Starting phenix.real_space_refine on Fri Dec 8 05:36:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv7_36670/12_2023/8jv7_36670_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv7_36670/12_2023/8jv7_36670.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv7_36670/12_2023/8jv7_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_36670/12_2023/8jv7_36670_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv7_36670/12_2023/8jv7_36670_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv7_36670/12_2023/8jv7_36670.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv7_36670/12_2023/8jv7_36670.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv7_36670/12_2023/8jv7_36670_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv7_36670/12_2023/8jv7_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-1.21rc1-5172/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: 4.54, per 1000 atoms: 0.63 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: 2.80 Conformation dependent library (CDL) restraints added in 1.4 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: 1.54 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: 2.03 Time building geometry restraints manager: 3.06 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: 1.020 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: 3.680 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 24.560 Find NCS groups from input model: 0.460 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.770 ------------------------------------------------------------------------------- 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 : 0.868 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 114 average time/residue: 0.1867 time to fit residues: 29.2311 Evaluate side-chains 103 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.818 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1495 time to fit residues: 2.5349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.0980 chunk 72 optimal weight: 0.0670 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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 C 268 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 7434 Z= 0.165 Angle : 0.466 5.754 10158 Z= 0.249 Chirality : 0.044 0.136 1125 Planarity : 0.004 0.037 1302 Dihedral : 7.006 69.888 1170 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.28 % Allowed : 29.05 % Favored : 66.67 % 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: 0.11 (0.28), residues: 954 helix: 1.59 (0.45), residues: 153 sheet: 0.57 (0.28), residues: 360 loop : -0.89 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 258 HIS 0.012 0.001 HIS C 268 PHE 0.009 0.001 PHE A 102 TYR 0.008 0.001 TYR C 273 ARG 0.005 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 123 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 0.773 Fit side-chains outliers start: 28 outliers final: 16 residues processed: 115 average time/residue: 0.1895 time to fit residues: 29.5252 Evaluate side-chains 106 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.753 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0944 time to fit residues: 3.4164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 72 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 70 optimal weight: 0.0010 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN C 268 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7434 Z= 0.144 Angle : 0.446 5.010 10158 Z= 0.239 Chirality : 0.044 0.142 1125 Planarity : 0.003 0.034 1302 Dihedral : 6.543 65.995 1170 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.75 % Allowed : 29.51 % Favored : 67.74 % 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: 0.21 (0.28), residues: 954 helix: 1.57 (0.45), 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 0.008 0.001 PHE A 102 TYR 0.010 0.001 TYR C 93 ARG 0.005 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 122 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.891 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 119 average time/residue: 0.1738 time to fit residues: 29.0460 Evaluate side-chains 105 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.851 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0698 time to fit residues: 2.5833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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: 0.7644 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7434 Z= 0.234 Angle : 0.506 4.510 10158 Z= 0.273 Chirality : 0.046 0.155 1125 Planarity : 0.004 0.033 1302 Dihedral : 6.481 59.200 1170 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.59 % Allowed : 29.51 % 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: 0.06 (0.28), residues: 954 helix: 1.34 (0.44), residues: 153 sheet: 0.72 (0.28), residues: 345 loop : -0.95 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 258 HIS 0.002 0.001 HIS B 201 PHE 0.014 0.001 PHE C 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 118 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 88 time to evaluate : 0.777 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 19 residues processed: 111 average time/residue: 0.1662 time to fit residues: 26.0833 Evaluate side-chains 99 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.775 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0713 time to fit residues: 3.4544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 0.4980 chunk 79 optimal weight: 0.0470 chunk 64 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 0.0870 chunk 83 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7434 Z= 0.137 Angle : 0.454 4.312 10158 Z= 0.245 Chirality : 0.044 0.130 1125 Planarity : 0.003 0.029 1302 Dihedral : 6.280 57.034 1170 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.75 % Allowed : 29.97 % Favored : 67.28 % 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: 0.16 (0.28), residues: 954 helix: 1.35 (0.44), residues: 153 sheet: 0.58 (0.28), residues: 354 loop : -0.68 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 258 HIS 0.001 0.000 HIS B 201 PHE 0.021 0.001 PHE C 122 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 107 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.838 Fit side-chains outliers start: 18 outliers final: 6 residues processed: 101 average time/residue: 0.1949 time to fit residues: 26.9566 Evaluate side-chains 86 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.863 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0686 time to fit residues: 1.9082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7434 Z= 0.240 Angle : 0.505 4.479 10158 Z= 0.272 Chirality : 0.046 0.151 1125 Planarity : 0.004 0.033 1302 Dihedral : 6.357 54.464 1170 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.36 % Allowed : 30.43 % Favored : 66.21 % 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 (0.28), residues: 954 helix: 1.31 (0.44), residues: 153 sheet: 0.42 (0.28), residues: 351 loop : -0.74 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 258 HIS 0.002 0.000 HIS B 201 PHE 0.015 0.001 PHE A 235 TYR 0.011 0.001 TYR C 93 ARG 0.003 0.000 ARG A 206 *********************** 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 102 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 1.012 Fit side-chains outliers start: 22 outliers final: 16 residues processed: 96 average time/residue: 0.1796 time to fit residues: 24.2139 Evaluate side-chains 94 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0735 time to fit residues: 3.2535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 0.0070 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 57 optimal weight: 0.0570 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 overall best weight: 1.1920 ------------------------------------------------------------------------------- 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: 0.7632 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7434 Z= 0.205 Angle : 0.485 4.429 10158 Z= 0.262 Chirality : 0.045 0.144 1125 Planarity : 0.003 0.030 1302 Dihedral : 6.301 53.228 1170 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.92 % Allowed : 31.65 % Favored : 67.43 % 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: 0.04 (0.28), residues: 954 helix: 1.23 (0.44), residues: 153 sheet: 0.43 (0.28), residues: 354 loop : -0.68 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 258 HIS 0.002 0.001 HIS B 201 PHE 0.017 0.001 PHE C 235 TYR 0.012 0.001 TYR C 93 ARG 0.006 0.000 ARG B 206 *********************** 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 88 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.858 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 87 average time/residue: 0.1856 time to fit residues: 22.5355 Evaluate side-chains 82 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 0.844 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0689 time to fit residues: 1.3737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7607 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7434 Z= 0.162 Angle : 0.471 4.362 10158 Z= 0.254 Chirality : 0.045 0.135 1125 Planarity : 0.003 0.031 1302 Dihedral : 6.207 52.563 1170 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.61 % Allowed : 32.11 % Favored : 67.28 % 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 (0.29), residues: 954 helix: 1.35 (0.44), residues: 153 sheet: 0.81 (0.30), residues: 309 loop : -0.64 (0.30), residues: 492 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 0.016 0.001 PHE C 344 TYR 0.012 0.001 TYR A 93 ARG 0.004 0.000 ARG A 206 *********************** 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 86 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.863 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 85 average time/residue: 0.1993 time to fit residues: 23.6154 Evaluate side-chains 82 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 0.827 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0788 time to fit residues: 1.3948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7612 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7434 Z= 0.169 Angle : 0.474 5.404 10158 Z= 0.256 Chirality : 0.045 0.135 1125 Planarity : 0.003 0.033 1302 Dihedral : 6.144 52.633 1170 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.31 % Allowed : 31.96 % Favored : 67.74 % 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: 0.30 (0.29), residues: 954 helix: 1.44 (0.43), residues: 153 sheet: 0.83 (0.30), residues: 309 loop : -0.60 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 258 HIS 0.002 0.000 HIS B 201 PHE 0.017 0.001 PHE C 344 TYR 0.011 0.001 TYR C 93 ARG 0.003 0.000 ARG A 206 *********************** 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 84 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.896 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 84 average time/residue: 0.1968 time to fit residues: 23.1946 Evaluate side-chains 81 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.854 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 76 optimal weight: 30.0000 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2794 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= 0.175 Angle : 0.480 4.933 10158 Z= 0.260 Chirality : 0.045 0.137 1125 Planarity : 0.003 0.034 1302 Dihedral : 6.159 52.583 1170 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.31 % Allowed : 32.26 % Favored : 67.43 % 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: 0.31 (0.29), residues: 954 helix: 1.47 (0.44), residues: 153 sheet: 0.83 (0.30), residues: 309 loop : -0.60 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 258 HIS 0.002 0.000 HIS B 201 PHE 0.015 0.001 PHE C 344 TYR 0.012 0.001 TYR A 93 ARG 0.003 0.000 ARG A 206 ********************** 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 84 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.801 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 83 average time/residue: 0.1854 time to fit residues: 21.3842 Evaluate side-chains 81 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.763 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 76 optimal weight: 30.0000 chunk 31 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.0370 chunk 66 optimal weight: 0.0040 chunk 4 optimal weight: 9.9990 overall best weight: 0.5270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.145776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.103855 restraints weight = 10784.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.107642 restraints weight = 6059.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110243 restraints weight = 4298.828| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7434 Z= 0.145 Angle : 0.468 5.455 10158 Z= 0.254 Chirality : 0.045 0.130 1125 Planarity : 0.003 0.033 1302 Dihedral : 6.029 52.596 1170 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.31 % Allowed : 32.72 % Favored : 66.97 % 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: 0.38 (0.29), residues: 954 helix: 1.59 (0.44), residues: 153 sheet: 0.86 (0.30), residues: 309 loop : -0.57 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 258 HIS 0.001 0.000 HIS B 201 PHE 0.014 0.001 PHE C 344 TYR 0.010 0.001 TYR A 93 ARG 0.003 0.000 ARG A 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1625.18 seconds wall clock time: 30 minutes 8.76 seconds (1808.76 seconds total)