Starting phenix.real_space_refine on Sat Feb 17 03:52:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irt_35685/02_2024/8irt_35685_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irt_35685/02_2024/8irt_35685.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irt_35685/02_2024/8irt_35685_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irt_35685/02_2024/8irt_35685_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irt_35685/02_2024/8irt_35685_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irt_35685/02_2024/8irt_35685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irt_35685/02_2024/8irt_35685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irt_35685/02_2024/8irt_35685_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irt_35685/02_2024/8irt_35685_neut_trim_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 S 69 5.16 5 C 5571 2.51 5 N 1485 2.21 5 O 1643 1.98 5 H 8669 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 208": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 242": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 313": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 134": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 150": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 219": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 251": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 304": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 314": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 98": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 180": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 191": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 128": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 219": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 222": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 391": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17437 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3572 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 2 Chain: "B" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5108 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "E" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3503 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 4369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4369 Unusual residues: {'R5F': 1} Inner-chain residues flagged as termini: ['pdbres="CYS R 400 "'] Classifications: {'peptide': 273, 'undetermined': 1, 'water': 2} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 262, None: 3} Not linked: pdbres="CYS R 400 " pdbres="R5F R 501 " Not linked: pdbres="R5F R 501 " pdbres="HOH R 601 " Not linked: pdbres="HOH R 601 " pdbres="HOH R 602 " Chain breaks: 1 Time building chain proxies: 7.74, per 1000 atoms: 0.44 Number of scatterers: 17437 At special positions: 0 Unit cell: (112.86, 132.715, 108.68, 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 69 16.00 O 1643 8.00 N 1485 7.00 C 5571 6.00 H 8669 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 103 " - pdb=" SG CYS R 181 " distance=2.04 Simple disulfide: pdb=" SG CYS R 355 " - pdb=" SG CYS R 358 " distance=2.02 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: 15.10 Conformation dependent library (CDL) restraints added in 2.3 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 12 sheets defined 36.0% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.863A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 231' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.343A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 350 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 47 removed outlier: 5.042A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 56 Processing helix chain 'R' and resid 58 through 60 No H-bonds generated for 'chain 'R' and resid 58 through 60' Processing helix chain 'R' and resid 63 through 80 removed outlier: 3.627A pdb=" N LEU R 67 " --> pdb=" O THR R 63 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL R 68 " --> pdb=" O THR R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 91 Processing helix chain 'R' and resid 100 through 133 removed outlier: 3.694A pdb=" N VAL R 132 " --> pdb=" O ARG R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 138 No H-bonds generated for 'chain 'R' and resid 135 through 138' Processing helix chain 'R' and resid 144 through 169 Proline residue: R 167 - end of helix Processing helix chain 'R' and resid 186 through 196 removed outlier: 4.827A pdb=" N TYR R 191 " --> pdb=" O ASP R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 222 Processing helix chain 'R' and resid 322 through 353 Proline residue: R 344 - end of helix Processing helix chain 'R' and resid 362 through 383 removed outlier: 3.800A pdb=" N ASN R 375 " --> pdb=" O LEU R 371 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER R 376 " --> pdb=" O GLY R 372 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA R 377 " --> pdb=" O TYR R 373 " (cutoff:3.500A) Proline residue: R 380 - end of helix Processing helix chain 'R' and resid 388 through 399 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.824A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.836A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.940A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.569A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.743A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.683A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.621A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.532A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.833A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.571A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 411 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.56 Time building geometry restraints manager: 15.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 8637 1.13 - 1.30: 1520 1.30 - 1.47: 3462 1.47 - 1.65: 3898 1.65 - 1.82: 98 Bond restraints: 17615 Sorted by residual: bond pdb=" C7 R5F R 501 " pdb=" C8 R5F R 501 " ideal model delta sigma weight residual 1.596 1.382 0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C6 R5F R 501 " pdb=" S1 R5F R 501 " ideal model delta sigma weight residual 1.555 1.737 -0.182 2.00e-02 2.50e+03 8.27e+01 bond pdb=" C9 R5F R 501 " pdb=" S1 R5F R 501 " ideal model delta sigma weight residual 1.555 1.717 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" NE2 GLN R 356 " pdb="HE22 GLN R 356 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE3 TRP E 36 " pdb=" HE3 TRP E 36 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 17610 not shown) Histogram of bond angle deviations from ideal: 88.70 - 97.93: 29 97.93 - 107.16: 1826 107.16 - 116.39: 19540 116.39 - 125.63: 9934 125.63 - 134.86: 363 Bond angle restraints: 31692 Sorted by residual: angle pdb=" C TYR B 105 " pdb=" CA TYR B 105 " pdb=" CB TYR B 105 " ideal model delta sigma weight residual 109.71 122.47 -12.76 1.83e+00 2.99e-01 4.86e+01 angle pdb=" N ASN A 269 " pdb=" CA ASN A 269 " pdb=" C ASN A 269 " ideal model delta sigma weight residual 113.18 121.46 -8.28 1.21e+00 6.83e-01 4.68e+01 angle pdb=" N ARG B 52 " pdb=" CA ARG B 52 " pdb=" C ARG B 52 " ideal model delta sigma weight residual 112.90 121.78 -8.88 1.31e+00 5.83e-01 4.59e+01 angle pdb=" C LEU B 51 " pdb=" CA LEU B 51 " pdb=" CB LEU B 51 " ideal model delta sigma weight residual 111.77 121.44 -9.67 1.52e+00 4.33e-01 4.05e+01 angle pdb=" C6 R5F R 501 " pdb=" S1 R5F R 501 " pdb=" C9 R5F R 501 " ideal model delta sigma weight residual 107.56 88.70 18.86 3.00e+00 1.11e-01 3.95e+01 ... (remaining 31687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7611 17.95 - 35.91: 446 35.91 - 53.86: 143 53.86 - 71.81: 126 71.81 - 89.77: 7 Dihedral angle restraints: 8333 sinusoidal: 4458 harmonic: 3875 Sorted by residual: dihedral pdb=" CA ASN A 311 " pdb=" C ASN A 311 " pdb=" N LYS A 312 " pdb=" CA LYS A 312 " ideal model delta harmonic sigma weight residual 180.00 150.13 29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA TYR R 138 " pdb=" C TYR R 138 " pdb=" N GLN R 139 " pdb=" CA GLN R 139 " ideal model delta harmonic sigma weight residual -180.00 -150.27 -29.73 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA TYR B 289 " pdb=" C TYR B 289 " pdb=" N ASP B 290 " pdb=" CA ASP B 290 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 8330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 889 0.086 - 0.173: 379 0.173 - 0.259: 90 0.259 - 0.345: 26 0.345 - 0.431: 5 Chirality restraints: 1389 Sorted by residual: chirality pdb=" CA SER B 334 " pdb=" N SER B 334 " pdb=" C SER B 334 " pdb=" CB SER B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CA THR R 357 " pdb=" N THR R 357 " pdb=" C THR R 357 " pdb=" CB THR R 357 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA ASP B 228 " pdb=" N ASP B 228 " pdb=" C ASP B 228 " pdb=" CB ASP B 228 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 1386 not shown) Planarity restraints: 2610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.404 2.00e-02 2.50e+03 1.59e-01 7.54e+02 pdb=" CG TYR B 105 " -0.228 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " -0.085 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " -0.169 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.062 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.176 2.00e-02 2.50e+03 pdb=" HD1 TYR B 105 " 0.005 2.00e-02 2.50e+03 pdb=" HD2 TYR B 105 " -0.090 2.00e-02 2.50e+03 pdb=" HE1 TYR B 105 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 TYR B 105 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 175 " -0.293 2.00e-02 2.50e+03 1.22e-01 4.45e+02 pdb=" CG TYR E 175 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR E 175 " 0.089 2.00e-02 2.50e+03 pdb=" CD2 TYR E 175 " 0.067 2.00e-02 2.50e+03 pdb=" CE1 TYR E 175 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR E 175 " 0.060 2.00e-02 2.50e+03 pdb=" CZ TYR E 175 " -0.038 2.00e-02 2.50e+03 pdb=" OH TYR E 175 " -0.202 2.00e-02 2.50e+03 pdb=" HD1 TYR E 175 " 0.149 2.00e-02 2.50e+03 pdb=" HD2 TYR E 175 " 0.079 2.00e-02 2.50e+03 pdb=" HE1 TYR E 175 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR E 175 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 47 " 0.026 2.00e-02 2.50e+03 1.05e-01 4.38e+02 pdb=" CG TRP E 47 " -0.098 2.00e-02 2.50e+03 pdb=" CD1 TRP E 47 " -0.079 2.00e-02 2.50e+03 pdb=" CD2 TRP E 47 " -0.086 2.00e-02 2.50e+03 pdb=" NE1 TRP E 47 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TRP E 47 " -0.098 2.00e-02 2.50e+03 pdb=" CE3 TRP E 47 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 47 " -0.074 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 47 " 0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP E 47 " -0.036 2.00e-02 2.50e+03 pdb=" HD1 TRP E 47 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP E 47 " 0.328 2.00e-02 2.50e+03 pdb=" HE3 TRP E 47 " 0.069 2.00e-02 2.50e+03 pdb=" HZ2 TRP E 47 " -0.063 2.00e-02 2.50e+03 pdb=" HZ3 TRP E 47 " 0.130 2.00e-02 2.50e+03 pdb=" HH2 TRP E 47 " -0.019 2.00e-02 2.50e+03 ... (remaining 2607 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1121 2.16 - 2.77: 30747 2.77 - 3.38: 52688 3.38 - 3.99: 71156 3.99 - 4.60: 103701 Nonbonded interactions: 259413 Sorted by model distance: nonbonded pdb=" HG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 1.550 1.850 nonbonded pdb=" HG1 THR B 274 " pdb=" O VAL B 315 " model vdw 1.557 1.850 nonbonded pdb=" HG SER B 147 " pdb=" O VAL B 187 " model vdw 1.560 1.850 nonbonded pdb=" OE2 GLU A 8 " pdb=" HH TYR E 175 " model vdw 1.577 1.850 nonbonded pdb=" OD2 ASP B 170 " pdb=" HG1 THR B 173 " model vdw 1.596 1.850 ... (remaining 259408 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.260 Extract box with map and model: 2.820 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 59.770 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.013 0.214 8946 Z= 0.826 Angle : 1.903 18.859 12126 Z= 1.255 Chirality : 0.103 0.431 1389 Planarity : 0.019 0.274 1527 Dihedral : 12.954 89.767 3198 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 3.33 % 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: -0.67 (0.24), residues: 1104 helix: -0.47 (0.22), residues: 388 sheet: -0.17 (0.31), residues: 264 loop : -0.36 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.121 0.025 TRP B 82 HIS 0.022 0.005 HIS B 54 PHE 0.105 0.018 PHE R 345 TYR 0.377 0.025 TYR B 105 ARG 0.014 0.002 ARG R 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8139 (m-40) cc_final: 0.7930 (m-40) REVERT: A 26 ASP cc_start: 0.7501 (m-30) cc_final: 0.7209 (m-30) REVERT: A 207 GLU cc_start: 0.7262 (tt0) cc_final: 0.6856 (tt0) REVERT: B 214 ARG cc_start: 0.6868 (mmp80) cc_final: 0.6569 (mmp-170) REVERT: G 14 LYS cc_start: 0.7418 (tptp) cc_final: 0.7070 (tttt) REVERT: R 170 PHE cc_start: 0.6066 (p90) cc_final: 0.5835 (p90) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 2.6652 time to fit residues: 587.6714 Evaluate side-chains 157 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 213 HIS A 294 ASN A 322 HIS B 35 ASN B 340 ASN E 171 ASN G 24 ASN R 47 ASN R 352 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8946 Z= 0.226 Angle : 0.614 7.271 12126 Z= 0.331 Chirality : 0.043 0.154 1389 Planarity : 0.004 0.041 1527 Dihedral : 7.127 65.896 1226 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.46 % Allowed : 7.80 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1104 helix: 1.40 (0.25), residues: 384 sheet: -0.12 (0.31), residues: 280 loop : 0.02 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.005 0.001 HIS R 137 PHE 0.025 0.002 PHE R 345 TYR 0.045 0.002 TYR B 105 ARG 0.005 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7652 (m-30) cc_final: 0.7365 (m-30) REVERT: A 244 HIS cc_start: 0.7647 (m-70) cc_final: 0.7415 (m-70) REVERT: B 23 LYS cc_start: 0.8416 (tptm) cc_final: 0.8192 (mmmm) REVERT: B 312 ASP cc_start: 0.7379 (m-30) cc_final: 0.7168 (m-30) REVERT: G 14 LYS cc_start: 0.7207 (tptp) cc_final: 0.6862 (tttt) REVERT: G 20 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.6881 (tttm) REVERT: R 113 MET cc_start: 0.7391 (mmt) cc_final: 0.7091 (mmt) outliers start: 14 outliers final: 9 residues processed: 175 average time/residue: 2.7472 time to fit residues: 512.0777 Evaluate side-chains 156 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 146 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 333 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 195 HIS A 331 ASN B 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8946 Z= 0.361 Angle : 0.617 6.452 12126 Z= 0.336 Chirality : 0.044 0.152 1389 Planarity : 0.004 0.045 1527 Dihedral : 6.801 76.852 1226 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.50 % Allowed : 10.41 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1104 helix: 1.65 (0.26), residues: 389 sheet: -0.26 (0.31), residues: 273 loop : -0.15 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.008 0.002 HIS A 213 PHE 0.021 0.002 PHE R 345 TYR 0.049 0.002 TYR B 105 ARG 0.008 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6544 (pp-130) REVERT: B 325 MET cc_start: 0.8251 (mmm) cc_final: 0.7989 (mmm) REVERT: E 19 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7850 (tptt) REVERT: E 234 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: G 14 LYS cc_start: 0.7235 (tptp) cc_final: 0.6890 (tttt) REVERT: G 32 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8065 (ttmt) REVERT: G 62 ARG cc_start: 0.6496 (OUTLIER) cc_final: 0.6133 (mtm110) REVERT: R 134 MET cc_start: 0.7051 (ttp) cc_final: 0.6841 (ttp) REVERT: R 170 PHE cc_start: 0.6416 (OUTLIER) cc_final: 0.5513 (p90) outliers start: 24 outliers final: 8 residues processed: 168 average time/residue: 2.8760 time to fit residues: 512.8539 Evaluate side-chains 153 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 195 HIS B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8946 Z= 0.272 Angle : 0.568 5.900 12126 Z= 0.303 Chirality : 0.042 0.149 1389 Planarity : 0.004 0.049 1527 Dihedral : 6.422 79.275 1226 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.39 % Allowed : 12.49 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.76 (0.26), residues: 1104 helix: 1.87 (0.26), residues: 391 sheet: -0.32 (0.31), residues: 275 loop : -0.07 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS A 213 PHE 0.019 0.002 PHE R 345 TYR 0.021 0.002 TYR B 105 ARG 0.006 0.000 ARG E 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 312 ASP cc_start: 0.7329 (m-30) cc_final: 0.6993 (m-30) REVERT: E 234 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: G 14 LYS cc_start: 0.7244 (tptp) cc_final: 0.6927 (tttt) REVERT: G 32 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8076 (ttmt) REVERT: R 113 MET cc_start: 0.7259 (mmt) cc_final: 0.7048 (mmp) REVERT: R 134 MET cc_start: 0.7113 (ttp) cc_final: 0.6773 (ttp) REVERT: R 170 PHE cc_start: 0.6394 (OUTLIER) cc_final: 0.5519 (p90) outliers start: 23 outliers final: 11 residues processed: 155 average time/residue: 2.6783 time to fit residues: 442.2764 Evaluate side-chains 150 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS R 387 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8946 Z= 0.256 Angle : 0.540 5.004 12126 Z= 0.290 Chirality : 0.041 0.148 1389 Planarity : 0.004 0.039 1527 Dihedral : 6.232 83.786 1226 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.60 % Allowed : 13.84 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1104 helix: 2.19 (0.26), residues: 384 sheet: -0.25 (0.31), residues: 276 loop : -0.02 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.006 0.001 HIS R 137 PHE 0.016 0.002 PHE R 345 TYR 0.017 0.002 TYR B 105 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6272 (OUTLIER) cc_final: 0.5874 (mt0) REVERT: B 217 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6626 (pp-130) REVERT: B 312 ASP cc_start: 0.7360 (m-30) cc_final: 0.7075 (m-30) REVERT: B 333 ASP cc_start: 0.8375 (p0) cc_final: 0.8165 (p0) REVERT: G 14 LYS cc_start: 0.7219 (tptp) cc_final: 0.6873 (tttt) REVERT: G 32 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8072 (ttmt) REVERT: G 62 ARG cc_start: 0.6530 (OUTLIER) cc_final: 0.6183 (mtt90) REVERT: R 113 MET cc_start: 0.7316 (mmt) cc_final: 0.7049 (mmp) REVERT: R 170 PHE cc_start: 0.6313 (OUTLIER) cc_final: 0.5449 (p90) outliers start: 25 outliers final: 14 residues processed: 156 average time/residue: 2.9687 time to fit residues: 491.6740 Evaluate side-chains 156 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS E 77 ASN R 65 ASN R 352 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8946 Z= 0.250 Angle : 0.535 5.106 12126 Z= 0.286 Chirality : 0.041 0.146 1389 Planarity : 0.004 0.071 1527 Dihedral : 6.158 86.055 1226 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.71 % Allowed : 13.84 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.06 (0.26), residues: 1104 helix: 2.31 (0.26), residues: 384 sheet: -0.23 (0.31), residues: 276 loop : -0.00 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 213 PHE 0.016 0.002 PHE R 345 TYR 0.012 0.001 TYR E 103 ARG 0.009 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 ARG cc_start: 0.7909 (mtm110) cc_final: 0.7693 (ptp90) REVERT: B 312 ASP cc_start: 0.7388 (m-30) cc_final: 0.7105 (m-30) REVERT: B 333 ASP cc_start: 0.8368 (p0) cc_final: 0.8134 (p0) REVERT: G 14 LYS cc_start: 0.7183 (tptp) cc_final: 0.6847 (tttt) REVERT: G 32 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8059 (ttmt) REVERT: G 62 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.6216 (mtt90) REVERT: R 113 MET cc_start: 0.7290 (mmt) cc_final: 0.7033 (mmp) REVERT: R 170 PHE cc_start: 0.6372 (OUTLIER) cc_final: 0.5564 (p90) outliers start: 26 outliers final: 15 residues processed: 163 average time/residue: 2.7400 time to fit residues: 475.6631 Evaluate side-chains 160 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS R 352 ASN R 387 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8946 Z= 0.188 Angle : 0.507 4.774 12126 Z= 0.269 Chirality : 0.041 0.147 1389 Planarity : 0.003 0.038 1527 Dihedral : 5.943 87.631 1226 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.19 % Allowed : 14.88 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.22 (0.26), residues: 1104 helix: 2.48 (0.27), residues: 385 sheet: -0.16 (0.31), residues: 282 loop : 0.07 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.013 0.001 PHE R 345 TYR 0.012 0.001 TYR R 191 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6257 (OUTLIER) cc_final: 0.5921 (mt0) REVERT: B 312 ASP cc_start: 0.7363 (m-30) cc_final: 0.7144 (m-30) REVERT: B 333 ASP cc_start: 0.8302 (p0) cc_final: 0.7976 (p0) REVERT: E 19 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7912 (tptt) REVERT: G 14 LYS cc_start: 0.7175 (tptp) cc_final: 0.6841 (tttt) REVERT: G 32 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8064 (ttmt) REVERT: G 62 ARG cc_start: 0.6561 (OUTLIER) cc_final: 0.6186 (mtt90) REVERT: R 113 MET cc_start: 0.7320 (mmt) cc_final: 0.7065 (mmp) REVERT: R 170 PHE cc_start: 0.6443 (OUTLIER) cc_final: 0.5747 (p90) outliers start: 21 outliers final: 14 residues processed: 158 average time/residue: 2.8299 time to fit residues: 475.0940 Evaluate side-chains 158 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Chi-restraints excluded: chain R residue 352 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS R 65 ASN R 352 ASN R 387 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8946 Z= 0.279 Angle : 0.544 5.262 12126 Z= 0.291 Chirality : 0.041 0.146 1389 Planarity : 0.003 0.036 1527 Dihedral : 6.076 89.332 1226 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.81 % Allowed : 14.67 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.18 (0.26), residues: 1104 helix: 2.47 (0.27), residues: 383 sheet: -0.18 (0.32), residues: 276 loop : 0.02 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS A 213 PHE 0.016 0.002 PHE R 345 TYR 0.012 0.002 TYR E 103 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6250 (OUTLIER) cc_final: 0.5946 (mt0) REVERT: B 217 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.6752 (pp-130) REVERT: B 312 ASP cc_start: 0.7389 (m-30) cc_final: 0.7124 (m-30) REVERT: B 333 ASP cc_start: 0.8381 (p0) cc_final: 0.8151 (p0) REVERT: E 19 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7924 (tptt) REVERT: G 14 LYS cc_start: 0.7177 (tptp) cc_final: 0.6852 (tttt) REVERT: G 32 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8061 (ttmt) REVERT: G 62 ARG cc_start: 0.6618 (OUTLIER) cc_final: 0.6254 (mtt90) REVERT: R 113 MET cc_start: 0.7335 (mmt) cc_final: 0.7091 (mmp) REVERT: R 170 PHE cc_start: 0.6578 (OUTLIER) cc_final: 0.6011 (p90) outliers start: 27 outliers final: 15 residues processed: 155 average time/residue: 2.7182 time to fit residues: 448.8449 Evaluate side-chains 160 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS R 387 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8946 Z= 0.176 Angle : 0.503 4.771 12126 Z= 0.266 Chirality : 0.040 0.147 1389 Planarity : 0.003 0.032 1527 Dihedral : 5.844 89.525 1226 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.19 % Allowed : 15.50 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.34 (0.26), residues: 1104 helix: 2.65 (0.27), residues: 384 sheet: -0.12 (0.31), residues: 282 loop : 0.07 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 349 PHE 0.012 0.001 PHE R 345 TYR 0.011 0.001 TYR A 230 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6317 (OUTLIER) cc_final: 0.6069 (mt0) REVERT: B 333 ASP cc_start: 0.8278 (p0) cc_final: 0.7934 (p0) REVERT: E 19 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7758 (tptt) REVERT: G 14 LYS cc_start: 0.7185 (tptp) cc_final: 0.6851 (tttt) REVERT: G 32 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8077 (ttmt) REVERT: G 62 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.6221 (mtt90) REVERT: R 113 MET cc_start: 0.7299 (mmt) cc_final: 0.7047 (mmp) REVERT: R 170 PHE cc_start: 0.6404 (OUTLIER) cc_final: 0.5958 (p90) outliers start: 21 outliers final: 14 residues processed: 153 average time/residue: 2.7025 time to fit residues: 440.6914 Evaluate side-chains 156 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS R 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8946 Z= 0.249 Angle : 0.535 5.332 12126 Z= 0.284 Chirality : 0.041 0.145 1389 Planarity : 0.003 0.036 1527 Dihedral : 5.937 87.639 1226 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.08 % Allowed : 15.50 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.27 (0.26), residues: 1104 helix: 2.62 (0.27), residues: 384 sheet: -0.16 (0.32), residues: 276 loop : -0.00 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 213 PHE 0.015 0.002 PHE R 345 TYR 0.012 0.001 TYR E 103 ARG 0.007 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6353 (OUTLIER) cc_final: 0.6092 (mt0) REVERT: B 333 ASP cc_start: 0.8361 (p0) cc_final: 0.8107 (p0) REVERT: E 19 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7903 (tptt) REVERT: G 14 LYS cc_start: 0.7186 (tptp) cc_final: 0.6862 (tttt) REVERT: G 32 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8066 (ttmt) REVERT: G 62 ARG cc_start: 0.6566 (OUTLIER) cc_final: 0.6202 (mtt90) REVERT: R 170 PHE cc_start: 0.6439 (OUTLIER) cc_final: 0.5851 (p90) outliers start: 20 outliers final: 15 residues processed: 149 average time/residue: 2.7248 time to fit residues: 432.9347 Evaluate side-chains 154 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 0.0020 chunk 16 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 overall best weight: 2.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 266 HIS R 387 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.170888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.124124 restraints weight = 25123.617| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.58 r_work: 0.3162 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8946 Z= 0.325 Angle : 0.572 5.609 12126 Z= 0.305 Chirality : 0.042 0.146 1389 Planarity : 0.004 0.049 1527 Dihedral : 6.120 88.004 1226 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.29 % Allowed : 15.82 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.09 (0.26), residues: 1104 helix: 2.44 (0.27), residues: 384 sheet: -0.26 (0.31), residues: 276 loop : -0.07 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 99 HIS 0.006 0.001 HIS A 213 PHE 0.017 0.002 PHE R 345 TYR 0.014 0.002 TYR E 103 ARG 0.006 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8305.44 seconds wall clock time: 146 minutes 16.00 seconds (8776.00 seconds total)