.46: 1742 1.46 - 1.57: 7696 1.57 - 1.69: 0 1.69 - 1.80: 44 Bond restraints: 14410 Sorted by residual: bond pdb=" CA HIS T 218 " pdb=" C HIS T 218 " ideal model delta sigma weight residual 1.532 1.519 0.014 9.60e-03 1.09e+04 2.06e+00 bond pdb=" CA HIS O 218 " pdb=" C HIS O 218 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.88e+00 bond pdb=" CA HIS g 218 " pdb=" C HIS g 218 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.86e+00 bond pdb=" CA HIS G 218 " pdb=" C HIS G 218 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.86e+00 bond pdb=" CA HIS A 218 " pdb=" C HIS A 218 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.83e+00 ... (remaining 14405 not shown) Histogram of bond angle deviations from ideal: 100.74 - 106.87: 594 106.87 - 113.00: 8325 113.00 - 119.12: 3489 119.12 - 125.25: 7040 125.25 - 131.38: 198 Bond angle restraints: 19646 Sorted by residual: angle pdb=" N VAL J 130 " pdb=" CA VAL J 130 " pdb=" C VAL J 130 " ideal model delta sigma weight residual 112.12 108.28 3.84 8.40e-01 1.42e+00 2.08e+01 angle pdb=" N VAL L 130 " pdb=" CA VAL L 130 " pdb=" C VAL L 130 " ideal model delta sigma weight residual 112.12 108.30 3.82 8.40e-01 1.42e+00 2.07e+01 angle pdb=" N VAL O 130 " pdb=" CA VAL O 130 " pdb=" C VAL O 130 " ideal model delta sigma weight residual 112.12 108.30 3.82 8.40e-01 1.42e+00 2.06e+01 angle pdb=" N VAL a 130 " pdb=" CA VAL a 130 " pdb=" C VAL a 130 " ideal model delta sigma weight residual 112.12 108.31 3.81 8.40e-01 1.42e+00 2.06e+01 angle pdb=" N VAL M 130 " pdb=" CA VAL M 130 " pdb=" C VAL M 130 " ideal model delta sigma weight residual 112.12 108.31 3.81 8.40e-01 1.42e+00 2.06e+01 ... (remaining 19641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 7832 16.44 - 32.88: 726 32.88 - 49.32: 176 49.32 - 65.76: 44 65.76 - 82.20: 22 Dihedral angle restraints: 8800 sinusoidal: 3322 harmonic: 5478 Sorted by residual: dihedral pdb=" CB GLU J 188 " pdb=" CG GLU J 188 " pdb=" CD GLU J 188 " pdb=" OE1 GLU J 188 " ideal model delta sinusoidal sigma weight residual 0.00 -82.20 82.20 1 3.00e+01 1.11e-03 9.22e+00 dihedral pdb=" CB GLU R 188 " pdb=" CG GLU R 188 " pdb=" CD GLU R 188 " pdb=" OE1 GLU R 188 " ideal model delta sinusoidal sigma weight residual 0.00 -82.16 82.16 1 3.00e+01 1.11e-03 9.21e+00 dihedral pdb=" CB GLU D 188 " pdb=" CG GLU D 188 " pdb=" CD GLU D 188 " pdb=" OE1 GLU D 188 " ideal model delta sinusoidal sigma weight residual 0.00 -82.16 82.16 1 3.00e+01 1.11e-03 9.21e+00 ... (remaining 8797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1365 0.028 - 0.055: 656 0.055 - 0.083: 284 0.083 - 0.110: 115 0.110 - 0.138: 22 Chirality restraints: 2442 Sorted by residual: chirality pdb=" CA VAL f 213 " pdb=" N VAL f 213 " pdb=" C VAL f 213 " pdb=" CB VAL f 213 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA VAL W 213 " pdb=" N VAL W 213 " pdb=" C VAL W 213 " pdb=" CB VAL W 213 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA VAL D 213 " pdb=" N VAL D 213 " pdb=" C VAL D 213 " pdb=" CB VAL D 213 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 2439 not shown) Planarity restraints: 2574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU T 181 " -0.012 5.00e-02 4.00e+02 1.87e-02 5.60e-01 pdb=" N PRO T 182 " 0.032 5.00e-02 4.00e+02 pdb=" CA PRO T 182 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO T 182 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU a 181 " -0.012 5.00e-02 4.00e+02 1.87e-02 5.59e-01 pdb=" N PRO a 182 " 0.032 5.00e-02 4.00e+02 pdb=" CA PRO a 182 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO a 182 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU d 181 " -0.012 5.00e-02 4.00e+02 1.87e-02 5.59e-01 pdb=" N PRO d 182 " 0.032 5.00e-02 4.00e+02 pdb=" CA PRO d 182 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO d 182 " -0.010 5.00e-02 4.00e+02 ... (remaining 2571 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 5059 2.84 - 3.35: 13320 3.35 - 3.87: 21809 3.87 - 4.38: 27851 4.38 - 4.90: 47853 Nonbonded interactions: 115892 Sorted by model distance: nonbonded pdb=" O SER D 175 " pdb=" OG SER D 175 " model vdw 2.321 2.440 nonbonded pdb=" O SER L 175 " pdb=" OG SER L 175 " model vdw 2.322 2.440 nonbonded pdb=" O SER F 175 " pdb=" OG SER F 175 " model vdw 2.322 2.440 nonbonded pdb=" O SER A 175 " pdb=" OG SER A 175 " model vdw 2.322 2.440 nonbonded pdb=" O SER I 175 " pdb=" OG SER I 175 " model vdw 2.322 2.440 ... (remaining 115887 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 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' } 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 22 5.16 5 C 8844 2.51 5 N 2530 2.21 5 O 2816 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: 3.790 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: 0.010 Extract box with map and model: 17.870 Check model and map are aligned: 0.000 Process input model: 38.060 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.140 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 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 : 0.006 0.041 14410 Z= 0.431 Angle : 0.708 4.709 19646 Z= 0.428 Chirality : 0.041 0.138 2442 Planarity : 0.003 0.019 2574 Dihedral : 15.042 82.197 5236 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer Outliers : 1.39 % 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: -5.48 (0.16), residues: 1848 helix: -4.59 (0.08), residues: 726 sheet: -3.31 (0.23), residues: 484 loop : -2.12 (0.21), residues: 638 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 447 time to evaluate : 1.577 Fit side-chains outliers start: 22 outliers final: 20 residues processed: 469 average time/residue: 0.3075 time to fit residues: 198.9558 Evaluate side-chains 411 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 391 time to evaluate : 1.520 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1234 time to fit residues: 6.8959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.7980 chunk 133 optimal weight: 0.2980 chunk 74 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 137 optimal weight: 0.5980 chunk 53 optimal weight: 0.3980 chunk 83 optimal weight: 0.1980 chunk 102 optimal weight: 0.8980 chunk 159 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 196 HIS C 196 HIS D 196 HIS F 190 GLN F 196 HIS G 190 GLN G 196 HIS I 190 GLN I 196 HIS J 196 HIS L 190 GLN M 190 GLN M 196 HIS O 190 GLN O 196 HIS P 190 GLN P 196 HIS R 190 GLN R 196 HIS T 196 HIS U 196 HIS W 190 GLN X 196 HIS Z 190 GLN Z 196 HIS a 196 HIS c 196 HIS d 190 GLN d 196 HIS f 190 GLN f 196 HIS g 196 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 14410 Z= 0.203 Angle : 0.535 8.331 19646 Z= 0.268 Chirality : 0.038 0.118 2442 Planarity : 0.004 0.017 2574 Dihedral : 3.964 11.867 2002 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 4.29 % 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: -3.92 (0.18), residues: 1848 helix: -2.81 (0.16), residues: 704 sheet: -2.88 (0.24), residues: 484 loop : -1.66 (0.22), residues: 660 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 429 time to evaluate : 1.680 Fit side-chains outliers start: 68 outliers final: 54 residues processed: 465 average time/residue: 0.2560 time to fit residues: 174.1615 Evaluate side-chains 413 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 359 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.1341 time to fit residues: 15.3005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 133 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 142 optimal weight: 0.1980 chunk 158 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 196 HIS W 196 HIS c 190 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 14410 Z= 0.262 Angle : 0.561 6.955 19646 Z= 0.275 Chirality : 0.040 0.121 2442 Planarity : 0.003 0.026 2574 Dihedral : 3.846 11.507 2002 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 2.27 % 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: -2.81 (0.19), residues: 1848 helix: -1.52 (0.19), residues: 726 sheet: -2.81 (0.23), residues: 528 loop : -0.82 (0.24), residues: 594 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 375 time to evaluate : 1.621 Fit side-chains outliers start: 36 outliers final: 26 residues processed: 392 average time/residue: 0.2675 time to fit residues: 149.9424 Evaluate side-chains 377 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 351 time to evaluate : 1.659 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1215 time to fit residues: 8.1969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 170 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 141 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 190 GLN M 190 GLN O 190 GLN P 190 GLN U 190 GLN c 190 GLN d 190 GLN f 190 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 14410 Z= 0.253 Angle : 0.564 8.315 19646 Z= 0.271 Chirality : 0.040 0.123 2442 Planarity : 0.003 0.029 2574 Dihedral : 3.720 10.913 2002 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 2.78 % 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: -2.02 (0.21), residues: 1848 helix: -0.76 (0.20), residues: 726 sheet: -2.53 (0.25), residues: 484 loop : -0.62 (0.26), residues: 638 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 353 time to evaluate : 1.681 Fit side-chains outliers start: 44 outliers final: 39 residues processed: 372 average time/residue: 0.2694 time to fit residues: 143.8570 Evaluate side-chains 363 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 324 time to evaluate : 1.813 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.1360 time to fit residues: 12.0346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 70 optimal weight: 0.4980 chunk 145 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 190 GLN f 190 GLN g 190 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 14410 Z= 0.302 Angle : 0.581 9.311 19646 Z= 0.278 Chirality : 0.040 0.121 2442 Planarity : 0.003 0.032 2574 Dihedral : 3.774 11.070 2002 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 4.10 % 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: -2.08 (0.21), residues: 1848 helix: -0.65 (0.20), residues: 726 sheet: -2.58 (0.24), residues: 528 loop : -0.67 (0.26), residues: 594 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 321 time to evaluate : 1.669 Fit side-chains outliers start: 65 outliers final: 59 residues processed: 362 average time/residue: 0.2703 time to fit residues: 140.0370 Evaluate side-chains 370 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 311 time to evaluate : 1.442 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.1200 time to fit residues: 15.3944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 141 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 190 GLN M 190 GLN O 190 GLN P 190 GLN c 190 GLN f 190 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 14410 Z= 0.264 Angle : 0.561 8.198 19646 Z= 0.272 Chirality : 0.039 0.118 2442 Planarity : 0.003 0.027 2574 Dihedral : 3.658 10.993 2002 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 2.53 % 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: -1.65 (0.21), residues: 1848 helix: -0.49 (0.20), residues: 726 sheet: -2.32 (0.26), residues: 484 loop : -0.38 (0.27), residues: 638 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 330 time to evaluate : 1.814 Fit side-chains outliers start: 40 outliers final: 22 residues processed: 347 average time/residue: 0.2598 time to fit residues: 131.1879 Evaluate side-chains 331 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 309 time to evaluate : 1.699 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1310 time to fit residues: 7.5656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 ASN P 190 GLN c 190 GLN g 190 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 14410 Z= 0.268 Angle : 0.560 7.868 19646 Z= 0.271 Chirality : 0.040 0.118 2442 Planarity : 0.003 0.026 2574 Dihedral : 3.624 11.705 2002 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 1.70 % 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: -1.53 (0.21), residues: 1848 helix: -0.45 (0.20), residues: 726 sheet: -2.22 (0.26), residues: 484 loop : -0.28 (0.27), residues: 638 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 321 time to evaluate : 1.764 Fit side-chains outliers start: 27 outliers final: 14 residues processed: 330 average time/residue: 0.2955 time to fit residues: 144.6899 Evaluate side-chains 326 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 312 time to evaluate : 1.793 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1354 time to fit residues: 5.9136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 133 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 190 GLN F 190 GLN M 190 GLN P 190 GLN U 190 GLN U 209 ASN W 190 GLN c 190 GLN g 190 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 14410 Z= 0.240 Angle : 0.546 7.237 19646 Z= 0.265 Chirality : 0.040 0.119 2442 Planarity : 0.003 0.031 2574 Dihedral : 3.529 12.753 2002 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 1.70 % 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: -1.36 (0.22), residues: 1848 helix: -0.35 (0.21), residues: 726 sheet: -2.11 (0.26), residues: 484 loop : -0.15 (0.27), residues: 638 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 345 time to evaluate : 1.795 Fit side-chains outliers start: 27 outliers final: 18 residues processed: 358 average time/residue: 0.2423 time to fit residues: 128.8109 Evaluate side-chains 348 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 330 time to evaluate : 1.629 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1268 time to fit residues: 6.4597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.3980 chunk 148 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 0.0670 chunk 48 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 157 optimal weight: 0.8980 chunk 103 optimal weight: 0.0170 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 190 GLN P 190 GLN g 190 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 14410 Z= 0.180 Angle : 0.522 9.926 19646 Z= 0.253 Chirality : 0.039 0.125 2442 Planarity : 0.003 0.042 2574 Dihedral : 3.290 12.372 2002 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 0.76 % 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: -0.97 (0.22), residues: 1848 helix: -0.16 (0.21), residues: 726 sheet: -1.99 (0.26), residues: 484 loop : 0.34 (0.28), residues: 638 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 371 time to evaluate : 1.600 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 376 average time/residue: 0.2196 time to fit residues: 125.9406 Evaluate side-chains 358 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 350 time to evaluate : 1.679 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1244 time to fit residues: 4.0745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 0.2980 chunk 102 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 116 optimal weight: 0.0000 chunk 175 optimal weight: 0.0370 chunk 161 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 190 GLN M 190 GLN P 190 GLN d 190 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 14410 Z= 0.185 Angle : 0.540 10.951 19646 Z= 0.260 Chirality : 0.039 0.128 2442 Planarity : 0.004 0.048 2574 Dihedral : 3.223 13.794 2002 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.57 % 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: -1.15 (0.21), residues: 1848 helix: -0.13 (0.20), residues: 748 sheet: -1.85 (0.26), residues: 484 loop : -0.22 (0.25), residues: 616 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 345 time to evaluate : 1.609 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 351 average time/residue: 0.2185 time to fit residues: 117.7842 Evaluate side-chains 348 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 343 time to evaluate : 1.624 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1433 time to fit residues: 3.4255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 chunk 58 optimal weight: 0.0030 chunk 143 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 190 GLN P 190 GLN W 190 GLN c 190 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123464 restraints weight = 15897.953| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.13 r_work: 0.3316 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 14410 Z= 0.220 Angle : 0.550 11.017 19646 Z= 0.264 Chirality : 0.040 0.125 2442 Planarity : 0.004 0.052 2574 Dihedral : 3.312 14.809 2002 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.82 % 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: -1.19 (0.21), residues: 1848 helix: 0.00 (0.21), residues: 726 sheet: -1.79 (0.27), residues: 484 loop : -0.57 (0.25), residues: 638 =============================================================================== Job complete usr+sys time: 3591.34 seconds wall clock time: 65 minutes 30.50 seconds (3930.50 seconds total)