Starting phenix.real_space_refine on Tue Feb 13 14:05:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1e_30939/02_2024/7e1e_30939.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1e_30939/02_2024/7e1e_30939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1e_30939/02_2024/7e1e_30939.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1e_30939/02_2024/7e1e_30939.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1e_30939/02_2024/7e1e_30939.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1e_30939/02_2024/7e1e_30939.pdb" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 Ca 6 9.91 5 S 36 5.16 5 C 4128 2.51 5 N 1092 2.21 5 O 1227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 67": "OE1" <-> "OE2" Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A ASP 131": "OD1" <-> "OD2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 158": "OD1" <-> "OD2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B ASP 131": "OD1" <-> "OD2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 306": "OD1" <-> "OD2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C ASP 129": "OD1" <-> "OD2" Residue "C ASP 131": "OD1" <-> "OD2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 158": "OD1" <-> "OD2" Residue "C PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ASP 276": "OD1" <-> "OD2" Residue "C TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 306": "OD1" <-> "OD2" Residue "C GLU 324": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6489 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2161 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 265} Chain: "B" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2161 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 265} Chain: "C" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2161 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 265} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.43, per 1000 atoms: 0.68 Number of scatterers: 6489 At special positions: 0 Unit cell: (91.4578, 87.5382, 78.3924, 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) Ca 6 19.99 S 36 16.00 O 1227 8.00 N 1092 7.00 C 4128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 85 " distance=2.02 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 299 " distance=2.02 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 278 " distance=2.04 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 245 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 56 " - pdb=" SG CYS B 85 " distance=2.02 Simple disulfide: pdb=" SG CYS B 109 " - pdb=" SG CYS B 299 " distance=2.02 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 278 " distance=2.04 Simple disulfide: pdb=" SG CYS B 242 " - pdb=" SG CYS B 245 " distance=2.03 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 56 " - pdb=" SG CYS C 85 " distance=2.02 Simple disulfide: pdb=" SG CYS C 109 " - pdb=" SG CYS C 299 " distance=2.02 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 278 " distance=2.04 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 245 " distance=2.03 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 284 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.64 Conformation dependent library (CDL) restraints added in 2.0 seconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1506 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 24.7% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 55 through 63 removed outlier: 3.823A pdb=" N ILE A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 removed outlier: 4.141A pdb=" N GLY A 91 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 157 Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 242 through 247 removed outlier: 4.019A pdb=" N LEU A 246 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 242 through 247' Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.837A pdb=" N HIS A 282 " --> pdb=" O ASN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'B' and resid 55 through 63 removed outlier: 3.823A pdb=" N ILE B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 4.142A pdb=" N GLY B 91 " --> pdb=" O ASN B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 157 Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 242 through 247 removed outlier: 4.018A pdb=" N LEU B 246 " --> pdb=" O CYS B 242 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 242 through 247' Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.836A pdb=" N HIS B 282 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'C' and resid 55 through 63 removed outlier: 3.823A pdb=" N ILE C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 removed outlier: 4.141A pdb=" N GLY C 91 " --> pdb=" O ASN C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 157 Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 233 through 241 Processing helix chain 'C' and resid 242 through 247 removed outlier: 4.020A pdb=" N LEU C 246 " --> pdb=" O CYS C 242 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 242 through 247' Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.836A pdb=" N HIS C 282 " --> pdb=" O ASN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 74 removed outlier: 25.097A pdb=" N PHE A 80 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 19.942A pdb=" N VAL A 100 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 13.344A pdb=" N GLN A 82 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ALA A 98 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE A 84 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 74 removed outlier: 25.097A pdb=" N PHE A 80 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 19.942A pdb=" N VAL A 100 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 13.344A pdb=" N GLN A 82 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ALA A 98 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE A 84 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE A 329 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER A 99 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL A 327 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ILE A 164 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A 184 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ARG A 185 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA A 267 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE A 259 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 249 through 251 Processing sheet with id=AA4, first strand: chain 'B' and resid 69 through 74 removed outlier: 25.098A pdb=" N PHE B 80 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 19.942A pdb=" N VAL B 100 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 13.344A pdb=" N GLN B 82 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ALA B 98 " --> pdb=" O GLN B 82 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE B 84 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 74 removed outlier: 25.098A pdb=" N PHE B 80 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 19.942A pdb=" N VAL B 100 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 13.344A pdb=" N GLN B 82 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ALA B 98 " --> pdb=" O GLN B 82 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE B 84 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 329 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER B 99 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL B 327 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ILE B 164 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE B 184 " --> pdb=" O HIS B 168 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG B 185 " --> pdb=" O ASP B 230 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA B 267 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE B 259 " --> pdb=" O PRO B 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 249 through 251 Processing sheet with id=AA7, first strand: chain 'C' and resid 69 through 74 removed outlier: 25.098A pdb=" N PHE C 80 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 19.942A pdb=" N VAL C 100 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 13.345A pdb=" N GLN C 82 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ALA C 98 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE C 84 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 69 through 74 removed outlier: 25.098A pdb=" N PHE C 80 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 19.942A pdb=" N VAL C 100 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 13.345A pdb=" N GLN C 82 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ALA C 98 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE C 84 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE C 329 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER C 99 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL C 327 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ILE C 164 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE C 184 " --> pdb=" O HIS C 168 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ARG C 185 " --> pdb=" O ASP C 230 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA C 267 " --> pdb=" O ARG C 257 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE C 259 " --> pdb=" O PRO C 265 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 249 through 251 201 hydrogen bonds defined for protein. 486 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.26 Time building geometry restraints manager: 5.85 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: 2106 1.34 - 1.47: 1823 1.47 - 1.59: 2701 1.59 - 1.71: 0 1.71 - 1.83: 39 Bond restraints: 6669 Sorted by residual: bond pdb=" CB PHE C 184 " pdb=" CG PHE C 184 " ideal model delta sigma weight residual 1.502 1.470 0.032 2.30e-02 1.89e+03 1.96e+00 bond pdb=" CB PHE A 184 " pdb=" CG PHE A 184 " ideal model delta sigma weight residual 1.502 1.470 0.032 2.30e-02 1.89e+03 1.92e+00 bond pdb=" CB PHE B 184 " pdb=" CG PHE B 184 " ideal model delta sigma weight residual 1.502 1.470 0.032 2.30e-02 1.89e+03 1.90e+00 bond pdb=" C TYR C 208 " pdb=" O TYR C 208 " ideal model delta sigma weight residual 1.240 1.223 0.017 1.24e-02 6.50e+03 1.78e+00 bond pdb=" C TYR A 208 " pdb=" O TYR A 208 " ideal model delta sigma weight residual 1.240 1.223 0.016 1.24e-02 6.50e+03 1.76e+00 ... (remaining 6664 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.04: 206 107.04 - 113.78: 3541 113.78 - 120.52: 2697 120.52 - 127.26: 2548 127.26 - 134.00: 92 Bond angle restraints: 9084 Sorted by residual: angle pdb=" CA CYS C 242 " pdb=" CB CYS C 242 " pdb=" SG CYS C 242 " ideal model delta sigma weight residual 114.40 122.46 -8.06 2.30e+00 1.89e-01 1.23e+01 angle pdb=" CA CYS B 242 " pdb=" CB CYS B 242 " pdb=" SG CYS B 242 " ideal model delta sigma weight residual 114.40 122.45 -8.05 2.30e+00 1.89e-01 1.23e+01 angle pdb=" CA CYS A 242 " pdb=" CB CYS A 242 " pdb=" SG CYS A 242 " ideal model delta sigma weight residual 114.40 122.45 -8.05 2.30e+00 1.89e-01 1.23e+01 angle pdb=" CB GLN B 177 " pdb=" CG GLN B 177 " pdb=" CD GLN B 177 " ideal model delta sigma weight residual 112.60 118.19 -5.59 1.70e+00 3.46e-01 1.08e+01 angle pdb=" CB GLN C 177 " pdb=" CG GLN C 177 " pdb=" CD GLN C 177 " ideal model delta sigma weight residual 112.60 118.18 -5.58 1.70e+00 3.46e-01 1.08e+01 ... (remaining 9079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.96: 3573 25.96 - 51.93: 234 51.93 - 77.89: 42 77.89 - 103.85: 6 103.85 - 129.82: 3 Dihedral angle restraints: 3858 sinusoidal: 1476 harmonic: 2382 Sorted by residual: dihedral pdb=" CA PHE C 207 " pdb=" C PHE C 207 " pdb=" N TYR C 208 " pdb=" CA TYR C 208 " ideal model delta harmonic sigma weight residual 180.00 50.18 129.82 0 5.00e+00 4.00e-02 6.74e+02 dihedral pdb=" CA PHE A 207 " pdb=" C PHE A 207 " pdb=" N TYR A 208 " pdb=" CA TYR A 208 " ideal model delta harmonic sigma weight residual 180.00 50.20 129.80 0 5.00e+00 4.00e-02 6.74e+02 dihedral pdb=" CA PHE B 207 " pdb=" C PHE B 207 " pdb=" N TYR B 208 " pdb=" CA TYR B 208 " ideal model delta harmonic sigma weight residual 180.00 50.24 129.76 0 5.00e+00 4.00e-02 6.73e+02 ... (remaining 3855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 543 0.037 - 0.074: 278 0.074 - 0.111: 118 0.111 - 0.148: 12 0.148 - 0.185: 6 Chirality restraints: 957 Sorted by residual: chirality pdb=" CA VAL C 258 " pdb=" N VAL C 258 " pdb=" C VAL C 258 " pdb=" CB VAL C 258 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA VAL B 258 " pdb=" N VAL B 258 " pdb=" C VAL B 258 " pdb=" CB VAL B 258 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA VAL A 258 " pdb=" N VAL A 258 " pdb=" C VAL A 258 " pdb=" CB VAL A 258 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.27e-01 ... (remaining 954 not shown) Planarity restraints: 1188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 217 " 0.063 5.00e-02 4.00e+02 9.51e-02 1.45e+01 pdb=" N PRO A 218 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO A 218 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 218 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 217 " -0.063 5.00e-02 4.00e+02 9.49e-02 1.44e+01 pdb=" N PRO B 218 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 218 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 218 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 217 " 0.063 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO C 218 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO C 218 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 218 " 0.051 5.00e-02 4.00e+02 ... (remaining 1185 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 385 2.70 - 3.25: 6803 3.25 - 3.80: 11014 3.80 - 4.35: 14816 4.35 - 4.90: 24438 Nonbonded interactions: 57456 Sorted by model distance: nonbonded pdb=" O LYS C 62 " pdb=" NZ LYS C 64 " model vdw 2.154 2.520 nonbonded pdb=" O LYS A 62 " pdb=" NZ LYS A 64 " model vdw 2.155 2.520 nonbonded pdb=" O LYS B 62 " pdb=" NZ LYS B 64 " model vdw 2.155 2.520 nonbonded pdb=" OG SER A 77 " pdb=" OE2 GLU B 144 " model vdw 2.159 2.440 nonbonded pdb=" OD1 ASP B 149 " pdb=" N ASP B 150 " model vdw 2.187 2.520 ... (remaining 57451 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 6.690 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: 5.400 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 41.750 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 6669 Z= 0.479 Angle : 0.858 8.062 9084 Z= 0.502 Chirality : 0.050 0.185 957 Planarity : 0.007 0.095 1188 Dihedral : 17.656 129.817 2307 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.03 % Favored : 90.61 % Rotamer: Outliers : 11.79 % Allowed : 5.82 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 15.38 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.23), residues: 831 helix: -3.33 (0.39), residues: 96 sheet: -1.21 (0.48), residues: 96 loop : -2.85 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 178 HIS 0.003 0.001 HIS B 101 PHE 0.015 0.002 PHE C 127 TYR 0.012 0.002 TYR C 201 ARG 0.015 0.001 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 171 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ASN cc_start: 0.8410 (m-40) cc_final: 0.8200 (m110) REVERT: A 305 PHE cc_start: 0.8203 (m-10) cc_final: 0.7900 (m-10) REVERT: B 202 PHE cc_start: 0.7975 (m-80) cc_final: 0.7761 (m-10) REVERT: B 307 TRP cc_start: 0.6919 (t-100) cc_final: 0.6679 (t-100) REVERT: B 321 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8808 (t) REVERT: C 314 VAL cc_start: 0.6846 (OUTLIER) cc_final: 0.6635 (m) REVERT: C 320 LYS cc_start: 0.8542 (tttm) cc_final: 0.8329 (ttmm) outliers start: 81 outliers final: 13 residues processed: 227 average time/residue: 0.2102 time to fit residues: 60.4522 Evaluate side-chains 118 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 299 CYS Chi-restraints excluded: chain C residue 314 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 282 HIS B 240 GLN B 277 ASN B 282 HIS C 122 ASN C 240 GLN ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6669 Z= 0.223 Angle : 0.661 7.469 9084 Z= 0.352 Chirality : 0.046 0.174 957 Planarity : 0.006 0.077 1188 Dihedral : 9.409 97.070 937 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.14 % Favored : 93.26 % Rotamer: Outliers : 4.66 % Allowed : 14.41 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.26), residues: 831 helix: -3.08 (0.39), residues: 117 sheet: -0.39 (0.46), residues: 120 loop : -2.31 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 94 HIS 0.009 0.002 HIS B 255 PHE 0.011 0.001 PHE A 80 TYR 0.024 0.002 TYR A 208 ARG 0.005 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 125 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8102 (ttmt) REVERT: B 79 GLN cc_start: 0.8953 (tt0) cc_final: 0.8651 (tt0) REVERT: B 142 ARG cc_start: 0.6632 (mtt90) cc_final: 0.6427 (mmt-90) REVERT: B 158 ASP cc_start: 0.7409 (t0) cc_final: 0.7083 (t0) REVERT: B 212 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.8152 (t80) REVERT: B 230 ASP cc_start: 0.7648 (m-30) cc_final: 0.7444 (m-30) REVERT: B 234 THR cc_start: 0.7406 (m) cc_final: 0.7048 (p) REVERT: B 307 TRP cc_start: 0.7238 (t-100) cc_final: 0.7023 (t-100) REVERT: C 202 PHE cc_start: 0.8253 (m-80) cc_final: 0.8010 (m-80) REVERT: C 231 PHE cc_start: 0.8158 (t80) cc_final: 0.7935 (t80) outliers start: 32 outliers final: 17 residues processed: 145 average time/residue: 0.2142 time to fit residues: 39.6606 Evaluate side-chains 122 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 299 CYS Chi-restraints excluded: chain C residue 323 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN C 122 ASN C 255 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6669 Z= 0.344 Angle : 0.697 7.055 9084 Z= 0.373 Chirality : 0.049 0.177 957 Planarity : 0.006 0.080 1188 Dihedral : 8.676 59.949 921 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.90 % Favored : 90.61 % Rotamer: Outliers : 5.39 % Allowed : 14.85 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 10.26 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.27), residues: 831 helix: -2.32 (0.47), residues: 90 sheet: -0.44 (0.44), residues: 120 loop : -2.17 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 94 HIS 0.006 0.001 HIS B 255 PHE 0.018 0.002 PHE A 330 TYR 0.017 0.002 TYR B 151 ARG 0.004 0.001 ARG B 297 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 113 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7927 (p0) REVERT: A 272 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8567 (pp) REVERT: B 212 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.8560 (t80) REVERT: C 62 LYS cc_start: 0.7942 (tptp) cc_final: 0.7694 (mtmm) REVERT: C 202 PHE cc_start: 0.8405 (m-80) cc_final: 0.8130 (m-80) REVERT: C 272 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8794 (pp) outliers start: 37 outliers final: 20 residues processed: 139 average time/residue: 0.2524 time to fit residues: 43.4358 Evaluate side-chains 112 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 293 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 70 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6669 Z= 0.263 Angle : 0.642 6.409 9084 Z= 0.340 Chirality : 0.047 0.173 957 Planarity : 0.006 0.076 1188 Dihedral : 7.947 50.135 916 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.58 % Favored : 91.82 % Rotamer: Outliers : 5.39 % Allowed : 17.03 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.28), residues: 831 helix: -2.43 (0.46), residues: 99 sheet: -0.21 (0.45), residues: 120 loop : -1.85 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 307 HIS 0.004 0.001 HIS B 255 PHE 0.013 0.001 PHE B 330 TYR 0.013 0.002 TYR A 208 ARG 0.005 0.001 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 108 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 ARG cc_start: 0.7848 (tmt170) cc_final: 0.7509 (tmt170) REVERT: A 272 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8515 (pp) REVERT: B 73 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8204 (mt) REVERT: B 148 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.7045 (m-30) REVERT: B 212 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.8390 (t80) REVERT: C 272 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8745 (pp) outliers start: 37 outliers final: 19 residues processed: 136 average time/residue: 0.2503 time to fit residues: 42.1807 Evaluate side-chains 113 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 295 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6669 Z= 0.257 Angle : 0.638 5.972 9084 Z= 0.339 Chirality : 0.047 0.163 957 Planarity : 0.006 0.075 1188 Dihedral : 7.635 50.111 914 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.18 % Favored : 91.10 % Rotamer: Outliers : 6.11 % Allowed : 16.30 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.28), residues: 831 helix: -2.28 (0.47), residues: 99 sheet: -0.21 (0.46), residues: 120 loop : -1.83 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 307 HIS 0.004 0.001 HIS B 187 PHE 0.013 0.001 PHE B 330 TYR 0.014 0.002 TYR B 208 ARG 0.015 0.001 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 99 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 ARG cc_start: 0.7870 (tmt170) cc_final: 0.7615 (tmt170) REVERT: A 272 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8632 (pp) REVERT: B 73 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8185 (mt) REVERT: B 148 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.6949 (m-30) REVERT: B 212 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8484 (t80) REVERT: B 310 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8239 (mt) REVERT: C 87 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7686 (mpp) REVERT: C 202 PHE cc_start: 0.8503 (m-80) cc_final: 0.8298 (m-80) outliers start: 42 outliers final: 24 residues processed: 127 average time/residue: 0.2553 time to fit residues: 40.1263 Evaluate side-chains 122 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 92 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 293 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6669 Z= 0.184 Angle : 0.614 7.893 9084 Z= 0.324 Chirality : 0.045 0.162 957 Planarity : 0.006 0.071 1188 Dihedral : 7.261 50.591 914 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.86 % Favored : 92.54 % Rotamer: Outliers : 3.78 % Allowed : 18.63 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.28), residues: 831 helix: -1.88 (0.49), residues: 96 sheet: -0.10 (0.46), residues: 120 loop : -1.77 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 94 HIS 0.004 0.001 HIS B 255 PHE 0.009 0.001 PHE B 259 TYR 0.013 0.001 TYR A 208 ARG 0.012 0.001 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8517 (pp) REVERT: B 148 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6938 (m-30) REVERT: B 212 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.8454 (t80) REVERT: B 310 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8177 (mt) REVERT: C 87 MET cc_start: 0.7905 (mpp) cc_final: 0.7459 (mpp) REVERT: C 315 GLU cc_start: 0.7065 (pm20) cc_final: 0.6651 (tp30) outliers start: 26 outliers final: 16 residues processed: 122 average time/residue: 0.2651 time to fit residues: 39.6652 Evaluate side-chains 116 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 310 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6669 Z= 0.292 Angle : 0.670 8.213 9084 Z= 0.353 Chirality : 0.047 0.167 957 Planarity : 0.006 0.074 1188 Dihedral : 7.480 50.975 914 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.70 % Favored : 91.58 % Rotamer: Outliers : 4.66 % Allowed : 19.51 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.28), residues: 831 helix: -2.22 (0.46), residues: 96 sheet: -0.26 (0.46), residues: 120 loop : -1.77 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 307 HIS 0.004 0.001 HIS A 255 PHE 0.013 0.001 PHE B 330 TYR 0.019 0.002 TYR B 208 ARG 0.005 0.001 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 98 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7902 (mp0) cc_final: 0.7467 (mp0) REVERT: A 272 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8680 (pp) REVERT: B 73 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8200 (mt) REVERT: B 148 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.6985 (m-30) REVERT: B 212 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.8362 (t80) REVERT: B 310 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8196 (mt) REVERT: C 87 MET cc_start: 0.7919 (mpp) cc_final: 0.7465 (mpp) REVERT: C 275 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7648 (mt) outliers start: 32 outliers final: 25 residues processed: 118 average time/residue: 0.2535 time to fit residues: 37.1092 Evaluate side-chains 124 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 93 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 310 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 7 optimal weight: 0.0170 chunk 61 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6669 Z= 0.179 Angle : 0.604 7.088 9084 Z= 0.320 Chirality : 0.045 0.165 957 Planarity : 0.006 0.072 1188 Dihedral : 7.103 51.358 914 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.62 % Favored : 92.78 % Rotamer: Outliers : 4.66 % Allowed : 19.36 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.28), residues: 831 helix: -2.03 (0.48), residues: 96 sheet: -0.14 (0.46), residues: 120 loop : -1.71 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 134 HIS 0.003 0.001 HIS A 255 PHE 0.009 0.001 PHE C 202 TYR 0.012 0.001 TYR B 208 ARG 0.005 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8609 (pp) REVERT: B 148 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.6928 (m-30) REVERT: B 212 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.8383 (t80) REVERT: B 310 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8182 (mt) REVERT: C 87 MET cc_start: 0.7937 (mpp) cc_final: 0.7496 (mpp) REVERT: C 257 ARG cc_start: 0.6711 (tmt170) cc_final: 0.5735 (ttp-170) REVERT: C 275 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7599 (mt) outliers start: 32 outliers final: 21 residues processed: 120 average time/residue: 0.2654 time to fit residues: 39.1843 Evaluate side-chains 121 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 310 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 0.1980 chunk 47 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6669 Z= 0.277 Angle : 0.656 7.808 9084 Z= 0.346 Chirality : 0.047 0.165 957 Planarity : 0.006 0.074 1188 Dihedral : 7.256 50.989 914 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.34 % Favored : 91.94 % Rotamer: Outliers : 4.95 % Allowed : 19.80 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.28), residues: 831 helix: -2.09 (0.47), residues: 96 sheet: -0.17 (0.45), residues: 120 loop : -1.72 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 307 HIS 0.004 0.001 HIS B 187 PHE 0.013 0.002 PHE C 202 TYR 0.021 0.002 TYR C 208 ARG 0.005 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 103 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8650 (ptmm) cc_final: 0.8382 (ptmm) REVERT: A 272 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8673 (pp) REVERT: B 73 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8199 (mt) REVERT: B 148 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.6960 (m-30) REVERT: B 212 TYR cc_start: 0.8870 (OUTLIER) cc_final: 0.8175 (t80) REVERT: B 310 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8207 (mt) REVERT: C 87 MET cc_start: 0.8041 (mpp) cc_final: 0.7601 (mpp) REVERT: C 275 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7746 (mt) outliers start: 34 outliers final: 26 residues processed: 123 average time/residue: 0.2461 time to fit residues: 37.7310 Evaluate side-chains 128 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 310 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6669 Z= 0.308 Angle : 0.694 9.224 9084 Z= 0.367 Chirality : 0.048 0.165 957 Planarity : 0.006 0.075 1188 Dihedral : 7.442 53.468 914 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.22 % Favored : 92.06 % Rotamer: Outliers : 4.66 % Allowed : 21.11 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.28), residues: 831 helix: -2.22 (0.46), residues: 99 sheet: -0.48 (0.54), residues: 87 loop : -1.58 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 307 HIS 0.004 0.001 HIS B 187 PHE 0.015 0.002 PHE B 330 TYR 0.036 0.002 TYR C 208 ARG 0.006 0.001 ARG C 257 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8238 (mt) REVERT: B 148 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7020 (m-30) REVERT: B 212 TYR cc_start: 0.8910 (OUTLIER) cc_final: 0.8236 (t80) REVERT: C 87 MET cc_start: 0.8014 (mpp) cc_final: 0.7575 (mpp) REVERT: C 257 ARG cc_start: 0.6866 (tmt170) cc_final: 0.6339 (ttm-80) REVERT: C 275 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7992 (mt) outliers start: 32 outliers final: 26 residues processed: 117 average time/residue: 0.2675 time to fit residues: 38.6338 Evaluate side-chains 124 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 94 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 310 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108577 restraints weight = 9664.074| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.79 r_work: 0.3221 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.5756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6669 Z= 0.287 Angle : 0.687 9.599 9084 Z= 0.363 Chirality : 0.048 0.172 957 Planarity : 0.006 0.075 1188 Dihedral : 7.400 53.271 914 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.82 % Favored : 91.46 % Rotamer: Outliers : 4.66 % Allowed : 21.25 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.28), residues: 831 helix: -2.22 (0.47), residues: 99 sheet: -0.49 (0.55), residues: 87 loop : -1.58 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 307 HIS 0.005 0.001 HIS B 187 PHE 0.018 0.002 PHE B 184 TYR 0.021 0.002 TYR C 208 ARG 0.005 0.001 ARG B 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1762.15 seconds wall clock time: 33 minutes 44.66 seconds (2024.66 seconds total)