Starting phenix.real_space_refine on Thu Jul 25 17:52:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdp_17617/07_2024/8pdp_17617.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdp_17617/07_2024/8pdp_17617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdp_17617/07_2024/8pdp_17617.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdp_17617/07_2024/8pdp_17617.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdp_17617/07_2024/8pdp_17617.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdp_17617/07_2024/8pdp_17617.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.047 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 70 5.49 5 S 130 5.16 5 C 18820 2.51 5 N 5190 2.21 5 O 5950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C GLU 360": "OE1" <-> "OE2" Residue "G GLU 20": "OE1" <-> "OE2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G GLU 215": "OE1" <-> "OE2" Residue "G GLU 298": "OE1" <-> "OE2" Residue "G GLU 360": "OE1" <-> "OE2" Residue "J GLU 20": "OE1" <-> "OE2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "J ARG 132": "NH1" <-> "NH2" Residue "J GLU 215": "OE1" <-> "OE2" Residue "J GLU 298": "OE1" <-> "OE2" Residue "J GLU 360": "OE1" <-> "OE2" Residue "M GLU 20": "OE1" <-> "OE2" Residue "M GLU 89": "OE1" <-> "OE2" Residue "M GLU 109": "OE1" <-> "OE2" Residue "M ARG 132": "NH1" <-> "NH2" Residue "M GLU 215": "OE1" <-> "OE2" Residue "M GLU 298": "OE1" <-> "OE2" Residue "M GLU 360": "OE1" <-> "OE2" Residue "P GLU 20": "OE1" <-> "OE2" Residue "P GLU 89": "OE1" <-> "OE2" Residue "P GLU 109": "OE1" <-> "OE2" Residue "P ARG 132": "NH1" <-> "NH2" Residue "P GLU 215": "OE1" <-> "OE2" Residue "P GLU 298": "OE1" <-> "OE2" Residue "P GLU 360": "OE1" <-> "OE2" Residue "S GLU 20": "OE1" <-> "OE2" Residue "S GLU 89": "OE1" <-> "OE2" Residue "S GLU 109": "OE1" <-> "OE2" Residue "S ARG 132": "NH1" <-> "NH2" Residue "S GLU 215": "OE1" <-> "OE2" Residue "S GLU 298": "OE1" <-> "OE2" Residue "S GLU 360": "OE1" <-> "OE2" Residue "V GLU 20": "OE1" <-> "OE2" Residue "V GLU 89": "OE1" <-> "OE2" Residue "V GLU 109": "OE1" <-> "OE2" Residue "V ARG 132": "NH1" <-> "NH2" Residue "V GLU 215": "OE1" <-> "OE2" Residue "V GLU 298": "OE1" <-> "OE2" Residue "V GLU 360": "OE1" <-> "OE2" Residue "Y GLU 20": "OE1" <-> "OE2" Residue "Y GLU 89": "OE1" <-> "OE2" Residue "Y GLU 109": "OE1" <-> "OE2" Residue "Y ARG 132": "NH1" <-> "NH2" Residue "Y GLU 215": "OE1" <-> "OE2" Residue "Y GLU 298": "OE1" <-> "OE2" Residue "Y GLU 360": "OE1" <-> "OE2" Residue "1 GLU 20": "OE1" <-> "OE2" Residue "1 GLU 89": "OE1" <-> "OE2" Residue "1 GLU 109": "OE1" <-> "OE2" Residue "1 ARG 132": "NH1" <-> "NH2" Residue "1 GLU 215": "OE1" <-> "OE2" Residue "1 GLU 298": "OE1" <-> "OE2" Residue "1 GLU 360": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 30160 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} 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: "C" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} 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: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} 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: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} 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} Chain: "M" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "O" 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: "P" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "R" 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: "S" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "U" 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: "V" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "X" 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: "Y" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "0" 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: "1" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "2" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "3" 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: 16.33, per 1000 atoms: 0.54 Number of scatterers: 30160 At special positions: 0 Unit cell: (192.15, 192.15, 89.25, 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 130 16.00 P 70 15.00 O 5950 8.00 N 5190 7.00 C 18820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.47 Conformation dependent library (CDL) restraints added in 5.6 seconds 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6880 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 20 sheets defined 69.2% alpha, 5.1% beta 0 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 10.49 Creating SS restraints... Processing helix chain 'A' and resid 9 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: 3.844A pdb=" N LEU A 47 " --> pdb=" O GLU A 43 " (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 142 removed outlier: 3.629A pdb=" N VAL A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.615A pdb=" N GLN A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.921A 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: 3.716A 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 268 removed outlier: 3.658A 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 280 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.521A 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 301 through 306 Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'B' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN B 13 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 14 " --> pdb=" O ILE B 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 10 through 14' Processing helix chain 'C' and resid 9 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: 3.844A pdb=" N LEU C 47 " --> pdb=" O GLU C 43 " (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 142 removed outlier: 3.628A pdb=" N VAL C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.615A pdb=" N GLN C 150 " --> pdb=" O PRO C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 171 removed outlier: 3.825A pdb=" N LYS C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 190 removed outlier: 3.922A 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: 3.716A 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 268 removed outlier: 3.658A 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 280 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 297 through 300 removed outlier: 3.522A 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 301 through 306 Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 344 through 361 Processing helix chain 'D' and resid 10 through 14 removed outlier: 3.528A pdb=" N GLN D 13 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU D 14 " --> pdb=" O ILE D 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 10 through 14' Processing helix chain 'G' and resid 9 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: 3.844A pdb=" N LEU G 47 " --> pdb=" O GLU G 43 " (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 142 removed outlier: 3.629A pdb=" N VAL G 124 " --> pdb=" O GLU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 151 removed outlier: 3.616A pdb=" N GLN G 150 " --> pdb=" O PRO G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS G 171 " --> pdb=" O LEU G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 190 removed outlier: 3.921A 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: 3.716A 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 268 removed outlier: 3.658A 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 280 Processing helix chain 'G' and resid 281 through 296 Processing helix chain 'G' and resid 297 through 300 removed outlier: 3.522A 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 301 through 306 Processing helix chain 'G' and resid 318 through 332 Processing helix chain 'G' and resid 344 through 361 Processing helix chain 'H' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN H 13 " --> pdb=" O ASP H 10 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU H 14 " --> pdb=" O ILE H 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 10 through 14' Processing helix chain 'J' and resid 9 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: 3.844A pdb=" N LEU J 47 " --> pdb=" O GLU J 43 " (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 142 removed outlier: 3.628A pdb=" N VAL J 124 " --> pdb=" O GLU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 151 removed outlier: 3.616A pdb=" N GLN J 150 " --> pdb=" O PRO J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS J 171 " --> pdb=" O LEU J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 190 removed outlier: 3.922A 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: 3.716A 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 268 removed outlier: 3.658A 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 280 Processing helix chain 'J' and resid 281 through 296 Processing helix chain 'J' and resid 297 through 300 removed outlier: 3.521A 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 301 through 306 Processing helix chain 'J' and resid 318 through 332 Processing helix chain 'J' and resid 344 through 361 Processing helix chain 'K' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN K 13 " --> pdb=" O ASP K 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU K 14 " --> pdb=" O ILE K 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 10 through 14' Processing helix chain 'M' and resid 9 through 20 Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 75 Processing helix chain 'M' and resid 75 through 86 Processing helix chain 'M' and resid 120 through 142 removed outlier: 3.628A pdb=" N VAL M 124 " --> pdb=" O GLU M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 151 removed outlier: 3.615A pdb=" N GLN M 150 " --> pdb=" O PRO M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 171 removed outlier: 3.825A pdb=" N LYS M 171 " --> pdb=" O LEU M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 190 removed outlier: 3.921A pdb=" N ARG M 189 " --> pdb=" O ARG M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 198 Processing helix chain 'M' and resid 202 through 217 Processing helix chain 'M' and resid 218 through 233 removed outlier: 3.716A pdb=" N SER M 222 " --> pdb=" O VAL M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 238 through 251 Processing helix chain 'M' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG M 260 " --> pdb=" O GLN M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 274 Processing helix chain 'M' and resid 275 through 280 Processing helix chain 'M' and resid 281 through 296 Processing helix chain 'M' and resid 297 through 300 removed outlier: 3.521A pdb=" N GLY M 300 " --> pdb=" O PRO M 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 297 through 300' Processing helix chain 'M' and resid 301 through 306 Processing helix chain 'M' and resid 318 through 332 Processing helix chain 'M' and resid 344 through 361 Processing helix chain 'N' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN N 13 " --> pdb=" O ASP N 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU N 14 " --> pdb=" O ILE N 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 10 through 14' Processing helix chain 'P' and resid 9 through 20 Processing helix chain 'P' and resid 37 through 39 No H-bonds generated for 'chain 'P' and resid 37 through 39' Processing helix chain 'P' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU P 47 " --> pdb=" O GLU P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 75 Processing helix chain 'P' and resid 75 through 86 Processing helix chain 'P' and resid 120 through 142 removed outlier: 3.629A pdb=" N VAL P 124 " --> pdb=" O GLU P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 151 removed outlier: 3.615A pdb=" N GLN P 150 " --> pdb=" O PRO P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS P 171 " --> pdb=" O LEU P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 175 through 190 removed outlier: 3.921A pdb=" N ARG P 189 " --> pdb=" O ARG P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 198 Processing helix chain 'P' and resid 202 through 217 Processing helix chain 'P' and resid 218 through 233 removed outlier: 3.716A pdb=" N SER P 222 " --> pdb=" O VAL P 218 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 251 Processing helix chain 'P' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG P 260 " --> pdb=" O GLN P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 274 Processing helix chain 'P' and resid 275 through 280 Processing helix chain 'P' and resid 281 through 296 Processing helix chain 'P' and resid 297 through 300 removed outlier: 3.521A pdb=" N GLY P 300 " --> pdb=" O PRO P 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 297 through 300' Processing helix chain 'P' and resid 301 through 306 Processing helix chain 'P' and resid 318 through 332 Processing helix chain 'P' and resid 344 through 361 Processing helix chain 'Q' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN Q 13 " --> pdb=" O ASP Q 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU Q 14 " --> pdb=" O ILE Q 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 10 through 14' Processing helix chain 'S' and resid 9 through 20 Processing helix chain 'S' and resid 37 through 39 No H-bonds generated for 'chain 'S' and resid 37 through 39' Processing helix chain 'S' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU S 47 " --> pdb=" O GLU S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 75 Processing helix chain 'S' and resid 75 through 86 Processing helix chain 'S' and resid 120 through 142 removed outlier: 3.629A pdb=" N VAL S 124 " --> pdb=" O GLU S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 151 removed outlier: 3.615A pdb=" N GLN S 150 " --> pdb=" O PRO S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 156 through 171 removed outlier: 3.825A pdb=" N LYS S 171 " --> pdb=" O LEU S 167 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 190 removed outlier: 3.922A pdb=" N ARG S 189 " --> pdb=" O ARG S 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 198 Processing helix chain 'S' and resid 202 through 217 Processing helix chain 'S' and resid 218 through 233 removed outlier: 3.716A pdb=" N SER S 222 " --> pdb=" O VAL S 218 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 251 Processing helix chain 'S' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG S 260 " --> pdb=" O GLN S 256 " (cutoff:3.500A) Processing helix chain 'S' and resid 270 through 274 Processing helix chain 'S' and resid 275 through 280 Processing helix chain 'S' and resid 281 through 296 Processing helix chain 'S' and resid 297 through 300 removed outlier: 3.522A pdb=" N GLY S 300 " --> pdb=" O PRO S 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 297 through 300' Processing helix chain 'S' and resid 301 through 306 Processing helix chain 'S' and resid 318 through 332 Processing helix chain 'S' and resid 344 through 361 Processing helix chain 'T' and resid 10 through 14 removed outlier: 3.528A pdb=" N GLN T 13 " --> pdb=" O ASP T 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU T 14 " --> pdb=" O ILE T 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 10 through 14' Processing helix chain 'V' and resid 9 through 20 Processing helix chain 'V' and resid 37 through 39 No H-bonds generated for 'chain 'V' and resid 37 through 39' Processing helix chain 'V' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU V 47 " --> pdb=" O GLU V 43 " (cutoff:3.500A) Processing helix chain 'V' and resid 61 through 75 Processing helix chain 'V' and resid 75 through 86 Processing helix chain 'V' and resid 120 through 142 removed outlier: 3.629A pdb=" N VAL V 124 " --> pdb=" O GLU V 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 151 removed outlier: 3.616A pdb=" N GLN V 150 " --> pdb=" O PRO V 147 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS V 171 " --> pdb=" O LEU V 167 " (cutoff:3.500A) Processing helix chain 'V' and resid 175 through 190 removed outlier: 3.921A pdb=" N ARG V 189 " --> pdb=" O ARG V 185 " (cutoff:3.500A) Processing helix chain 'V' and resid 191 through 198 Processing helix chain 'V' and resid 202 through 217 Processing helix chain 'V' and resid 218 through 233 removed outlier: 3.716A pdb=" N SER V 222 " --> pdb=" O VAL V 218 " (cutoff:3.500A) Processing helix chain 'V' and resid 238 through 251 Processing helix chain 'V' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG V 260 " --> pdb=" O GLN V 256 " (cutoff:3.500A) Processing helix chain 'V' and resid 270 through 274 Processing helix chain 'V' and resid 275 through 280 Processing helix chain 'V' and resid 281 through 296 Processing helix chain 'V' and resid 297 through 300 removed outlier: 3.522A pdb=" N GLY V 300 " --> pdb=" O PRO V 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 297 through 300' Processing helix chain 'V' and resid 301 through 306 Processing helix chain 'V' and resid 318 through 332 Processing helix chain 'V' and resid 344 through 361 Processing helix chain 'W' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN W 13 " --> pdb=" O ASP W 10 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU W 14 " --> pdb=" O ILE W 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 10 through 14' Processing helix chain 'Y' and resid 9 through 20 Processing helix chain 'Y' and resid 37 through 39 No H-bonds generated for 'chain 'Y' and resid 37 through 39' Processing helix chain 'Y' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU Y 47 " --> pdb=" O GLU Y 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 61 through 75 Processing helix chain 'Y' and resid 75 through 86 Processing helix chain 'Y' and resid 120 through 142 removed outlier: 3.629A pdb=" N VAL Y 124 " --> pdb=" O GLU Y 120 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 151 removed outlier: 3.616A pdb=" N GLN Y 150 " --> pdb=" O PRO Y 147 " (cutoff:3.500A) Processing helix chain 'Y' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS Y 171 " --> pdb=" O LEU Y 167 " (cutoff:3.500A) Processing helix chain 'Y' and resid 175 through 190 removed outlier: 3.922A pdb=" N ARG Y 189 " --> pdb=" O ARG Y 185 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 198 Processing helix chain 'Y' and resid 202 through 217 Processing helix chain 'Y' and resid 218 through 233 removed outlier: 3.715A pdb=" N SER Y 222 " --> pdb=" O VAL Y 218 " (cutoff:3.500A) Processing helix chain 'Y' and resid 238 through 251 Processing helix chain 'Y' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG Y 260 " --> pdb=" O GLN Y 256 " (cutoff:3.500A) Processing helix chain 'Y' and resid 270 through 274 Processing helix chain 'Y' and resid 275 through 280 Processing helix chain 'Y' and resid 281 through 296 Processing helix chain 'Y' and resid 297 through 300 removed outlier: 3.522A pdb=" N GLY Y 300 " --> pdb=" O PRO Y 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 297 through 300' Processing helix chain 'Y' and resid 301 through 306 Processing helix chain 'Y' and resid 318 through 332 Processing helix chain 'Y' and resid 344 through 361 Processing helix chain 'Z' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN Z 13 " --> pdb=" O ASP Z 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU Z 14 " --> pdb=" O ILE Z 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 10 through 14' Processing helix chain '1' and resid 9 through 20 Processing helix chain '1' and resid 37 through 39 No H-bonds generated for 'chain '1' and resid 37 through 39' Processing helix chain '1' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU 1 47 " --> pdb=" O GLU 1 43 " (cutoff:3.500A) Processing helix chain '1' and resid 61 through 75 Processing helix chain '1' and resid 75 through 86 Processing helix chain '1' and resid 120 through 142 removed outlier: 3.628A pdb=" N VAL 1 124 " --> pdb=" O GLU 1 120 " (cutoff:3.500A) Processing helix chain '1' and resid 147 through 151 removed outlier: 3.615A pdb=" N GLN 1 150 " --> pdb=" O PRO 1 147 " (cutoff:3.500A) Processing helix chain '1' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS 1 171 " --> pdb=" O LEU 1 167 " (cutoff:3.500A) Processing helix chain '1' and resid 175 through 190 removed outlier: 3.921A pdb=" N ARG 1 189 " --> pdb=" O ARG 1 185 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 198 Processing helix chain '1' and resid 202 through 217 Processing helix chain '1' and resid 218 through 233 removed outlier: 3.716A pdb=" N SER 1 222 " --> pdb=" O VAL 1 218 " (cutoff:3.500A) Processing helix chain '1' and resid 238 through 251 Processing helix chain '1' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG 1 260 " --> pdb=" O GLN 1 256 " (cutoff:3.500A) Processing helix chain '1' and resid 270 through 274 Processing helix chain '1' and resid 275 through 280 Processing helix chain '1' and resid 281 through 296 Processing helix chain '1' and resid 297 through 300 removed outlier: 3.521A pdb=" N GLY 1 300 " --> pdb=" O PRO 1 297 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 297 through 300' Processing helix chain '1' and resid 301 through 306 Processing helix chain '1' and resid 318 through 332 Processing helix chain '1' and resid 344 through 361 Processing helix chain '2' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN 2 13 " --> pdb=" O ASP 2 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU 2 14 " --> pdb=" O ILE 2 11 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 10 through 14' Processing sheet with id=1, first strand: chain 'A' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR A 33 " --> pdb=" O VAL A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=1 Processing sheet with id=2, first strand: chain 'A' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU A 111 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR C 33 " --> pdb=" O VAL C 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=3 Processing sheet with id=4, first strand: chain 'C' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU C 111 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'G' and resid 32 through 35 removed outlier: 6.188A pdb=" N THR G 33 " --> pdb=" O VAL G 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=5 Processing sheet with id=6, first strand: chain 'G' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU G 111 " --> pdb=" O LEU G 100 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'J' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR J 33 " --> pdb=" O VAL J 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=7 Processing sheet with id=8, first strand: chain 'J' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU J 111 " --> pdb=" O LEU J 100 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'M' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR M 33 " --> pdb=" O VAL M 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=9 Processing sheet with id=10, first strand: chain 'M' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU M 111 " --> pdb=" O LEU M 100 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'P' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR P 33 " --> pdb=" O VAL P 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=11 Processing sheet with id=12, first strand: chain 'P' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU P 111 " --> pdb=" O LEU P 100 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'S' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR S 33 " --> pdb=" O VAL S 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=13 Processing sheet with id=14, first strand: chain 'S' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU S 111 " --> pdb=" O LEU S 100 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'V' and resid 32 through 35 removed outlier: 6.188A pdb=" N THR V 33 " --> pdb=" O VAL V 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=15 Processing sheet with id=16, first strand: chain 'V' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU V 111 " --> pdb=" O LEU V 100 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'Y' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR Y 33 " --> pdb=" O VAL Y 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=17 Processing sheet with id=18, first strand: chain 'Y' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU Y 111 " --> pdb=" O LEU Y 100 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain '1' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR 1 33 " --> pdb=" O VAL 1 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=19 Processing sheet with id=20, first strand: chain '1' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU 1 111 " --> pdb=" O LEU 1 100 " (cutoff:3.500A) 1680 hydrogen bonds defined for protein. 4920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 12.31 Time building geometry restraints manager: 12.55 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: 9700 1.34 - 1.46: 5244 1.46 - 1.57: 15416 1.57 - 1.69: 130 1.69 - 1.81: 230 Bond restraints: 30720 Sorted by residual: bond pdb=" C ALA M 310 " pdb=" N GLY M 311 " ideal model delta sigma weight residual 1.335 1.325 0.010 9.80e-03 1.04e+04 1.06e+00 bond pdb=" C ALA 1 310 " pdb=" N GLY 1 311 " ideal model delta sigma weight residual 1.335 1.325 0.010 9.80e-03 1.04e+04 1.06e+00 bond pdb=" C ALA G 310 " pdb=" N GLY G 311 " ideal model delta sigma weight residual 1.335 1.325 0.010 9.80e-03 1.04e+04 1.06e+00 bond pdb=" C ALA V 310 " pdb=" N GLY V 311 " ideal model delta sigma weight residual 1.335 1.325 0.010 9.80e-03 1.04e+04 1.06e+00 bond pdb=" C ALA S 310 " pdb=" N GLY S 311 " ideal model delta sigma weight residual 1.335 1.325 0.010 9.80e-03 1.04e+04 1.04e+00 ... (remaining 30715 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.39: 904 106.39 - 113.27: 17212 113.27 - 120.14: 10791 120.14 - 127.01: 12589 127.01 - 133.89: 214 Bond angle restraints: 41710 Sorted by residual: angle pdb=" N LYS V 55 " pdb=" CA LYS V 55 " pdb=" CB LYS V 55 " ideal model delta sigma weight residual 109.87 113.28 -3.41 1.63e+00 3.76e-01 4.38e+00 angle pdb=" N LYS G 55 " pdb=" CA LYS G 55 " pdb=" CB LYS G 55 " ideal model delta sigma weight residual 109.87 113.28 -3.41 1.63e+00 3.76e-01 4.38e+00 angle pdb=" N LYS Y 55 " pdb=" CA LYS Y 55 " pdb=" CB LYS Y 55 " ideal model delta sigma weight residual 109.87 113.27 -3.40 1.63e+00 3.76e-01 4.34e+00 angle pdb=" N LYS J 55 " pdb=" CA LYS J 55 " pdb=" CB LYS J 55 " ideal model delta sigma weight residual 109.87 113.27 -3.40 1.63e+00 3.76e-01 4.34e+00 angle pdb=" N LYS S 55 " pdb=" CA LYS S 55 " pdb=" CB LYS S 55 " ideal model delta sigma weight residual 109.87 113.25 -3.38 1.63e+00 3.76e-01 4.30e+00 ... (remaining 41705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 17029 16.59 - 33.19: 1401 33.19 - 49.78: 300 49.78 - 66.37: 110 66.37 - 82.96: 120 Dihedral angle restraints: 18960 sinusoidal: 8250 harmonic: 10710 Sorted by residual: dihedral pdb=" CA ALA J 251 " pdb=" C ALA J 251 " pdb=" N TYR J 252 " pdb=" CA TYR J 252 " ideal model delta harmonic sigma weight residual -180.00 -162.38 -17.62 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ALA Y 251 " pdb=" C ALA Y 251 " pdb=" N TYR Y 252 " pdb=" CA TYR Y 252 " ideal model delta harmonic sigma weight residual -180.00 -162.38 -17.62 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ALA 1 251 " pdb=" C ALA 1 251 " pdb=" N TYR 1 252 " pdb=" CA TYR 1 252 " ideal model delta harmonic sigma weight residual -180.00 -162.38 -17.62 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 18957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2857 0.031 - 0.062: 1457 0.062 - 0.094: 418 0.094 - 0.125: 150 0.125 - 0.156: 38 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CB VAL C 35 " pdb=" CA VAL C 35 " pdb=" CG1 VAL C 35 " pdb=" CG2 VAL C 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CB VAL S 35 " pdb=" CA VAL S 35 " pdb=" CG1 VAL S 35 " pdb=" CG2 VAL S 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CB VAL M 35 " pdb=" CA VAL M 35 " pdb=" CG1 VAL M 35 " pdb=" CG2 VAL M 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 4917 not shown) Planarity restraints: 5050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C F 73 " -0.025 2.00e-02 2.50e+03 1.26e-02 3.57e+00 pdb=" N1 C F 73 " 0.025 2.00e-02 2.50e+03 pdb=" C2 C F 73 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C F 73 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C F 73 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C F 73 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C F 73 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C F 73 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C F 73 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C U 73 " -0.025 2.00e-02 2.50e+03 1.26e-02 3.57e+00 pdb=" N1 C U 73 " 0.025 2.00e-02 2.50e+03 pdb=" C2 C U 73 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C U 73 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C U 73 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C U 73 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C U 73 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C U 73 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C U 73 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C I 73 " -0.025 2.00e-02 2.50e+03 1.25e-02 3.53e+00 pdb=" N1 C I 73 " 0.025 2.00e-02 2.50e+03 pdb=" C2 C I 73 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C I 73 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C I 73 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C I 73 " -0.002 2.00e-02 2.50e+03 pdb=" N4 C I 73 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C I 73 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C I 73 " 0.005 2.00e-02 2.50e+03 ... (remaining 5047 not shown) Histogram of nonbonded interaction distances: 0.57 - 1.43: 120 1.43 - 2.30: 200 2.30 - 3.17: 26141 3.17 - 4.03: 81053 4.03 - 4.90: 150190 Warning: very small nonbonded interaction distances. Nonbonded interactions: 257704 Sorted by model distance: nonbonded pdb=" CE1 TYR Y 23 " pdb=" CZ ARG 1 78 " model vdw 0.568 3.570 nonbonded pdb=" CE1 TYR J 23 " pdb=" CZ ARG M 78 " model vdw 0.568 3.570 nonbonded pdb=" CE1 TYR G 23 " pdb=" CZ ARG J 78 " model vdw 0.568 3.570 nonbonded pdb=" CE1 TYR A 23 " pdb=" CZ ARG C 78 " model vdw 0.568 3.570 nonbonded pdb=" CE1 TYR P 23 " pdb=" CZ ARG S 78 " model vdw 0.568 3.570 ... (remaining 257699 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 '0' selection = chain '3' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' } ncs_group { reference = chain '1' selection = chain 'A' selection = chain 'C' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Y' } ncs_group { reference = chain '2' selection = chain 'B' selection = chain 'D' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.130 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: 0.000 Extract box with map and model: 0.500 Check model and map are aligned: 0.000 Set scattering table: 0.170 Process input model: 88.830 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 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 : 0.004 0.032 30720 Z= 0.272 Angle : 0.583 5.983 41710 Z= 0.329 Chirality : 0.042 0.156 4920 Planarity : 0.003 0.028 5050 Dihedral : 14.904 82.962 12080 Min Nonbonded Distance : 0.568 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: 0.66 (0.14), residues: 3640 helix: 1.16 (0.11), residues: 2270 sheet: -0.79 (0.30), residues: 210 loop : -0.63 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 123 HIS 0.005 0.001 HIS G 15 PHE 0.014 0.002 PHE C 169 TYR 0.018 0.002 TYR V 53 ARG 0.015 0.001 ARG J 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 437 time to evaluate : 3.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.6685 (tp30) cc_final: 0.6247 (mm-30) REVERT: C 55 LYS cc_start: 0.7701 (mppt) cc_final: 0.7427 (mppt) REVERT: C 180 LEU cc_start: 0.8539 (mt) cc_final: 0.8254 (mt) REVERT: J 85 ASN cc_start: 0.8590 (m-40) cc_final: 0.8216 (m110) REVERT: J 249 MET cc_start: 0.8336 (mmt) cc_final: 0.8045 (mmp) REVERT: J 281 GLU cc_start: 0.6960 (tp30) cc_final: 0.6746 (tp30) REVERT: K 12 TYR cc_start: 0.7451 (m-80) cc_final: 0.7173 (m-10) REVERT: K 16 MET cc_start: 0.4604 (mmm) cc_final: 0.4281 (mmt) REVERT: M 200 ARG cc_start: 0.7529 (ptp90) cc_final: 0.7326 (ptt-90) REVERT: N 12 TYR cc_start: 0.7298 (m-80) cc_final: 0.7067 (m-10) REVERT: P 281 GLU cc_start: 0.6681 (tp30) cc_final: 0.6243 (mm-30) REVERT: S 55 LYS cc_start: 0.7698 (mppt) cc_final: 0.7427 (mppt) REVERT: S 180 LEU cc_start: 0.8541 (mt) cc_final: 0.8249 (mt) REVERT: Y 85 ASN cc_start: 0.8590 (m-40) cc_final: 0.8219 (m110) REVERT: Y 249 MET cc_start: 0.8335 (mmt) cc_final: 0.8044 (mmp) REVERT: Y 281 GLU cc_start: 0.6962 (tp30) cc_final: 0.6750 (tp30) REVERT: Z 12 TYR cc_start: 0.7452 (m-80) cc_final: 0.7174 (m-10) REVERT: Z 16 MET cc_start: 0.4605 (mmm) cc_final: 0.4276 (mmt) REVERT: 2 12 TYR cc_start: 0.7300 (m-80) cc_final: 0.7070 (m-10) outliers start: 0 outliers final: 2 residues processed: 437 average time/residue: 1.5663 time to fit residues: 792.5848 Evaluate side-chains 301 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 299 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain S residue 22 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.5980 chunk 272 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 282 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 171 optimal weight: 0.0670 chunk 210 optimal weight: 0.6980 chunk 326 optimal weight: 3.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 112 GLN A 306 GLN A 365 ASN C 42 GLN C 112 GLN C 306 GLN C 365 ASN G 42 GLN G 112 GLN G 306 GLN G 365 ASN J 112 GLN J 306 GLN J 365 ASN M 42 GLN M 85 ASN M 112 GLN M 279 GLN M 306 GLN M 365 ASN P 42 GLN P 112 GLN P 306 GLN P 365 ASN S 42 GLN S 112 GLN S 306 GLN S 365 ASN V 42 GLN V 112 GLN V 306 GLN V 365 ASN Y 112 GLN Y 306 GLN Y 365 ASN 1 42 GLN 1 85 ASN 1 112 GLN 1 279 GLN 1 306 GLN 1 365 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 30720 Z= 0.193 Angle : 0.549 8.247 41710 Z= 0.289 Chirality : 0.041 0.219 4920 Planarity : 0.004 0.044 5050 Dihedral : 11.411 74.057 5116 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.82 % Allowed : 7.78 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.14), residues: 3640 helix: 1.66 (0.11), residues: 2310 sheet: -0.67 (0.31), residues: 210 loop : -0.36 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 123 HIS 0.003 0.001 HIS V 275 PHE 0.011 0.001 PHE A 169 TYR 0.028 0.002 TYR G 354 ARG 0.004 0.000 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 319 time to evaluate : 3.448 Fit side-chains REVERT: A 281 GLU cc_start: 0.6518 (tp30) cc_final: 0.6281 (mm-30) REVERT: C 339 ARG cc_start: 0.7800 (mtp85) cc_final: 0.7540 (mtp180) REVERT: G 281 GLU cc_start: 0.6241 (tp30) cc_final: 0.5962 (mm-30) REVERT: J 281 GLU cc_start: 0.6450 (tp30) cc_final: 0.6230 (mm-30) REVERT: K 12 TYR cc_start: 0.7385 (m-80) cc_final: 0.7066 (m-10) REVERT: M 200 ARG cc_start: 0.7412 (ptp90) cc_final: 0.7186 (ptt-90) REVERT: M 281 GLU cc_start: 0.6441 (tp30) cc_final: 0.6205 (mm-30) REVERT: P 281 GLU cc_start: 0.6524 (tp30) cc_final: 0.6286 (mm-30) REVERT: S 339 ARG cc_start: 0.7800 (mtp85) cc_final: 0.7538 (mtp180) REVERT: V 281 GLU cc_start: 0.6240 (tp30) cc_final: 0.5962 (mm-30) REVERT: Y 281 GLU cc_start: 0.6450 (tp30) cc_final: 0.6232 (mm-30) REVERT: Z 12 TYR cc_start: 0.7384 (m-80) cc_final: 0.7067 (m-10) REVERT: 1 281 GLU cc_start: 0.6441 (tp30) cc_final: 0.6205 (mm-30) outliers start: 26 outliers final: 14 residues processed: 325 average time/residue: 1.4643 time to fit residues: 556.7929 Evaluate side-chains 308 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 294 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain 1 residue 32 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 222 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 327 optimal weight: 0.9980 chunk 353 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 chunk 324 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 262 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 30720 Z= 0.338 Angle : 0.610 7.104 41710 Z= 0.313 Chirality : 0.044 0.181 4920 Planarity : 0.004 0.050 5050 Dihedral : 11.363 74.707 5110 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.84 % Allowed : 8.35 % Favored : 89.81 % 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: 1.12 (0.14), residues: 3640 helix: 1.48 (0.11), residues: 2310 sheet: -0.62 (0.34), residues: 210 loop : -0.43 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 261 HIS 0.004 0.001 HIS V 275 PHE 0.017 0.002 PHE A 169 TYR 0.037 0.002 TYR S 53 ARG 0.006 0.001 ARG Y 221 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 333 time to evaluate : 3.455 Fit side-chains REVERT: C 281 GLU cc_start: 0.6455 (tp30) cc_final: 0.6082 (mt-10) REVERT: G 148 GLN cc_start: 0.6547 (tm-30) cc_final: 0.6331 (tm-30) REVERT: G 281 GLU cc_start: 0.6404 (tp30) cc_final: 0.6204 (mm-30) REVERT: K 12 TYR cc_start: 0.7501 (m-80) cc_final: 0.7179 (m-10) REVERT: M 200 ARG cc_start: 0.7596 (ptp90) cc_final: 0.7286 (ptt-90) REVERT: M 215 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: S 281 GLU cc_start: 0.6456 (tp30) cc_final: 0.6081 (mt-10) REVERT: V 148 GLN cc_start: 0.6541 (tm-30) cc_final: 0.6327 (tm-30) REVERT: Z 12 TYR cc_start: 0.7498 (m-80) cc_final: 0.7178 (m-10) REVERT: 1 215 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.6974 (mp0) outliers start: 58 outliers final: 45 residues processed: 358 average time/residue: 1.3525 time to fit residues: 573.8036 Evaluate side-chains 347 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 300 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 53 TYR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 53 TYR Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 215 GLU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 53 TYR Chi-restraints excluded: chain V residue 95 THR Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 332 LEU Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 53 TYR Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 215 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 0.9980 chunk 246 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 156 optimal weight: 0.3980 chunk 219 optimal weight: 3.9990 chunk 328 optimal weight: 3.9990 chunk 347 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 311 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 320 ASN G 150 GLN G 344 ASN M 320 ASN P 150 GLN V 150 GLN ** V 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 320 ASN 1 320 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30720 Z= 0.210 Angle : 0.539 8.272 41710 Z= 0.277 Chirality : 0.040 0.196 4920 Planarity : 0.003 0.050 5050 Dihedral : 11.282 74.225 5110 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.93 % Allowed : 10.03 % Favored : 88.04 % 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: 1.38 (0.14), residues: 3640 helix: 1.74 (0.11), residues: 2310 sheet: -0.78 (0.33), residues: 210 loop : -0.41 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 261 HIS 0.003 0.001 HIS V 275 PHE 0.012 0.002 PHE P 224 TYR 0.035 0.002 TYR M 53 ARG 0.007 0.000 ARG G 341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 311 time to evaluate : 3.436 Fit side-chains REVERT: C 94 LEU cc_start: 0.7513 (tp) cc_final: 0.7227 (mp) REVERT: C 339 ARG cc_start: 0.7815 (mtp85) cc_final: 0.7534 (mtp180) REVERT: G 148 GLN cc_start: 0.6568 (tm-30) cc_final: 0.6307 (tm-30) REVERT: K 12 TYR cc_start: 0.7510 (m-80) cc_final: 0.7185 (m-10) REVERT: M 200 ARG cc_start: 0.7446 (ptp90) cc_final: 0.7228 (ptt-90) REVERT: S 94 LEU cc_start: 0.7510 (tp) cc_final: 0.7224 (mp) REVERT: S 339 ARG cc_start: 0.7811 (mtp85) cc_final: 0.7532 (mtp180) REVERT: V 53 TYR cc_start: 0.5876 (p90) cc_final: 0.5672 (OUTLIER) REVERT: V 148 GLN cc_start: 0.6561 (tm-30) cc_final: 0.6304 (tm-30) REVERT: Z 12 TYR cc_start: 0.7507 (m-80) cc_final: 0.7183 (m-10) REVERT: 1 215 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6910 (mp0) outliers start: 61 outliers final: 46 residues processed: 339 average time/residue: 1.3013 time to fit residues: 524.4637 Evaluate side-chains 338 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 292 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain P residue 10 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain S residue 347 LEU Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 332 LEU Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain 1 residue 10 ASP Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 215 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 259 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 296 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 312 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 30720 Z= 0.273 Angle : 0.575 9.127 41710 Z= 0.290 Chirality : 0.041 0.151 4920 Planarity : 0.004 0.051 5050 Dihedral : 11.264 74.477 5110 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.41 % Allowed : 10.60 % Favored : 86.99 % 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: 1.29 (0.14), residues: 3640 helix: 1.71 (0.11), residues: 2310 sheet: -1.40 (0.31), residues: 230 loop : -0.39 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 261 HIS 0.004 0.001 HIS V 275 PHE 0.015 0.002 PHE A 169 TYR 0.025 0.002 TYR 1 53 ARG 0.006 0.000 ARG V 341 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 292 time to evaluate : 3.521 Fit side-chains REVERT: G 148 GLN cc_start: 0.6593 (tm-30) cc_final: 0.6353 (tm-30) REVERT: M 200 ARG cc_start: 0.7506 (ptp90) cc_final: 0.7273 (ptt-90) REVERT: M 215 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: S 339 ARG cc_start: 0.7830 (mtp85) cc_final: 0.7543 (mtp180) REVERT: V 148 GLN cc_start: 0.6592 (tm-30) cc_final: 0.6354 (tm-30) REVERT: 1 215 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6867 (mp0) outliers start: 76 outliers final: 64 residues processed: 334 average time/residue: 1.2792 time to fit residues: 509.9735 Evaluate side-chains 356 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 290 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 215 GLU Chi-restraints excluded: chain P residue 10 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 175 THR Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 332 LEU Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 175 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 10 ASP Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 215 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 0.9990 chunk 313 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 348 optimal weight: 0.9990 chunk 289 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30720 Z= 0.220 Angle : 0.564 9.817 41710 Z= 0.281 Chirality : 0.040 0.193 4920 Planarity : 0.003 0.053 5050 Dihedral : 11.223 74.267 5110 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.47 % Allowed : 11.49 % Favored : 86.04 % 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: 1.43 (0.14), residues: 3640 helix: 1.79 (0.11), residues: 2330 sheet: -1.48 (0.31), residues: 230 loop : -0.24 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 261 HIS 0.003 0.001 HIS V 275 PHE 0.013 0.002 PHE 1 169 TYR 0.026 0.002 TYR Z 12 ARG 0.007 0.000 ARG G 341 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 294 time to evaluate : 3.214 Fit side-chains REVERT: C 339 ARG cc_start: 0.7831 (mtp85) cc_final: 0.7512 (mtp180) REVERT: D 16 MET cc_start: 0.4396 (mmm) cc_final: 0.4056 (mmp) REVERT: G 148 GLN cc_start: 0.6714 (tm-30) cc_final: 0.6466 (tm-30) REVERT: K 16 MET cc_start: 0.4407 (mmm) cc_final: 0.3475 (mmp) REVERT: M 200 ARG cc_start: 0.7501 (ptp90) cc_final: 0.7249 (ptt-90) REVERT: N 16 MET cc_start: 0.4592 (mmm) cc_final: 0.3523 (mmp) REVERT: S 339 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7538 (mtp180) REVERT: T 16 MET cc_start: 0.4392 (mmm) cc_final: 0.4059 (mmp) REVERT: V 148 GLN cc_start: 0.6715 (tm-30) cc_final: 0.6468 (tm-30) REVERT: Z 16 MET cc_start: 0.4407 (mmm) cc_final: 0.3474 (mmp) REVERT: 1 215 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: 2 16 MET cc_start: 0.4283 (mmm) cc_final: 0.3234 (mmp) outliers start: 78 outliers final: 68 residues processed: 339 average time/residue: 1.2628 time to fit residues: 511.1236 Evaluate side-chains 353 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 284 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 10 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 10 ASP Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 175 THR Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 332 LEU Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 175 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 10 ASP Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 215 GLU Chi-restraints excluded: chain 1 residue 342 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 198 optimal weight: 0.5980 chunk 254 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 293 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 346 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 211 optimal weight: 0.2980 chunk 160 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30720 Z= 0.179 Angle : 0.541 9.914 41710 Z= 0.270 Chirality : 0.038 0.180 4920 Planarity : 0.003 0.053 5050 Dihedral : 11.193 74.017 5110 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.34 % Allowed : 12.22 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.14), residues: 3640 helix: 1.98 (0.11), residues: 2330 sheet: -1.51 (0.30), residues: 230 loop : -0.22 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Y 123 HIS 0.003 0.001 HIS C 56 PHE 0.011 0.001 PHE A 224 TYR 0.021 0.001 TYR V 338 ARG 0.008 0.000 ARG V 341 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 284 time to evaluate : 3.171 Fit side-chains REVERT: C 339 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7503 (mtp180) REVERT: J 94 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7098 (mp) REVERT: M 200 ARG cc_start: 0.7485 (ptp90) cc_final: 0.7226 (ptt-90) REVERT: S 339 ARG cc_start: 0.7813 (mtp85) cc_final: 0.7501 (mtp180) REVERT: W 16 MET cc_start: 0.3693 (mmm) cc_final: 0.3239 (mmp) REVERT: Y 94 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7093 (mp) outliers start: 74 outliers final: 56 residues processed: 329 average time/residue: 1.2963 time to fit residues: 509.3064 Evaluate side-chains 329 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 271 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 10 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 10 ASP Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 175 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 10 ASP Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 342 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 220 optimal weight: 0.9990 chunk 236 optimal weight: 0.7980 chunk 171 optimal weight: 0.0370 chunk 32 optimal weight: 3.9990 chunk 272 optimal weight: 0.7980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 270 ASN P 270 ASN ** V 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 270 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30720 Z= 0.192 Angle : 0.570 11.946 41710 Z= 0.279 Chirality : 0.039 0.152 4920 Planarity : 0.003 0.055 5050 Dihedral : 11.161 74.079 5110 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.25 % Allowed : 13.01 % Favored : 84.75 % 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: 1.70 (0.14), residues: 3640 helix: 2.02 (0.11), residues: 2330 sheet: -1.48 (0.31), residues: 230 loop : -0.16 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Y 123 HIS 0.002 0.001 HIS G 275 PHE 0.011 0.002 PHE 1 169 TYR 0.022 0.001 TYR V 338 ARG 0.006 0.000 ARG S 341 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 286 time to evaluate : 3.031 Fit side-chains REVERT: C 339 ARG cc_start: 0.7818 (mtp85) cc_final: 0.7527 (mtp180) REVERT: G 272 MET cc_start: 0.5158 (OUTLIER) cc_final: 0.4368 (tmt) REVERT: J 94 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7148 (mp) REVERT: K 12 TYR cc_start: 0.6838 (m-10) cc_final: 0.6543 (m-10) REVERT: M 200 ARG cc_start: 0.7485 (ptp90) cc_final: 0.7225 (ptt-90) REVERT: N 16 MET cc_start: 0.4199 (mmm) cc_final: 0.3510 (mmp) REVERT: S 339 ARG cc_start: 0.7814 (mtp85) cc_final: 0.7528 (mtp180) REVERT: V 272 MET cc_start: 0.5184 (OUTLIER) cc_final: 0.4368 (tmt) REVERT: Y 94 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7164 (mp) REVERT: Z 12 TYR cc_start: 0.6832 (m-10) cc_final: 0.6540 (m-10) REVERT: 2 16 MET cc_start: 0.4286 (mmm) cc_final: 0.3472 (mmp) outliers start: 71 outliers final: 59 residues processed: 327 average time/residue: 1.4040 time to fit residues: 558.2294 Evaluate side-chains 334 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 271 time to evaluate : 3.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 272 MET Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 10 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 10 ASP Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 175 THR Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 272 MET Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 175 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 10 ASP Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 342 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 0.7980 chunk 332 optimal weight: 4.9990 chunk 303 optimal weight: 0.6980 chunk 323 optimal weight: 2.9990 chunk 194 optimal weight: 0.0770 chunk 140 optimal weight: 5.9990 chunk 253 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 292 optimal weight: 0.7980 chunk 305 optimal weight: 0.8980 chunk 322 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 150 GLN C 270 ASN ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 GLN M 150 GLN M 270 ASN S 150 GLN S 270 ASN ** V 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 150 GLN 1 150 GLN 1 270 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30720 Z= 0.185 Angle : 0.573 12.507 41710 Z= 0.279 Chirality : 0.038 0.153 4920 Planarity : 0.004 0.055 5050 Dihedral : 11.154 74.024 5110 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.18 % Allowed : 13.20 % Favored : 84.62 % 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: 1.78 (0.14), residues: 3640 helix: 2.07 (0.11), residues: 2330 sheet: -1.39 (0.31), residues: 230 loop : -0.13 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 123 HIS 0.002 0.001 HIS J 275 PHE 0.011 0.001 PHE M 169 TYR 0.021 0.001 TYR V 338 ARG 0.005 0.000 ARG 1 341 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 280 time to evaluate : 3.173 Fit side-chains REVERT: B 16 MET cc_start: 0.3893 (mmm) cc_final: 0.3194 (mmp) REVERT: C 339 ARG cc_start: 0.7791 (mtp85) cc_final: 0.7501 (mtp180) REVERT: C 341 ARG cc_start: 0.7531 (ptm-80) cc_final: 0.6997 (mtp-110) REVERT: G 272 MET cc_start: 0.5189 (OUTLIER) cc_final: 0.4393 (tmt) REVERT: K 12 TYR cc_start: 0.6777 (m-10) cc_final: 0.6515 (m-10) REVERT: M 200 ARG cc_start: 0.7476 (ptp90) cc_final: 0.7216 (ptt-90) REVERT: N 16 MET cc_start: 0.4316 (mmm) cc_final: 0.3439 (mmp) REVERT: Q 16 MET cc_start: 0.3897 (mmm) cc_final: 0.3196 (mmp) REVERT: S 339 ARG cc_start: 0.7789 (mtp85) cc_final: 0.7448 (mtp180) REVERT: S 341 ARG cc_start: 0.7530 (ptm-80) cc_final: 0.6995 (mtp-110) REVERT: V 272 MET cc_start: 0.5197 (OUTLIER) cc_final: 0.4386 (tmt) REVERT: W 16 MET cc_start: 0.3942 (mmm) cc_final: 0.3246 (mmp) REVERT: Z 12 TYR cc_start: 0.6770 (m-10) cc_final: 0.6511 (m-10) REVERT: Z 16 MET cc_start: 0.4162 (mmm) cc_final: 0.3477 (mmp) REVERT: 2 16 MET cc_start: 0.4352 (mmm) cc_final: 0.3632 (mmp) outliers start: 69 outliers final: 57 residues processed: 320 average time/residue: 1.3225 time to fit residues: 505.3884 Evaluate side-chains 338 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 279 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 272 MET Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 10 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 10 ASP Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 175 THR Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 272 MET Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 175 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 0.5980 chunk 341 optimal weight: 0.6980 chunk 208 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 237 optimal weight: 0.3980 chunk 358 optimal weight: 0.9990 chunk 330 optimal weight: 0.6980 chunk 285 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 328 ASN ** V 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 328 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30720 Z= 0.185 Angle : 0.582 13.069 41710 Z= 0.282 Chirality : 0.038 0.177 4920 Planarity : 0.003 0.053 5050 Dihedral : 11.128 74.019 5110 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.96 % Allowed : 13.83 % Favored : 84.21 % 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: 1.87 (0.14), residues: 3640 helix: 2.13 (0.11), residues: 2330 sheet: -1.33 (0.31), residues: 230 loop : -0.07 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 123 HIS 0.003 0.001 HIS J 275 PHE 0.011 0.001 PHE M 169 TYR 0.020 0.001 TYR V 338 ARG 0.008 0.000 ARG 1 341 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 277 time to evaluate : 3.244 Fit side-chains REVERT: A 341 ARG cc_start: 0.7012 (ptm-80) cc_final: 0.6088 (mtp-110) REVERT: B 16 MET cc_start: 0.3936 (mmm) cc_final: 0.3408 (mmp) REVERT: C 339 ARG cc_start: 0.7811 (mtp85) cc_final: 0.7519 (mtp180) REVERT: C 341 ARG cc_start: 0.7479 (ptm-80) cc_final: 0.7000 (mtm110) REVERT: G 272 MET cc_start: 0.5300 (OUTLIER) cc_final: 0.4682 (tmt) REVERT: G 341 ARG cc_start: 0.6971 (ptm-80) cc_final: 0.6035 (mtm-85) REVERT: J 341 ARG cc_start: 0.7228 (ptm-80) cc_final: 0.6458 (mtm-85) REVERT: K 12 TYR cc_start: 0.6726 (m-10) cc_final: 0.6516 (m-10) REVERT: M 200 ARG cc_start: 0.7478 (ptp90) cc_final: 0.7202 (ptt-90) REVERT: P 341 ARG cc_start: 0.7009 (ptm-80) cc_final: 0.6088 (mtp-110) REVERT: Q 16 MET cc_start: 0.3942 (mmm) cc_final: 0.3408 (mmp) REVERT: S 339 ARG cc_start: 0.7806 (mtp85) cc_final: 0.7518 (mtp180) REVERT: S 341 ARG cc_start: 0.7469 (ptm-80) cc_final: 0.6991 (mtm110) REVERT: V 341 ARG cc_start: 0.6967 (ptm-80) cc_final: 0.6072 (mtm-85) REVERT: W 16 MET cc_start: 0.3938 (mmm) cc_final: 0.3406 (mmp) REVERT: Y 341 ARG cc_start: 0.7170 (ptm-80) cc_final: 0.6399 (mtm-85) REVERT: Z 12 TYR cc_start: 0.6742 (m-10) cc_final: 0.6528 (m-10) outliers start: 62 outliers final: 59 residues processed: 314 average time/residue: 1.3258 time to fit residues: 494.8547 Evaluate side-chains 336 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 276 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 272 MET Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 10 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 10 ASP Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 175 THR Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 175 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 10 ASP Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 9.9990 chunk 304 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 263 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 286 optimal weight: 0.1980 chunk 119 optimal weight: 0.9990 chunk 293 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.184747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.134969 restraints weight = 34484.154| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.82 r_work: 0.3300 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30720 Z= 0.193 Angle : 0.577 13.164 41710 Z= 0.281 Chirality : 0.039 0.185 4920 Planarity : 0.003 0.053 5050 Dihedral : 11.101 74.083 5110 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.03 % Allowed : 13.67 % Favored : 84.30 % 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: 1.89 (0.14), residues: 3640 helix: 2.12 (0.11), residues: 2330 sheet: -1.18 (0.32), residues: 230 loop : -0.05 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 123 HIS 0.003 0.001 HIS V 275 PHE 0.012 0.002 PHE M 169 TYR 0.021 0.001 TYR V 338 ARG 0.007 0.000 ARG G 341 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9603.14 seconds wall clock time: 170 minutes 22.75 seconds (10222.75 seconds total)