Starting phenix.real_space_refine on Fri Jul 26 12:21:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdn_17615/07_2024/8pdn_17615.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdn_17615/07_2024/8pdn_17615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdn_17615/07_2024/8pdn_17615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdn_17615/07_2024/8pdn_17615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdn_17615/07_2024/8pdn_17615.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdn_17615/07_2024/8pdn_17615.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 84 5.49 5 S 132 5.16 5 C 20700 2.51 5 N 5724 2.21 5 O 6588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C GLU 287": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C GLU 346": "OE1" <-> "OE2" Residue "C GLU 360": "OE1" <-> "OE2" Residue "D GLU 43": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "D GLU 287": "OE1" <-> "OE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D GLU 346": "OE1" <-> "OE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "E GLU 43": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 215": "OE1" <-> "OE2" Residue "E GLU 287": "OE1" <-> "OE2" Residue "E GLU 298": "OE1" <-> "OE2" Residue "E GLU 346": "OE1" <-> "OE2" Residue "E GLU 360": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F GLU 215": "OE1" <-> "OE2" Residue "F GLU 287": "OE1" <-> "OE2" Residue "F GLU 298": "OE1" <-> "OE2" Residue "F GLU 346": "OE1" <-> "OE2" Residue "F GLU 360": "OE1" <-> "OE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "G GLU 215": "OE1" <-> "OE2" Residue "G GLU 287": "OE1" <-> "OE2" Residue "G GLU 298": "OE1" <-> "OE2" Residue "G GLU 346": "OE1" <-> "OE2" Residue "G GLU 360": "OE1" <-> "OE2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H GLU 215": "OE1" <-> "OE2" Residue "H GLU 287": "OE1" <-> "OE2" Residue "H GLU 298": "OE1" <-> "OE2" Residue "H GLU 346": "OE1" <-> "OE2" Residue "H GLU 360": "OE1" <-> "OE2" Residue "I GLU 43": "OE1" <-> "OE2" Residue "I GLU 89": "OE1" <-> "OE2" Residue "I GLU 215": "OE1" <-> "OE2" Residue "I GLU 287": "OE1" <-> "OE2" Residue "I GLU 298": "OE1" <-> "OE2" Residue "I GLU 346": "OE1" <-> "OE2" Residue "I GLU 360": "OE1" <-> "OE2" Residue "J GLU 43": "OE1" <-> "OE2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J GLU 215": "OE1" <-> "OE2" Residue "J GLU 287": "OE1" <-> "OE2" Residue "J GLU 298": "OE1" <-> "OE2" Residue "J GLU 346": "OE1" <-> "OE2" Residue "J GLU 360": "OE1" <-> "OE2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K GLU 89": "OE1" <-> "OE2" Residue "K GLU 215": "OE1" <-> "OE2" Residue "K GLU 287": "OE1" <-> "OE2" Residue "K GLU 298": "OE1" <-> "OE2" Residue "K GLU 346": "OE1" <-> "OE2" Residue "K GLU 360": "OE1" <-> "OE2" Residue "L GLU 43": "OE1" <-> "OE2" Residue "L GLU 89": "OE1" <-> "OE2" Residue "L GLU 215": "OE1" <-> "OE2" Residue "L GLU 287": "OE1" <-> "OE2" Residue "L GLU 298": "OE1" <-> "OE2" Residue "L GLU 346": "OE1" <-> "OE2" Residue "L GLU 360": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 33228 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "B" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "C" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "D" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "E" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "F" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "G" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "H" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "I" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "J" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "K" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "L" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "a" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "b" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "c" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "d" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "e" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "f" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "g" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "h" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "i" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "j" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "k" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "l" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Time building chain proxies: 17.56, per 1000 atoms: 0.53 Number of scatterers: 33228 At special positions: 0 Unit cell: (126, 201.6, 202.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 84 15.00 O 6588 8.00 N 5724 7.00 C 20700 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 Atom "ATOM 31692 O5' C b 400 .*. O " rejected from bonding due to valence issues. Atom "ATOM 31972 O5' C d 400 .*. O " rejected from bonding due to valence issues. Atom "ATOM 31832 O5' C c 400 .*. O " rejected from bonding due to valence issues. Atom "ATOM 32112 O5' C e 400 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.56 Conformation dependent library (CDL) restraints added in 5.2 seconds 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7560 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 24 sheets defined 69.9% alpha, 2.4% beta 0 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 9.68 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.896A pdb=" N LEU A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 120 through 141 Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'A' and resid 175 through 191 removed outlier: 4.142A pdb=" N ARG A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.846A pdb=" N SER A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 256 through 269 removed outlier: 3.593A pdb=" N ARG A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.820A pdb=" N GLY A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 344 through 360 Processing helix chain 'B' and resid 11 through 20 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.896A pdb=" N LEU B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 75 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 120 through 141 Processing helix chain 'B' and resid 156 through 170 Processing helix chain 'B' and resid 175 through 191 removed outlier: 4.143A pdb=" N ARG B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 198 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 233 removed outlier: 3.846A pdb=" N SER B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 251 Processing helix chain 'B' and resid 256 through 269 removed outlier: 3.592A pdb=" N ARG B 260 " --> pdb=" O GLN B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLN B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 300 removed outlier: 3.820A pdb=" N GLY B 300 " --> pdb=" O PRO B 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 318 through 332 Processing helix chain 'B' and resid 344 through 360 Processing helix chain 'C' and resid 11 through 20 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.896A pdb=" N LEU C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 120 through 141 Processing helix chain 'C' and resid 156 through 170 Processing helix chain 'C' and resid 175 through 191 removed outlier: 4.142A pdb=" N ARG C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 218 through 233 removed outlier: 3.844A pdb=" N SER C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 256 through 269 removed outlier: 3.593A pdb=" N ARG C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 275 through 296 removed outlier: 4.684A pdb=" N LYS C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLN C 284 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 300 removed outlier: 3.820A pdb=" N GLY C 300 " --> pdb=" O PRO C 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 344 through 360 Processing helix chain 'D' and resid 11 through 20 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 51 removed outlier: 3.896A pdb=" N LEU D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 75 Processing helix chain 'D' and resid 75 through 86 Processing helix chain 'D' and resid 120 through 141 Processing helix chain 'D' and resid 156 through 170 Processing helix chain 'D' and resid 175 through 191 removed outlier: 4.143A pdb=" N ARG D 189 " --> pdb=" O ARG D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 218 through 233 removed outlier: 3.846A pdb=" N SER D 222 " --> pdb=" O VAL D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 251 Processing helix chain 'D' and resid 256 through 269 removed outlier: 3.593A pdb=" N ARG D 260 " --> pdb=" O GLN D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 275 through 296 removed outlier: 4.682A pdb=" N LYS D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLN D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 300 removed outlier: 3.822A pdb=" N GLY D 300 " --> pdb=" O PRO D 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 297 through 300' Processing helix chain 'D' and resid 318 through 332 Processing helix chain 'D' and resid 344 through 360 Processing helix chain 'E' and resid 11 through 20 Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 40 through 51 removed outlier: 3.895A pdb=" N LEU E 46 " --> pdb=" O GLN E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 75 Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 120 through 141 Processing helix chain 'E' and resid 156 through 170 Processing helix chain 'E' and resid 175 through 191 removed outlier: 4.144A pdb=" N ARG E 189 " --> pdb=" O ARG E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 198 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 218 through 233 removed outlier: 3.847A pdb=" N SER E 222 " --> pdb=" O VAL E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 251 Processing helix chain 'E' and resid 256 through 269 removed outlier: 3.592A pdb=" N ARG E 260 " --> pdb=" O GLN E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 274 Processing helix chain 'E' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS E 283 " --> pdb=" O GLN E 279 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLN E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 300 removed outlier: 3.820A pdb=" N GLY E 300 " --> pdb=" O PRO E 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 297 through 300' Processing helix chain 'E' and resid 318 through 332 Processing helix chain 'E' and resid 344 through 360 Processing helix chain 'F' and resid 11 through 20 Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 40 through 51 removed outlier: 3.896A pdb=" N LEU F 46 " --> pdb=" O GLN F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 75 Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 120 through 141 Processing helix chain 'F' and resid 156 through 170 Processing helix chain 'F' and resid 175 through 191 removed outlier: 4.143A pdb=" N ARG F 189 " --> pdb=" O ARG F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 198 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 218 through 233 removed outlier: 3.845A pdb=" N SER F 222 " --> pdb=" O VAL F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 251 Processing helix chain 'F' and resid 256 through 269 removed outlier: 3.592A pdb=" N ARG F 260 " --> pdb=" O GLN F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 274 Processing helix chain 'F' and resid 275 through 296 removed outlier: 4.682A pdb=" N LYS F 283 " --> pdb=" O GLN F 279 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLN F 284 " --> pdb=" O ALA F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 300 removed outlier: 3.821A pdb=" N GLY F 300 " --> pdb=" O PRO F 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 297 through 300' Processing helix chain 'F' and resid 318 through 332 Processing helix chain 'F' and resid 344 through 360 Processing helix chain 'G' and resid 11 through 20 Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 40 through 51 removed outlier: 3.894A pdb=" N LEU G 46 " --> pdb=" O GLN G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 75 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 120 through 141 Processing helix chain 'G' and resid 156 through 170 Processing helix chain 'G' and resid 175 through 191 removed outlier: 4.142A pdb=" N ARG G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 198 Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 218 through 233 removed outlier: 3.845A pdb=" N SER G 222 " --> pdb=" O VAL G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 251 Processing helix chain 'G' and resid 256 through 269 removed outlier: 3.592A pdb=" N ARG G 260 " --> pdb=" O GLN G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 274 Processing helix chain 'G' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS G 283 " --> pdb=" O GLN G 279 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLN G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 300 removed outlier: 3.821A pdb=" N GLY G 300 " --> pdb=" O PRO G 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 297 through 300' Processing helix chain 'G' and resid 318 through 332 Processing helix chain 'G' and resid 344 through 360 Processing helix chain 'H' and resid 11 through 20 Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 40 through 51 removed outlier: 3.896A pdb=" N LEU H 46 " --> pdb=" O GLN H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 75 Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 120 through 141 Processing helix chain 'H' and resid 156 through 170 Processing helix chain 'H' and resid 175 through 191 removed outlier: 4.142A pdb=" N ARG H 189 " --> pdb=" O ARG H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 198 Processing helix chain 'H' and resid 202 through 217 Processing helix chain 'H' and resid 218 through 233 removed outlier: 3.846A pdb=" N SER H 222 " --> pdb=" O VAL H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 251 Processing helix chain 'H' and resid 256 through 269 removed outlier: 3.593A pdb=" N ARG H 260 " --> pdb=" O GLN H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 274 Processing helix chain 'H' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS H 283 " --> pdb=" O GLN H 279 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLN H 284 " --> pdb=" O ALA H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 300 removed outlier: 3.821A pdb=" N GLY H 300 " --> pdb=" O PRO H 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 297 through 300' Processing helix chain 'H' and resid 318 through 332 Processing helix chain 'H' and resid 344 through 360 Processing helix chain 'I' and resid 11 through 20 Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'I' and resid 40 through 51 removed outlier: 3.895A pdb=" N LEU I 46 " --> pdb=" O GLN I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 75 Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 120 through 141 Processing helix chain 'I' and resid 156 through 170 Processing helix chain 'I' and resid 175 through 191 removed outlier: 4.142A pdb=" N ARG I 189 " --> pdb=" O ARG I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 198 Processing helix chain 'I' and resid 202 through 217 Processing helix chain 'I' and resid 218 through 233 removed outlier: 3.846A pdb=" N SER I 222 " --> pdb=" O VAL I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 251 Processing helix chain 'I' and resid 256 through 269 removed outlier: 3.593A pdb=" N ARG I 260 " --> pdb=" O GLN I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 274 Processing helix chain 'I' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS I 283 " --> pdb=" O GLN I 279 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLN I 284 " --> pdb=" O ALA I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 300 removed outlier: 3.821A pdb=" N GLY I 300 " --> pdb=" O PRO I 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 297 through 300' Processing helix chain 'I' and resid 318 through 332 Processing helix chain 'I' and resid 344 through 360 Processing helix chain 'J' and resid 11 through 20 Processing helix chain 'J' and resid 37 through 39 No H-bonds generated for 'chain 'J' and resid 37 through 39' Processing helix chain 'J' and resid 40 through 51 removed outlier: 3.895A pdb=" N LEU J 46 " --> pdb=" O GLN J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 75 Processing helix chain 'J' and resid 75 through 86 Processing helix chain 'J' and resid 120 through 141 Processing helix chain 'J' and resid 156 through 170 Processing helix chain 'J' and resid 175 through 191 removed outlier: 4.141A pdb=" N ARG J 189 " --> pdb=" O ARG J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 198 Processing helix chain 'J' and resid 202 through 217 Processing helix chain 'J' and resid 218 through 233 removed outlier: 3.846A pdb=" N SER J 222 " --> pdb=" O VAL J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 251 Processing helix chain 'J' and resid 256 through 269 removed outlier: 3.594A pdb=" N ARG J 260 " --> pdb=" O GLN J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 274 Processing helix chain 'J' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS J 283 " --> pdb=" O GLN J 279 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLN J 284 " --> pdb=" O ALA J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 300 removed outlier: 3.820A pdb=" N GLY J 300 " --> pdb=" O PRO J 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 297 through 300' Processing helix chain 'J' and resid 318 through 332 Processing helix chain 'J' and resid 344 through 360 Processing helix chain 'K' and resid 11 through 20 Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 40 through 51 removed outlier: 3.896A pdb=" N LEU K 46 " --> pdb=" O GLN K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 75 Processing helix chain 'K' and resid 75 through 86 Processing helix chain 'K' and resid 120 through 141 Processing helix chain 'K' and resid 156 through 170 Processing helix chain 'K' and resid 175 through 191 removed outlier: 4.142A pdb=" N ARG K 189 " --> pdb=" O ARG K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 198 Processing helix chain 'K' and resid 202 through 217 Processing helix chain 'K' and resid 218 through 233 removed outlier: 3.845A pdb=" N SER K 222 " --> pdb=" O VAL K 218 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 251 Processing helix chain 'K' and resid 256 through 269 removed outlier: 3.592A pdb=" N ARG K 260 " --> pdb=" O GLN K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 274 Processing helix chain 'K' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS K 283 " --> pdb=" O GLN K 279 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLN K 284 " --> pdb=" O ALA K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 300 removed outlier: 3.821A pdb=" N GLY K 300 " --> pdb=" O PRO K 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 297 through 300' Processing helix chain 'K' and resid 318 through 332 Processing helix chain 'K' and resid 344 through 360 Processing helix chain 'L' and resid 11 through 20 Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing helix chain 'L' and resid 40 through 51 removed outlier: 3.895A pdb=" N LEU L 46 " --> pdb=" O GLN L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 75 Processing helix chain 'L' and resid 75 through 86 Processing helix chain 'L' and resid 120 through 141 Processing helix chain 'L' and resid 156 through 170 Processing helix chain 'L' and resid 175 through 191 removed outlier: 4.143A pdb=" N ARG L 189 " --> pdb=" O ARG L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 198 Processing helix chain 'L' and resid 202 through 217 Processing helix chain 'L' and resid 218 through 233 removed outlier: 3.845A pdb=" N SER L 222 " --> pdb=" O VAL L 218 " (cutoff:3.500A) Processing helix chain 'L' and resid 238 through 251 Processing helix chain 'L' and resid 256 through 269 removed outlier: 3.593A pdb=" N ARG L 260 " --> pdb=" O GLN L 256 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS L 283 " --> pdb=" O GLN L 279 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLN L 284 " --> pdb=" O ALA L 280 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 300 removed outlier: 3.821A pdb=" N GLY L 300 " --> pdb=" O PRO L 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 297 through 300' Processing helix chain 'L' and resid 318 through 332 Processing helix chain 'L' and resid 344 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.299A pdb=" N THR A 33 " --> pdb=" O VAL A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.695A pdb=" N ARG A 96 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 34 removed outlier: 6.299A pdb=" N THR B 33 " --> pdb=" O VAL B 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.695A pdb=" N ARG B 96 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.298A pdb=" N THR C 33 " --> pdb=" O VAL C 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.695A pdb=" N ARG C 96 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 32 through 34 removed outlier: 6.298A pdb=" N THR D 33 " --> pdb=" O VAL D 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.696A pdb=" N ARG D 96 " --> pdb=" O ASP D 115 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 32 through 34 removed outlier: 6.298A pdb=" N THR E 33 " --> pdb=" O VAL E 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.695A pdb=" N ARG E 96 " --> pdb=" O ASP E 115 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 32 through 34 removed outlier: 6.298A pdb=" N THR F 33 " --> pdb=" O VAL F 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 96 through 98 removed outlier: 3.694A pdb=" N ARG F 96 " --> pdb=" O ASP F 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 32 through 34 removed outlier: 6.298A pdb=" N THR G 33 " --> pdb=" O VAL G 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 96 through 98 removed outlier: 3.694A pdb=" N ARG G 96 " --> pdb=" O ASP G 115 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 32 through 34 removed outlier: 6.300A pdb=" N THR H 33 " --> pdb=" O VAL H 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'H' and resid 96 through 98 removed outlier: 3.695A pdb=" N ARG H 96 " --> pdb=" O ASP H 115 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 32 through 34 removed outlier: 6.299A pdb=" N THR I 33 " --> pdb=" O VAL I 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 96 through 98 removed outlier: 3.695A pdb=" N ARG I 96 " --> pdb=" O ASP I 115 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 32 through 34 removed outlier: 6.299A pdb=" N THR J 33 " --> pdb=" O VAL J 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'J' and resid 96 through 98 removed outlier: 3.696A pdb=" N ARG J 96 " --> pdb=" O ASP J 115 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 32 through 34 removed outlier: 6.298A pdb=" N THR K 33 " --> pdb=" O VAL K 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'K' and resid 96 through 98 removed outlier: 3.696A pdb=" N ARG K 96 " --> pdb=" O ASP K 115 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 32 through 34 removed outlier: 6.299A pdb=" N THR L 33 " --> pdb=" O VAL L 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'L' and resid 96 through 98 removed outlier: 3.695A pdb=" N ARG L 96 " --> pdb=" O ASP L 115 " (cutoff:3.500A) 1969 hydrogen bonds defined for protein. 5799 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 10.64 Time building geometry restraints manager: 13.76 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: 10673 1.34 - 1.46: 5006 1.46 - 1.57: 17825 1.57 - 1.69: 156 1.69 - 1.81: 228 Bond restraints: 33888 Sorted by residual: bond pdb=" C VAL K 35 " pdb=" N THR K 36 " ideal model delta sigma weight residual 1.331 1.302 0.028 1.24e-02 6.50e+03 5.21e+00 bond pdb=" C VAL I 35 " pdb=" N THR I 36 " ideal model delta sigma weight residual 1.331 1.303 0.028 1.24e-02 6.50e+03 5.06e+00 bond pdb=" C VAL A 35 " pdb=" N THR A 36 " ideal model delta sigma weight residual 1.331 1.303 0.028 1.24e-02 6.50e+03 4.96e+00 bond pdb=" C VAL H 35 " pdb=" N THR H 36 " ideal model delta sigma weight residual 1.331 1.303 0.028 1.24e-02 6.50e+03 4.94e+00 bond pdb=" C VAL B 35 " pdb=" N THR B 36 " ideal model delta sigma weight residual 1.331 1.303 0.027 1.24e-02 6.50e+03 4.90e+00 ... (remaining 33883 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.43: 985 106.43 - 113.34: 19075 113.34 - 120.24: 12675 120.24 - 127.14: 13152 127.14 - 134.04: 217 Bond angle restraints: 46104 Sorted by residual: angle pdb=" C LEU A 52 " pdb=" N TYR A 53 " pdb=" CA TYR A 53 " ideal model delta sigma weight residual 122.60 115.36 7.24 1.56e+00 4.11e-01 2.16e+01 angle pdb=" C LEU B 52 " pdb=" N TYR B 53 " pdb=" CA TYR B 53 " ideal model delta sigma weight residual 122.60 115.43 7.17 1.56e+00 4.11e-01 2.12e+01 angle pdb=" C LEU L 52 " pdb=" N TYR L 53 " pdb=" CA TYR L 53 " ideal model delta sigma weight residual 122.60 115.44 7.16 1.56e+00 4.11e-01 2.11e+01 angle pdb=" C LEU C 52 " pdb=" N TYR C 53 " pdb=" CA TYR C 53 " ideal model delta sigma weight residual 122.60 115.45 7.15 1.56e+00 4.11e-01 2.10e+01 angle pdb=" C LEU K 52 " pdb=" N TYR K 53 " pdb=" CA TYR K 53 " ideal model delta sigma weight residual 122.60 115.45 7.15 1.56e+00 4.11e-01 2.10e+01 ... (remaining 46099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 18479 17.53 - 35.07: 1861 35.07 - 52.60: 276 52.60 - 70.13: 120 70.13 - 87.67: 132 Dihedral angle restraints: 20868 sinusoidal: 9084 harmonic: 11784 Sorted by residual: dihedral pdb=" CA TYR F 59 " pdb=" C TYR F 59 " pdb=" N LYS F 60 " pdb=" CA LYS F 60 " ideal model delta harmonic sigma weight residual 180.00 -163.32 -16.68 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA TYR L 59 " pdb=" C TYR L 59 " pdb=" N LYS L 60 " pdb=" CA LYS L 60 " ideal model delta harmonic sigma weight residual -180.00 -163.35 -16.65 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA TYR B 59 " pdb=" C TYR B 59 " pdb=" N LYS B 60 " pdb=" CA LYS B 60 " ideal model delta harmonic sigma weight residual -180.00 -163.36 -16.64 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 20865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3456 0.036 - 0.072: 1463 0.072 - 0.108: 350 0.108 - 0.144: 138 0.144 - 0.180: 29 Chirality restraints: 5436 Sorted by residual: chirality pdb=" CB VAL K 35 " pdb=" CA VAL K 35 " pdb=" CG1 VAL K 35 " pdb=" CG2 VAL K 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" CB VAL I 35 " pdb=" CA VAL I 35 " pdb=" CG1 VAL I 35 " pdb=" CG2 VAL I 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CB VAL B 35 " pdb=" CA VAL B 35 " pdb=" CG1 VAL B 35 " pdb=" CG2 VAL B 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.66e-01 ... (remaining 5433 not shown) Planarity restraints: 5580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 198 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO L 199 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO L 199 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 199 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 198 " 0.033 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO B 199 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 199 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 199 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 198 " -0.033 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO H 199 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 199 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 199 " -0.028 5.00e-02 4.00e+02 ... (remaining 5577 not shown) Histogram of nonbonded interaction distances: 0.98 - 1.77: 20 1.77 - 2.55: 363 2.55 - 3.33: 42337 3.33 - 4.12: 83623 4.12 - 4.90: 155072 Warning: very small nonbonded interaction distances. Nonbonded interactions: 281415 Sorted by model distance: nonbonded pdb=" CG2 VAL A 190 " pdb=" O5' C b 400 " model vdw 0.984 3.460 nonbonded pdb=" CE MET B 337 " pdb=" CZ ARG L 78 " model vdw 1.076 3.690 nonbonded pdb=" CG2 VAL A 190 " pdb=" P C b 400 " model vdw 1.162 3.820 nonbonded pdb=" O THR G 236 " pdb=" NH1 ARG H 27 " model vdw 1.208 2.520 nonbonded pdb=" O THR F 236 " pdb=" NH1 ARG G 27 " model vdw 1.209 2.520 ... (remaining 281410 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' } 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' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.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' } pdb_interpretation.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' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 4.910 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: 0.040 Extract box with map and model: 1.280 Check model and map are aligned: 0.250 Set scattering table: 0.320 Process input model: 86.620 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5862 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 : 0.007 0.064 33888 Z= 0.437 Angle : 0.662 7.243 46104 Z= 0.394 Chirality : 0.044 0.180 5436 Planarity : 0.005 0.051 5580 Dihedral : 15.878 87.665 13308 Min Nonbonded Distance : 0.984 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.42 (0.13), residues: 4020 helix: 0.73 (0.10), residues: 2784 sheet: -1.17 (0.32), residues: 180 loop : -0.41 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 123 HIS 0.004 0.001 HIS L 275 PHE 0.014 0.002 PHE K 169 TYR 0.032 0.003 TYR G 53 ARG 0.008 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.4412 (mtm) cc_final: 0.3660 (mtp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1982 time to fit residues: 11.8611 Evaluate side-chains 21 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.301 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0062 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 7.9990 chunk 300 optimal weight: 8.9990 chunk 166 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 310 optimal weight: 7.9990 chunk 120 optimal weight: 0.0050 chunk 188 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 359 optimal weight: 7.9990 overall best weight: 3.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 HIS ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 HIS Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33888 Z= 0.245 Angle : 0.604 5.930 46104 Z= 0.326 Chirality : 0.040 0.127 5436 Planarity : 0.005 0.044 5580 Dihedral : 12.154 73.737 5760 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.35 % Allowed : 4.53 % Favored : 95.12 % 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: 1.30 (0.14), residues: 4020 helix: 1.41 (0.10), residues: 2832 sheet: -1.55 (0.30), residues: 180 loop : -0.05 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 123 HIS 0.004 0.001 HIS J 220 PHE 0.015 0.002 PHE I 169 TYR 0.019 0.002 TYR C 252 ARG 0.004 0.001 ARG J 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 170 THR cc_start: 0.8982 (p) cc_final: 0.8325 (t) REVERT: F 191 LEU cc_start: 0.9013 (mt) cc_final: 0.8592 (mt) REVERT: F 301 LEU cc_start: 0.7382 (mt) cc_final: 0.6980 (mp) outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 0.1811 time to fit residues: 24.1893 Evaluate side-chains 65 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.292 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0067 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 199 optimal weight: 5.9990 chunk 111 optimal weight: 0.0870 chunk 299 optimal weight: 0.0670 chunk 244 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 360 optimal weight: 8.9990 chunk 389 optimal weight: 2.9990 chunk 320 optimal weight: 0.9990 chunk 357 optimal weight: 0.2980 chunk 122 optimal weight: 0.5980 chunk 289 optimal weight: 0.6980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.5747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33888 Z= 0.273 Angle : 0.753 10.394 46104 Z= 0.383 Chirality : 0.043 0.170 5436 Planarity : 0.012 0.213 5580 Dihedral : 12.334 73.568 5760 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.13), residues: 4020 helix: 1.21 (0.10), residues: 2748 sheet: -2.23 (0.27), residues: 228 loop : -0.17 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 261 HIS 0.002 0.001 HIS B 275 PHE 0.012 0.001 PHE J 244 TYR 0.022 0.002 TYR H 227 ARG 0.011 0.001 ARG J 305 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 14 LYS cc_start: 0.8563 (mttt) cc_final: 0.8300 (mmtt) REVERT: F 191 LEU cc_start: 0.8821 (mt) cc_final: 0.8487 (mt) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1659 time to fit residues: 16.7586 Evaluate side-chains 60 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.315 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0067 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 355 optimal weight: 5.9990 chunk 270 optimal weight: 0.5980 chunk 186 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 171 optimal weight: 0.0060 chunk 241 optimal weight: 7.9990 chunk 361 optimal weight: 0.0040 chunk 382 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 342 optimal weight: 0.2980 chunk 103 optimal weight: 7.9990 overall best weight: 0.7810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 moved from start: 0.6748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33888 Z= 0.222 Angle : 0.700 7.610 46104 Z= 0.366 Chirality : 0.043 0.166 5436 Planarity : 0.009 0.168 5580 Dihedral : 12.737 73.692 5760 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.35 % Allowed : 3.83 % Favored : 95.82 % 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: 0.57 (0.13), residues: 4020 helix: 1.08 (0.10), residues: 2736 sheet: -2.54 (0.24), residues: 228 loop : -0.58 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 261 HIS 0.005 0.001 HIS I 15 PHE 0.014 0.001 PHE B 244 TYR 0.041 0.003 TYR G 13 ARG 0.006 0.001 ARG B 305 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 161 LEU cc_start: 0.8989 (pp) cc_final: 0.8778 (pp) REVERT: F 167 LEU cc_start: 0.9321 (mt) cc_final: 0.9112 (tp) REVERT: F 272 MET cc_start: 0.7469 (mpp) cc_final: 0.5887 (mmm) REVERT: F 294 GLU cc_start: 0.8078 (mp0) cc_final: 0.7815 (mp0) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.1324 time to fit residues: 12.0431 Evaluate side-chains 47 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.292 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0065 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 318 optimal weight: 0.0070 chunk 217 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 285 optimal weight: 7.9990 chunk 157 optimal weight: 0.0370 chunk 326 optimal weight: 6.9990 chunk 264 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 195 optimal weight: 4.9990 chunk 343 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 overall best weight: 1.1478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 81 GLN F 269 ASN F 275 HIS ** F 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 0.7381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33888 Z= 0.203 Angle : 0.649 6.624 46104 Z= 0.350 Chirality : 0.042 0.157 5436 Planarity : 0.007 0.118 5580 Dihedral : 12.861 73.590 5760 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.70 % Allowed : 0.70 % Favored : 98.61 % 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: 0.65 (0.13), residues: 4020 helix: 1.16 (0.10), residues: 2748 sheet: -2.49 (0.25), residues: 228 loop : -0.66 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 261 HIS 0.002 0.001 HIS J 220 PHE 0.017 0.002 PHE I 169 TYR 0.015 0.002 TYR I 23 ARG 0.004 0.001 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 74 average time/residue: 0.1377 time to fit residues: 12.2986 Evaluate side-chains 50 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.291 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0059 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 128 optimal weight: 0.0270 chunk 344 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 94 optimal weight: 0.0270 chunk 383 optimal weight: 2.9990 chunk 318 optimal weight: 0.9980 chunk 177 optimal weight: 0.9980 chunk 31 optimal weight: 0.0070 chunk 126 optimal weight: 0.0050 chunk 201 optimal weight: 1.9990 overall best weight: 0.2128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.8013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33888 Z= 0.239 Angle : 0.730 9.945 46104 Z= 0.383 Chirality : 0.043 0.168 5436 Planarity : 0.012 0.246 5580 Dihedral : 13.200 73.411 5760 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 24.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.35 % Allowed : 2.79 % Favored : 96.86 % 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: 0.87 (0.14), residues: 4020 helix: 1.34 (0.10), residues: 2724 sheet: -2.54 (0.26), residues: 228 loop : -0.53 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 261 HIS 0.003 0.001 HIS B 15 PHE 0.015 0.002 PHE I 169 TYR 0.040 0.003 TYR D 59 ARG 0.004 0.001 ARG G 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: F 58 ASP cc_start: 0.6556 (t0) cc_final: 0.6152 (t0) REVERT: F 278 VAL cc_start: 0.8968 (t) cc_final: 0.8765 (t) outliers start: 1 outliers final: 0 residues processed: 67 average time/residue: 0.1333 time to fit residues: 10.9147 Evaluate side-chains 43 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.272 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0061 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 369 optimal weight: 0.0470 chunk 43 optimal weight: 8.9990 chunk 218 optimal weight: 0.7980 chunk 279 optimal weight: 1.9990 chunk 216 optimal weight: 0.4980 chunk 322 optimal weight: 0.0040 chunk 213 optimal weight: 0.0570 chunk 381 optimal weight: 0.0670 chunk 238 optimal weight: 6.9990 chunk 232 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 overall best weight: 0.1346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5863 moved from start: 0.8529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33888 Z= 0.204 Angle : 0.708 8.296 46104 Z= 0.376 Chirality : 0.043 0.168 5436 Planarity : 0.010 0.192 5580 Dihedral : 12.786 73.495 5760 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 0.90 (0.14), residues: 4020 helix: 1.39 (0.10), residues: 2724 sheet: -2.53 (0.27), residues: 228 loop : -0.59 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 261 HIS 0.005 0.001 HIS B 303 PHE 0.016 0.001 PHE L 244 TYR 0.013 0.002 TYR J 211 ARG 0.004 0.001 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.320 Fit side-chains REVERT: F 44 ILE cc_start: 0.8806 (tp) cc_final: 0.8391 (tp) REVERT: F 92 VAL cc_start: 0.5590 (t) cc_final: 0.5340 (p) REVERT: F 161 LEU cc_start: 0.8839 (pp) cc_final: 0.8621 (pp) REVERT: F 278 VAL cc_start: 0.8959 (t) cc_final: 0.8735 (t) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1226 time to fit residues: 9.4320 Evaluate side-chains 42 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.288 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0061 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 236 optimal weight: 0.7980 chunk 152 optimal weight: 0.7980 chunk 227 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 74 optimal weight: 0.0980 chunk 73 optimal weight: 9.9990 chunk 242 optimal weight: 9.9990 chunk 260 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 35 optimal weight: 30.0000 chunk 300 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5881 moved from start: 0.8967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33888 Z= 0.219 Angle : 0.717 8.068 46104 Z= 0.375 Chirality : 0.043 0.156 5436 Planarity : 0.008 0.154 5580 Dihedral : 12.756 73.296 5760 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: 0.95 (0.14), residues: 4020 helix: 1.45 (0.10), residues: 2724 sheet: -2.43 (0.30), residues: 228 loop : -0.67 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 261 HIS 0.005 0.002 HIS C 303 PHE 0.014 0.001 PHE K 244 TYR 0.030 0.002 TYR I 252 ARG 0.003 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.319 Fit side-chains REVERT: F 44 ILE cc_start: 0.8868 (tp) cc_final: 0.8141 (tp) REVERT: F 149 ASN cc_start: 0.6855 (p0) cc_final: 0.6603 (p0) REVERT: F 272 MET cc_start: 0.8031 (mtm) cc_final: 0.7827 (mtm) REVERT: F 278 VAL cc_start: 0.8966 (t) cc_final: 0.8644 (p) REVERT: F 295 MET cc_start: 0.7664 (mmm) cc_final: 0.6749 (mmm) REVERT: F 299 SER cc_start: 0.8258 (p) cc_final: 0.7863 (m) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1224 time to fit residues: 9.7876 Evaluate side-chains 41 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.325 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0070 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 347 optimal weight: 0.0060 chunk 365 optimal weight: 0.6980 chunk 333 optimal weight: 8.9990 chunk 355 optimal weight: 0.0870 chunk 214 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 279 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 321 optimal weight: 0.8980 chunk 336 optimal weight: 0.9980 chunk 354 optimal weight: 0.7980 overall best weight: 0.4974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 0.9295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33888 Z= 0.233 Angle : 0.768 14.393 46104 Z= 0.393 Chirality : 0.044 0.198 5436 Planarity : 0.008 0.144 5580 Dihedral : 12.672 73.361 5760 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: 0.62 (0.14), residues: 4020 helix: 1.26 (0.10), residues: 2808 sheet: -2.53 (0.29), residues: 228 loop : -1.19 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 261 HIS 0.022 0.004 HIS D 15 PHE 0.013 0.001 PHE K 244 TYR 0.011 0.002 TYR I 23 ARG 0.005 0.001 ARG L 339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: F 44 ILE cc_start: 0.8752 (tp) cc_final: 0.8111 (tt) REVERT: F 161 LEU cc_start: 0.8782 (pp) cc_final: 0.7902 (pp) REVERT: F 272 MET cc_start: 0.8192 (mtm) cc_final: 0.7927 (mtm) REVERT: F 278 VAL cc_start: 0.8921 (t) cc_final: 0.8639 (p) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1246 time to fit residues: 9.3347 Evaluate side-chains 41 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.312 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0066 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 233 optimal weight: 7.9990 chunk 376 optimal weight: 4.9990 chunk 229 optimal weight: 0.0050 chunk 178 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 394 optimal weight: 3.9990 chunk 363 optimal weight: 7.9990 chunk 314 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 242 optimal weight: 6.9990 chunk 192 optimal weight: 20.0000 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 148 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5960 moved from start: 0.9544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33888 Z= 0.252 Angle : 0.767 13.830 46104 Z= 0.397 Chirality : 0.043 0.192 5436 Planarity : 0.008 0.142 5580 Dihedral : 12.939 73.263 5760 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 23.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 0.68 (0.14), residues: 4020 helix: 1.33 (0.10), residues: 2808 sheet: -2.79 (0.30), residues: 228 loop : -1.19 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 261 HIS 0.004 0.001 HIS G 220 PHE 0.010 0.001 PHE K 244 TYR 0.013 0.002 TYR B 23 ARG 0.005 0.001 ARG C 339 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: F 272 MET cc_start: 0.8213 (mtm) cc_final: 0.7770 (mtm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1224 time to fit residues: 8.8575 Evaluate side-chains 38 residues out of total 287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.288 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0058 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 249 optimal weight: 6.9990 chunk 334 optimal weight: 0.4980 chunk 96 optimal weight: 0.6980 chunk 289 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 314 optimal weight: 0.0270 chunk 131 optimal weight: 0.0050 chunk 323 optimal weight: 0.0670 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 148 GLN ** F 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.085001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.071597 restraints weight = 11024.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.073596 restraints weight = 7291.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.075063 restraints weight = 5237.560| |-----------------------------------------------------------------------------| r_work (final): 0.3340 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.068094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.066499 restraints weight = 2081.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.067270 restraints weight = 671.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.067645 restraints weight = 270.921| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.9881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33888 Z= 0.218 Angle : 0.749 13.611 46104 Z= 0.383 Chirality : 0.043 0.172 5436 Planarity : 0.007 0.129 5580 Dihedral : 12.748 73.463 5760 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: 0.61 (0.14), residues: 4020 helix: 1.29 (0.10), residues: 2808 sheet: -2.74 (0.31), residues: 228 loop : -1.26 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 261 HIS 0.007 0.002 HIS K 303 PHE 0.008 0.001 PHE G 244 TYR 0.011 0.001 TYR E 23 ARG 0.003 0.000 ARG I 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4353.23 seconds wall clock time: 81 minutes 8.65 seconds (4868.65 seconds total)