Starting phenix.real_space_refine on Mon Mar 11 05:54:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv7_36670/03_2024/8jv7_36670_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv7_36670/03_2024/8jv7_36670.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv7_36670/03_2024/8jv7_36670_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv7_36670/03_2024/8jv7_36670_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv7_36670/03_2024/8jv7_36670_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv7_36670/03_2024/8jv7_36670.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv7_36670/03_2024/8jv7_36670.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv7_36670/03_2024/8jv7_36670_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv7_36670/03_2024/8jv7_36670_updated.pdb" } resolution = 3.6 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= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 45 5.16 5 C 4638 2.51 5 N 1215 2.21 5 O 1344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 89": "OD1" <-> "OD2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 132": "OD1" <-> "OD2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 89": "OD1" <-> "OD2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C ASP 240": "OD1" <-> "OD2" Residue "C PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7245 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2354 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2354 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 101 Chain: "C" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2354 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 101 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'NAG': 2, 'UO6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'NAG': 2, 'UO6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'NAG': 2, 'UO6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.11, per 1000 atoms: 0.57 Number of scatterers: 7245 At special positions: 0 Unit cell: (84.66, 87.98, 108.73, 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 45 16.00 P 3 15.00 O 1344 8.00 N 1215 7.00 C 4638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.04 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS C 226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 269 " 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 Links applied NAG-ASN " NAG A 401 " - " ASN A 187 " " NAG A 402 " - " ASN A 213 " " NAG B 401 " - " ASN B 187 " " NAG B 402 " - " ASN B 213 " " NAG C 401 " - " ASN C 187 " " NAG C 402 " - " ASN C 213 " Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.3 seconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1770 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 19 sheets defined 17.0% alpha, 35.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 32 through 48 removed outlier: 3.596A pdb=" N PHE A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 removed outlier: 4.057A pdb=" N GLU A 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 237 Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 331 through 349 Processing helix chain 'B' and resid 33 through 48 removed outlier: 4.190A pdb=" N PHE B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 183 through 186 removed outlier: 3.808A pdb=" N GLU B 186 " --> pdb=" O ASN B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 183 through 186' Processing helix chain 'B' and resid 231 through 238 removed outlier: 3.604A pdb=" N THR B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 245 No H-bonds generated for 'chain 'B' and resid 242 through 245' Processing helix chain 'B' and resid 330 through 349 Processing helix chain 'C' and resid 32 through 48 removed outlier: 3.515A pdb=" N PHE C 38 " --> pdb=" O HIS C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 187 removed outlier: 4.082A pdb=" N GLU C 186 " --> pdb=" O ASN C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 238 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 331 through 349 Processing sheet with id= A, first strand: chain 'A' and resid 52 through 55 removed outlier: 6.627A pdb=" N GLY A 250 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASP A 318 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET A 252 " --> pdb=" O ASP A 318 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU A 320 " --> pdb=" O MET A 252 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE A 254 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N PHE A 322 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE A 256 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N THR A 324 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N TRP A 258 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLY A 326 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N CYS A 260 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N PHE A 328 " --> pdb=" O CYS A 260 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 58 through 65 removed outlier: 4.160A pdb=" N TYR A 203 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 69 through 77 Processing sheet with id= D, first strand: chain 'A' and resid 101 through 103 Processing sheet with id= E, first strand: chain 'A' and resid 107 through 111 Processing sheet with id= F, first strand: chain 'A' and resid 115 through 119 Processing sheet with id= G, first strand: chain 'A' and resid 152 through 156 removed outlier: 6.454A pdb=" N LEU A 159 " --> pdb=" O TYR A 155 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 52 through 55 removed outlier: 6.609A pdb=" N GLY B 250 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ASP B 318 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N MET B 252 " --> pdb=" O ASP B 318 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU B 320 " --> pdb=" O MET B 252 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE B 254 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE B 322 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE B 256 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR B 324 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP B 258 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N GLY B 326 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N CYS B 260 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N PHE B 328 " --> pdb=" O CYS B 260 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 58 through 65 removed outlier: 4.072A pdb=" N TYR B 203 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 69 through 77 Processing sheet with id= K, first strand: chain 'B' and resid 115 through 119 Processing sheet with id= L, first strand: chain 'B' and resid 152 through 154 Processing sheet with id= M, first strand: chain 'B' and resid 292 through 301 removed outlier: 6.063A pdb=" N ILE B 315 " --> pdb=" O MET B 105 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N MET B 105 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE B 317 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N PHE B 103 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 52 through 55 removed outlier: 6.827A pdb=" N GLY C 250 " --> pdb=" O ARG C 316 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ASP C 318 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET C 252 " --> pdb=" O ASP C 318 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU C 320 " --> pdb=" O MET C 252 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE C 254 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N PHE C 322 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE C 256 " --> pdb=" O PHE C 322 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N THR C 324 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TRP C 258 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLY C 326 " --> pdb=" O TRP C 258 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N CYS C 260 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N PHE C 328 " --> pdb=" O CYS C 260 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP C 259 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG C 270 " --> pdb=" O ASP C 259 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 58 through 66 removed outlier: 3.852A pdb=" N THR C 189 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR C 203 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 69 through 77 Processing sheet with id= Q, first strand: chain 'C' and resid 115 through 120 Processing sheet with id= R, first strand: chain 'C' and resid 152 through 154 Processing sheet with id= S, first strand: chain 'C' and resid 292 through 301 removed outlier: 6.428A pdb=" N ILE C 315 " --> pdb=" O MET C 105 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N MET C 105 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N PHE C 317 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N PHE C 103 " --> pdb=" O PHE C 317 " (cutoff:3.500A) 267 hydrogen bonds defined for protein. 738 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: 1.89 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1149 1.31 - 1.44: 2190 1.44 - 1.57: 4040 1.57 - 1.69: 4 1.69 - 1.82: 51 Bond restraints: 7434 Sorted by residual: bond pdb=" CB PRO A 142 " pdb=" CG PRO A 142 " ideal model delta sigma weight residual 1.492 1.624 -0.132 5.00e-02 4.00e+02 6.98e+00 bond pdb=" C06 UO6 C 403 " pdb=" N07 UO6 C 403 " ideal model delta sigma weight residual 1.352 1.318 0.034 2.00e-02 2.50e+03 2.83e+00 bond pdb=" C06 UO6 A 403 " pdb=" N07 UO6 A 403 " ideal model delta sigma weight residual 1.352 1.319 0.033 2.00e-02 2.50e+03 2.77e+00 bond pdb=" C04 UO6 B 403 " pdb=" C05 UO6 B 403 " ideal model delta sigma weight residual 1.355 1.388 -0.033 2.00e-02 2.50e+03 2.77e+00 bond pdb=" C04 UO6 A 403 " pdb=" C05 UO6 A 403 " ideal model delta sigma weight residual 1.355 1.388 -0.033 2.00e-02 2.50e+03 2.74e+00 ... (remaining 7429 not shown) Histogram of bond angle deviations from ideal: 98.86 - 106.07: 150 106.07 - 113.27: 3957 113.27 - 120.48: 2823 120.48 - 127.69: 3171 127.69 - 134.90: 57 Bond angle restraints: 10158 Sorted by residual: angle pdb=" CA PRO A 142 " pdb=" N PRO A 142 " pdb=" CD PRO A 142 " ideal model delta sigma weight residual 112.00 100.14 11.86 1.40e+00 5.10e-01 7.17e+01 angle pdb=" O17 UO6 B 403 " pdb=" S16 UO6 B 403 " pdb=" O18 UO6 B 403 " ideal model delta sigma weight residual 111.28 101.06 10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" O17 UO6 C 403 " pdb=" S16 UO6 C 403 " pdb=" O18 UO6 C 403 " ideal model delta sigma weight residual 111.28 101.06 10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" O17 UO6 A 403 " pdb=" S16 UO6 A 403 " pdb=" O18 UO6 A 403 " ideal model delta sigma weight residual 111.28 101.09 10.19 3.00e+00 1.11e-01 1.15e+01 angle pdb=" O17 UO6 B 403 " pdb=" S16 UO6 B 403 " pdb=" O19 UO6 B 403 " ideal model delta sigma weight residual 101.20 111.37 -10.17 3.00e+00 1.11e-01 1.15e+01 ... (remaining 10153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 3746 17.58 - 35.16: 443 35.16 - 52.74: 126 52.74 - 70.33: 37 70.33 - 87.91: 7 Dihedral angle restraints: 4359 sinusoidal: 1590 harmonic: 2769 Sorted by residual: dihedral pdb=" CB CYS B 135 " pdb=" SG CYS B 135 " pdb=" SG CYS B 162 " pdb=" CB CYS B 162 " ideal model delta sinusoidal sigma weight residual -86.00 -167.65 81.65 1 1.00e+01 1.00e-02 8.21e+01 dihedral pdb=" CB CYS C 135 " pdb=" SG CYS C 135 " pdb=" SG CYS C 162 " pdb=" CB CYS C 162 " ideal model delta sinusoidal sigma weight residual -86.00 -154.33 68.33 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CB CYS B 216 " pdb=" SG CYS B 216 " pdb=" SG CYS B 226 " pdb=" CB CYS B 226 " ideal model delta sinusoidal sigma weight residual -86.00 -152.28 66.28 1 1.00e+01 1.00e-02 5.74e+01 ... (remaining 4356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 825 0.044 - 0.088: 208 0.088 - 0.131: 86 0.131 - 0.175: 5 0.175 - 0.219: 1 Chirality restraints: 1125 Sorted by residual: chirality pdb=" CA PRO A 142 " pdb=" N PRO A 142 " pdb=" C PRO A 142 " pdb=" CB PRO A 142 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE A 254 " pdb=" N ILE A 254 " pdb=" C ILE A 254 " pdb=" CB ILE A 254 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA ILE C 58 " pdb=" N ILE C 58 " pdb=" C ILE C 58 " pdb=" CB ILE C 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 1122 not shown) Planarity restraints: 1308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 141 " 0.061 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO A 142 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 237 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" CD GLU A 237 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU A 237 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 237 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 55 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO B 56 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 56 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 56 " 0.025 5.00e-02 4.00e+02 ... (remaining 1305 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 197 2.70 - 3.25: 6707 3.25 - 3.80: 10888 3.80 - 4.35: 13161 4.35 - 4.90: 22749 Nonbonded interactions: 53702 Sorted by model distance: nonbonded pdb=" O GLY A 67 " pdb=" OH TYR A 93 " model vdw 2.147 2.440 nonbonded pdb=" O GLY C 67 " pdb=" OH TYR C 93 " model vdw 2.172 2.440 nonbonded pdb=" O GLY B 67 " pdb=" OH TYR B 93 " model vdw 2.223 2.440 nonbonded pdb=" OD2 ASP A 197 " pdb=" NH2 ARG C 276 " model vdw 2.251 2.520 nonbonded pdb=" O LYS B 136 " pdb=" NE2 GLN B 148 " model vdw 2.255 2.520 ... (remaining 53697 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.760 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 21.730 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 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 : 0.003 0.132 7434 Z= 0.242 Angle : 0.633 11.856 10158 Z= 0.331 Chirality : 0.045 0.219 1125 Planarity : 0.005 0.085 1302 Dihedral : 16.859 87.906 2544 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.38 % Allowed : 31.50 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.06 (0.28), residues: 954 helix: 1.50 (0.45), residues: 153 sheet: 0.56 (0.30), residues: 315 loop : -0.96 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 167 HIS 0.012 0.001 HIS A 268 PHE 0.014 0.001 PHE B 266 TYR 0.011 0.001 TYR C 93 ARG 0.005 0.001 ARG C 276 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 0.853 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 114 average time/residue: 0.1862 time to fit residues: 29.0649 Evaluate side-chains 103 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 344 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 0.0670 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 225 GLN B 116 GLN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7434 Z= 0.192 Angle : 0.481 5.742 10158 Z= 0.257 Chirality : 0.045 0.140 1125 Planarity : 0.004 0.037 1302 Dihedral : 7.537 68.095 1186 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.66 % Allowed : 27.83 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.09 (0.28), residues: 954 helix: 1.61 (0.45), residues: 153 sheet: 0.57 (0.28), residues: 357 loop : -0.92 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 258 HIS 0.012 0.001 HIS C 268 PHE 0.010 0.001 PHE C 344 TYR 0.010 0.001 TYR C 273 ARG 0.004 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 91 time to evaluate : 0.802 Fit side-chains REVERT: B 34 HIS cc_start: 0.8252 (OUTLIER) cc_final: 0.7983 (m-70) REVERT: C 237 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7565 (tm-30) outliers start: 37 outliers final: 21 residues processed: 116 average time/residue: 0.1642 time to fit residues: 26.6167 Evaluate side-chains 106 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 344 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 70 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN B 194 ASN C 268 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7434 Z= 0.144 Angle : 0.441 4.898 10158 Z= 0.236 Chirality : 0.044 0.135 1125 Planarity : 0.003 0.034 1302 Dihedral : 6.841 63.992 1174 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.35 % Allowed : 28.29 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.24 (0.28), residues: 954 helix: 1.73 (0.46), residues: 153 sheet: 0.63 (0.28), residues: 360 loop : -0.78 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 258 HIS 0.012 0.001 HIS C 268 PHE 0.009 0.001 PHE A 102 TYR 0.010 0.001 TYR C 93 ARG 0.006 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 91 time to evaluate : 0.815 Fit side-chains REVERT: A 237 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7600 (tm-30) REVERT: A 252 MET cc_start: 0.8459 (mmt) cc_final: 0.7972 (tpp) REVERT: B 34 HIS cc_start: 0.8271 (OUTLIER) cc_final: 0.7962 (m-70) REVERT: C 237 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7637 (tm-30) outliers start: 35 outliers final: 23 residues processed: 118 average time/residue: 0.1800 time to fit residues: 29.2980 Evaluate side-chains 109 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 344 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 45 optimal weight: 0.0770 chunk 9 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 overall best weight: 1.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN B 267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7434 Z= 0.217 Angle : 0.488 4.622 10158 Z= 0.261 Chirality : 0.045 0.149 1125 Planarity : 0.004 0.034 1302 Dihedral : 6.840 59.166 1174 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 7.95 % Allowed : 26.30 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.17 (0.28), residues: 954 helix: 1.57 (0.44), residues: 153 sheet: 0.76 (0.28), residues: 345 loop : -0.92 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 258 HIS 0.002 0.001 HIS B 201 PHE 0.011 0.001 PHE B 235 TYR 0.012 0.001 TYR C 93 ARG 0.005 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 86 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7861 (t80) cc_final: 0.7534 (t80) REVERT: A 237 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7610 (tm-30) REVERT: A 252 MET cc_start: 0.8774 (mmt) cc_final: 0.8126 (tpp) REVERT: B 34 HIS cc_start: 0.8317 (OUTLIER) cc_final: 0.8085 (m-70) REVERT: C 112 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7685 (mt-10) REVERT: C 122 PHE cc_start: 0.8196 (t80) cc_final: 0.7938 (t80) REVERT: C 237 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7758 (tm-30) outliers start: 52 outliers final: 32 residues processed: 128 average time/residue: 0.1519 time to fit residues: 27.9594 Evaluate side-chains 114 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 81 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 315 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 79 optimal weight: 0.4980 chunk 64 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 0.2980 chunk 83 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 116 GLN B 116 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7434 Z= 0.232 Angle : 0.494 4.396 10158 Z= 0.266 Chirality : 0.046 0.146 1125 Planarity : 0.004 0.032 1302 Dihedral : 6.405 54.782 1170 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 7.65 % Allowed : 27.37 % Favored : 64.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.01 (0.28), residues: 954 helix: 1.46 (0.43), residues: 153 sheet: 0.56 (0.28), residues: 342 loop : -0.93 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 258 HIS 0.002 0.001 HIS B 201 PHE 0.017 0.001 PHE C 344 TYR 0.010 0.001 TYR A 93 ARG 0.004 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 78 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7876 (t80) cc_final: 0.7542 (t80) REVERT: A 237 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7684 (tm-30) REVERT: A 252 MET cc_start: 0.8733 (mmt) cc_final: 0.8173 (tpp) REVERT: B 34 HIS cc_start: 0.8355 (OUTLIER) cc_final: 0.8139 (m-70) REVERT: B 206 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6895 (mtt-85) REVERT: C 122 PHE cc_start: 0.8188 (t80) cc_final: 0.7910 (t80) REVERT: C 237 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7901 (tm-30) outliers start: 50 outliers final: 40 residues processed: 117 average time/residue: 0.1632 time to fit residues: 27.0757 Evaluate side-chains 117 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 75 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 315 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.8980 chunk 18 optimal weight: 0.0980 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7434 Z= 0.184 Angle : 0.468 4.348 10158 Z= 0.251 Chirality : 0.045 0.142 1125 Planarity : 0.003 0.031 1302 Dihedral : 6.293 53.408 1170 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 6.73 % Allowed : 27.98 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.13 (0.28), residues: 954 helix: 1.57 (0.44), residues: 153 sheet: 0.68 (0.28), residues: 339 loop : -0.88 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 258 HIS 0.002 0.000 HIS A 62 PHE 0.013 0.001 PHE C 344 TYR 0.013 0.001 TYR C 93 ARG 0.005 0.000 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 81 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7897 (t80) cc_final: 0.7573 (t80) REVERT: A 237 GLU cc_start: 0.8383 (tm-30) cc_final: 0.7669 (tm-30) REVERT: B 132 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8028 (m-30) REVERT: B 206 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6897 (mtt-85) REVERT: C 122 PHE cc_start: 0.8154 (t80) cc_final: 0.7871 (t80) REVERT: C 237 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7926 (tm-30) outliers start: 44 outliers final: 32 residues processed: 113 average time/residue: 0.1536 time to fit residues: 25.0826 Evaluate side-chains 113 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 79 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 266 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 20.0000 chunk 52 optimal weight: 0.0070 chunk 67 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 51 optimal weight: 0.0010 chunk 92 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 42 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.1606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7434 Z= 0.199 Angle : 0.479 4.451 10158 Z= 0.257 Chirality : 0.045 0.140 1125 Planarity : 0.003 0.031 1302 Dihedral : 6.281 52.667 1170 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 6.57 % Allowed : 27.52 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.08 (0.29), residues: 954 helix: 1.57 (0.43), residues: 153 sheet: 0.35 (0.28), residues: 357 loop : -0.69 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 258 HIS 0.002 0.001 HIS B 201 PHE 0.012 0.001 PHE C 242 TYR 0.010 0.001 TYR C 93 ARG 0.003 0.000 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 80 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7915 (t80) cc_final: 0.7582 (t80) REVERT: A 237 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7712 (tm-30) REVERT: B 132 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8131 (m-30) REVERT: B 206 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6910 (mtt-85) REVERT: C 122 PHE cc_start: 0.8131 (t80) cc_final: 0.7824 (t80) REVERT: C 237 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7946 (tm-30) REVERT: C 252 MET cc_start: 0.7914 (tpp) cc_final: 0.7701 (tpp) outliers start: 43 outliers final: 32 residues processed: 113 average time/residue: 0.1524 time to fit residues: 24.9281 Evaluate side-chains 113 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 79 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 266 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.7651 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7434 Z= 0.187 Angle : 0.476 4.507 10158 Z= 0.256 Chirality : 0.045 0.177 1125 Planarity : 0.003 0.031 1302 Dihedral : 6.239 52.497 1170 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.81 % Allowed : 27.68 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.12 (0.29), residues: 954 helix: 1.63 (0.44), residues: 153 sheet: 0.37 (0.29), residues: 360 loop : -0.67 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 258 HIS 0.002 0.000 HIS B 201 PHE 0.011 0.001 PHE C 344 TYR 0.012 0.001 TYR B 93 ARG 0.004 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 85 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7912 (t80) cc_final: 0.7583 (t80) REVERT: A 237 GLU cc_start: 0.8447 (tm-30) cc_final: 0.7748 (tm-30) REVERT: B 122 PHE cc_start: 0.7706 (t80) cc_final: 0.7061 (t80) REVERT: B 132 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8141 (m-30) REVERT: B 206 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6923 (mtt-85) REVERT: B 252 MET cc_start: 0.7370 (tpp) cc_final: 0.7114 (tpp) REVERT: C 122 PHE cc_start: 0.8137 (t80) cc_final: 0.7817 (t80) REVERT: C 237 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7934 (tm-30) outliers start: 38 outliers final: 33 residues processed: 112 average time/residue: 0.1534 time to fit residues: 24.7396 Evaluate side-chains 120 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 85 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 266 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 51 optimal weight: 0.0060 chunk 37 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 overall best weight: 1.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7434 Z= 0.289 Angle : 0.543 5.702 10158 Z= 0.292 Chirality : 0.047 0.175 1125 Planarity : 0.004 0.034 1302 Dihedral : 6.487 52.690 1170 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.96 % Allowed : 27.68 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.02 (0.29), residues: 954 helix: 1.56 (0.43), residues: 150 sheet: 0.23 (0.29), residues: 360 loop : -0.66 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 258 HIS 0.003 0.001 HIS B 201 PHE 0.015 0.002 PHE C 242 TYR 0.014 0.001 TYR C 93 ARG 0.003 0.000 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 79 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7861 (t80) cc_final: 0.7506 (t80) REVERT: A 237 GLU cc_start: 0.8528 (tm-30) cc_final: 0.7755 (tm-30) REVERT: B 122 PHE cc_start: 0.7697 (t80) cc_final: 0.7046 (t80) REVERT: B 132 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8189 (m-30) REVERT: B 186 GLU cc_start: 0.8357 (pt0) cc_final: 0.8077 (pt0) REVERT: B 206 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6666 (mtt-85) REVERT: B 252 MET cc_start: 0.7807 (tpp) cc_final: 0.7523 (tpp) REVERT: C 122 PHE cc_start: 0.8133 (t80) cc_final: 0.7831 (t80) REVERT: C 237 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7940 (tm-30) outliers start: 39 outliers final: 32 residues processed: 108 average time/residue: 0.1574 time to fit residues: 24.2776 Evaluate side-chains 109 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 75 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 321 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 88 optimal weight: 0.2980 chunk 76 optimal weight: 30.0000 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7653 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7434 Z= 0.166 Angle : 0.485 5.345 10158 Z= 0.261 Chirality : 0.045 0.180 1125 Planarity : 0.003 0.035 1302 Dihedral : 6.313 52.359 1170 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.74 % Allowed : 29.20 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.08 (0.29), residues: 954 helix: 1.63 (0.44), residues: 153 sheet: 0.36 (0.29), residues: 354 loop : -0.71 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 258 HIS 0.002 0.000 HIS B 201 PHE 0.011 0.001 PHE A 102 TYR 0.013 0.001 TYR A 93 ARG 0.003 0.000 ARG A 230 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 87 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7913 (t80) cc_final: 0.7566 (t80) REVERT: A 237 GLU cc_start: 0.8492 (tm-30) cc_final: 0.7710 (tm-30) REVERT: B 122 PHE cc_start: 0.7674 (t80) cc_final: 0.7022 (t80) REVERT: B 132 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8245 (m-30) REVERT: B 206 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6995 (mtt-85) REVERT: C 122 PHE cc_start: 0.8134 (t80) cc_final: 0.7817 (t80) REVERT: C 237 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7913 (tm-30) outliers start: 31 outliers final: 27 residues processed: 108 average time/residue: 0.1601 time to fit residues: 24.8309 Evaluate side-chains 114 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 85 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 266 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.0670 chunk 70 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 30.0000 chunk 31 optimal weight: 5.9990 chunk 78 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 66 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.144406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.103251 restraints weight = 10684.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.107001 restraints weight = 5921.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.109439 restraints weight = 4164.625| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 7434 Z= 0.143 Angle : 0.468 6.490 10158 Z= 0.251 Chirality : 0.045 0.179 1125 Planarity : 0.003 0.036 1302 Dihedral : 6.096 52.610 1170 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.43 % Allowed : 29.20 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.23 (0.29), residues: 954 helix: 1.82 (0.44), residues: 153 sheet: 0.46 (0.29), residues: 354 loop : -0.67 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 258 HIS 0.001 0.000 HIS A 62 PHE 0.016 0.001 PHE C 235 TYR 0.011 0.001 TYR A 93 ARG 0.003 0.000 ARG A 230 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1641.99 seconds wall clock time: 30 minutes 37.57 seconds (1837.57 seconds total)