Starting phenix.real_space_refine on Wed Feb 14 06:20:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5h_33014/02_2024/7x5h_33014_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5h_33014/02_2024/7x5h_33014.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5h_33014/02_2024/7x5h_33014_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5h_33014/02_2024/7x5h_33014_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5h_33014/02_2024/7x5h_33014_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5h_33014/02_2024/7x5h_33014.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5h_33014/02_2024/7x5h_33014.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5h_33014/02_2024/7x5h_33014_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5h_33014/02_2024/7x5h_33014_neut_updated.pdb" } resolution = 3.1 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= 0.005 sd= 0.133 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5568 2.51 5 N 1496 2.21 5 O 1642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 153": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8768 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1807 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 427 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2121 Unusual residues: {'8K3': 1} Classifications: {'peptide': 274, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 9, 'TRANS': 264, None: 1} Not linked: pdbres="PHE R 353 " pdbres="8K3 R 601 " Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 58 Time building chain proxies: 4.80, per 1000 atoms: 0.55 Number of scatterers: 8768 At special positions: 0 Unit cell: (118.881, 124.236, 106.029, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1642 8.00 N 1496 7.00 C 5568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 192 " distance=2.00 Simple disulfide: pdb=" SG CYS R 311 " - pdb=" SG CYS R 313 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 1.6 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 12 sheets defined 36.3% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.902A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 230 removed outlier: 3.726A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.760A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.761A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.654A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 removed outlier: 4.658A pdb=" N LYS C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'R' and resid 40 through 67 Processing helix chain 'R' and resid 69 through 71 No H-bonds generated for 'chain 'R' and resid 69 through 71' Processing helix chain 'R' and resid 74 through 92 removed outlier: 4.357A pdb=" N LEU R 78 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL R 79 " --> pdb=" O PRO R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 103 removed outlier: 3.801A pdb=" N SER R 103 " --> pdb=" O VAL R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 144 removed outlier: 3.676A pdb=" N GLN R 115 " --> pdb=" O ARG R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 178 removed outlier: 3.636A pdb=" N CYS R 156 " --> pdb=" O ARG R 152 " (cutoff:3.500A) Proline residue: R 176 - end of helix Processing helix chain 'R' and resid 198 through 208 removed outlier: 3.611A pdb=" N PHE R 203 " --> pdb=" O SER R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 232 Processing helix chain 'R' and resid 277 through 310 Proline residue: R 300 - end of helix Proline residue: R 309 - end of helix Processing helix chain 'R' and resid 317 through 339 removed outlier: 3.922A pdb=" N SER R 331 " --> pdb=" O GLY R 327 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE R 332 " --> pdb=" O TYR R 328 " (cutoff:3.500A) Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 343 through 352 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 7.329A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.992A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.042A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.852A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.967A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.795A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.440A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 45 through 52 removed outlier: 6.935A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.501A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.575A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.747A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1215 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: 2.85 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1432 1.31 - 1.45: 2498 1.45 - 1.58: 4935 1.58 - 1.71: 0 1.71 - 1.84: 88 Bond restraints: 8953 Sorted by residual: bond pdb=" C04 8K3 R 601 " pdb=" C08 8K3 R 601 " ideal model delta sigma weight residual 1.365 1.532 -0.167 2.00e-02 2.50e+03 7.00e+01 bond pdb=" C10 8K3 R 601 " pdb=" C11 8K3 R 601 " ideal model delta sigma weight residual 1.386 1.439 -0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" N CYS R 114 " pdb=" CA CYS R 114 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.25e+00 bond pdb=" N PHE E 68 " pdb=" CA PHE E 68 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.21e-02 6.83e+03 6.12e+00 bond pdb=" C09 8K3 R 601 " pdb=" C10 8K3 R 601 " ideal model delta sigma weight residual 1.386 1.434 -0.048 2.00e-02 2.50e+03 5.74e+00 ... (remaining 8948 not shown) Histogram of bond angle deviations from ideal: 99.99 - 107.50: 282 107.50 - 115.02: 5307 115.02 - 122.53: 5380 122.53 - 130.04: 1093 130.04 - 137.56: 71 Bond angle restraints: 12133 Sorted by residual: angle pdb=" C03 8K3 R 601 " pdb=" C04 8K3 R 601 " pdb=" C08 8K3 R 601 " ideal model delta sigma weight residual 139.25 124.10 15.15 3.00e+00 1.11e-01 2.55e+01 angle pdb=" C03 8K3 R 601 " pdb=" C04 8K3 R 601 " pdb=" C05 8K3 R 601 " ideal model delta sigma weight residual 112.74 124.15 -11.41 3.00e+00 1.11e-01 1.45e+01 angle pdb=" C05 8K3 R 601 " pdb=" N06 8K3 R 601 " pdb=" C07 8K3 R 601 " ideal model delta sigma weight residual 108.08 119.31 -11.23 3.00e+00 1.11e-01 1.40e+01 angle pdb=" N VAL A 201 " pdb=" CA VAL A 201 " pdb=" C VAL A 201 " ideal model delta sigma weight residual 112.17 108.64 3.53 9.50e-01 1.11e+00 1.38e+01 angle pdb=" N VAL E 64 " pdb=" CA VAL E 64 " pdb=" C VAL E 64 " ideal model delta sigma weight residual 113.53 110.13 3.40 9.80e-01 1.04e+00 1.20e+01 ... (remaining 12128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4779 17.94 - 35.88: 404 35.88 - 53.81: 90 53.81 - 71.75: 10 71.75 - 89.69: 9 Dihedral angle restraints: 5292 sinusoidal: 2024 harmonic: 3268 Sorted by residual: dihedral pdb=" CA CYS R 311 " pdb=" C CYS R 311 " pdb=" N SER R 312 " pdb=" CA SER R 312 " ideal model delta harmonic sigma weight residual 180.00 143.08 36.92 0 5.00e+00 4.00e-02 5.45e+01 dihedral pdb=" CB CYS R 311 " pdb=" SG CYS R 311 " pdb=" SG CYS R 313 " pdb=" CB CYS R 313 " ideal model delta sinusoidal sigma weight residual -86.00 -48.18 -37.82 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CB GLU A 33 " pdb=" CG GLU A 33 " pdb=" CD GLU A 33 " pdb=" OE1 GLU A 33 " ideal model delta sinusoidal sigma weight residual 0.00 -89.69 89.69 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1115 0.045 - 0.090: 179 0.090 - 0.135: 71 0.135 - 0.180: 3 0.180 - 0.225: 1 Chirality restraints: 1369 Sorted by residual: chirality pdb=" CA CYS R 192 " pdb=" N CYS R 192 " pdb=" C CYS R 192 " pdb=" CB CYS R 192 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE R 315 " pdb=" N ILE R 315 " pdb=" C ILE R 315 " pdb=" CB ILE R 315 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 1366 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO B 39 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 54 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C THR R 54 " 0.032 2.00e-02 2.50e+03 pdb=" O THR R 54 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE R 55 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 197 " 0.102 9.50e-02 1.11e+02 4.58e-02 1.47e+00 pdb=" NE ARG B 197 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG B 197 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 197 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 197 " 0.001 2.00e-02 2.50e+03 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 244 2.70 - 3.25: 8808 3.25 - 3.80: 14006 3.80 - 4.35: 18344 4.35 - 4.90: 31686 Nonbonded interactions: 73088 Sorted by model distance: nonbonded pdb=" O SER A 44 " pdb=" ND2 ASN A 269 " model vdw 2.148 2.520 nonbonded pdb=" O SER C 57 " pdb=" NH2 ARG C 62 " model vdw 2.167 2.520 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.180 2.520 nonbonded pdb=" OD1 ASP A 341 " pdb=" NH1 ARG R 230 " model vdw 2.205 2.520 nonbonded pdb=" NH2 ARG B 46 " pdb=" OE2 GLU C 63 " model vdw 2.212 2.520 ... (remaining 73083 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 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: 2.170 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.840 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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 0.167 8953 Z= 0.178 Angle : 0.524 15.154 12133 Z= 0.278 Chirality : 0.039 0.225 1369 Planarity : 0.003 0.049 1537 Dihedral : 14.215 89.688 3176 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.26), residues: 1112 helix: 3.55 (0.26), residues: 388 sheet: 0.71 (0.29), residues: 284 loop : 0.51 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 325 HIS 0.002 0.000 HIS E 35 PHE 0.008 0.001 PHE A 189 TYR 0.007 0.001 TYR E 60 ARG 0.008 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 58 ASN cc_start: 0.8378 (m110) cc_final: 0.8120 (m110) REVERT: R 117 TRP cc_start: 0.7679 (t60) cc_final: 0.7459 (t60) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2632 time to fit residues: 53.3265 Evaluate side-chains 140 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 237 ASN B 239 ASN E 39 GLN E 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8953 Z= 0.167 Angle : 0.474 6.277 12133 Z= 0.252 Chirality : 0.041 0.145 1369 Planarity : 0.003 0.044 1537 Dihedral : 3.668 30.593 1218 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.49 % Allowed : 9.68 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.26), residues: 1112 helix: 3.28 (0.26), residues: 389 sheet: 0.63 (0.29), residues: 278 loop : 0.32 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 325 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE B 199 TYR 0.016 0.001 TYR B 105 ARG 0.004 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 333 GLN cc_start: 0.8217 (tp40) cc_final: 0.7995 (tp40) REVERT: E 220 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6197 (mp0) outliers start: 14 outliers final: 9 residues processed: 156 average time/residue: 0.2646 time to fit residues: 54.0354 Evaluate side-chains 150 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 205 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 81 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 32 GLN B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8953 Z= 0.286 Angle : 0.522 7.213 12133 Z= 0.281 Chirality : 0.043 0.172 1369 Planarity : 0.003 0.041 1537 Dihedral : 4.097 28.481 1218 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.70 % Allowed : 12.23 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.25), residues: 1112 helix: 3.08 (0.26), residues: 383 sheet: 0.37 (0.28), residues: 294 loop : 0.17 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS B 311 PHE 0.022 0.002 PHE E 68 TYR 0.025 0.002 TYR B 105 ARG 0.004 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 1.034 Fit side-chains REVERT: A 253 ILE cc_start: 0.9012 (tp) cc_final: 0.8756 (tp) REVERT: A 273 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7712 (tt) REVERT: A 333 GLN cc_start: 0.8320 (tp40) cc_final: 0.8060 (tp40) REVERT: E 220 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6397 (mp0) REVERT: R 276 ARG cc_start: 0.6266 (mmm-85) cc_final: 0.5735 (mtt-85) outliers start: 16 outliers final: 10 residues processed: 161 average time/residue: 0.2813 time to fit residues: 58.5814 Evaluate side-chains 156 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 205 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 67 optimal weight: 0.0270 chunk 101 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 204 GLN B 32 GLN B 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8953 Z= 0.136 Angle : 0.453 7.027 12133 Z= 0.245 Chirality : 0.040 0.183 1369 Planarity : 0.003 0.040 1537 Dihedral : 3.781 17.679 1218 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.91 % Allowed : 12.98 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.25), residues: 1112 helix: 3.12 (0.26), residues: 381 sheet: 0.37 (0.28), residues: 296 loop : 0.01 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 325 HIS 0.003 0.001 HIS A 188 PHE 0.010 0.001 PHE A 189 TYR 0.012 0.001 TYR E 60 ARG 0.008 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 1.004 Fit side-chains REVERT: A 253 ILE cc_start: 0.9000 (tp) cc_final: 0.8739 (tp) REVERT: A 273 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7734 (tt) REVERT: A 333 GLN cc_start: 0.8229 (tp40) cc_final: 0.8003 (tp40) REVERT: B 127 LYS cc_start: 0.9116 (mmtm) cc_final: 0.8910 (mmtp) REVERT: B 273 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8597 (mm) REVERT: B 322 ASP cc_start: 0.8003 (t0) cc_final: 0.7721 (m-30) REVERT: E 82 GLN cc_start: 0.7888 (tp-100) cc_final: 0.7464 (tp-100) REVERT: E 220 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: R 276 ARG cc_start: 0.6385 (mmm-85) cc_final: 0.5505 (mtt-85) outliers start: 18 outliers final: 10 residues processed: 160 average time/residue: 0.2607 time to fit residues: 54.5124 Evaluate side-chains 160 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 74 optimal weight: 30.0000 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 32 GLN B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8953 Z= 0.320 Angle : 0.538 7.204 12133 Z= 0.289 Chirality : 0.043 0.198 1369 Planarity : 0.004 0.041 1537 Dihedral : 4.177 19.071 1218 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.77 % Allowed : 13.51 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1112 helix: 2.85 (0.26), residues: 383 sheet: 0.18 (0.28), residues: 299 loop : -0.11 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 325 HIS 0.007 0.001 HIS A 188 PHE 0.021 0.002 PHE R 203 TYR 0.019 0.002 TYR B 105 ARG 0.006 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 1.021 Fit side-chains REVERT: A 253 ILE cc_start: 0.9068 (tp) cc_final: 0.8804 (tp) REVERT: A 273 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7751 (tt) REVERT: B 322 ASP cc_start: 0.8147 (t0) cc_final: 0.7903 (m-30) REVERT: E 220 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6495 (mp0) REVERT: R 117 TRP cc_start: 0.7710 (t60) cc_final: 0.7494 (t60) REVERT: R 276 ARG cc_start: 0.6327 (mmm-85) cc_final: 0.5428 (mtt-85) outliers start: 26 outliers final: 16 residues processed: 163 average time/residue: 0.2646 time to fit residues: 56.1717 Evaluate side-chains 157 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 205 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 89 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 176 GLN E 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8953 Z= 0.239 Angle : 0.498 7.184 12133 Z= 0.270 Chirality : 0.042 0.214 1369 Planarity : 0.003 0.041 1537 Dihedral : 4.092 19.212 1218 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.77 % Allowed : 14.26 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.25), residues: 1112 helix: 2.90 (0.26), residues: 383 sheet: 0.19 (0.28), residues: 296 loop : -0.23 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP R 325 HIS 0.005 0.001 HIS E 35 PHE 0.016 0.001 PHE R 203 TYR 0.011 0.001 TYR B 105 ARG 0.006 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 1.004 Fit side-chains REVERT: A 253 ILE cc_start: 0.9039 (tp) cc_final: 0.8749 (tp) REVERT: A 273 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7672 (tt) REVERT: B 322 ASP cc_start: 0.8150 (t0) cc_final: 0.7871 (m-30) REVERT: R 117 TRP cc_start: 0.7727 (t60) cc_final: 0.7484 (t60) REVERT: R 276 ARG cc_start: 0.6407 (mmm-85) cc_final: 0.5466 (mtt-85) outliers start: 26 outliers final: 19 residues processed: 163 average time/residue: 0.2688 time to fit residues: 57.0337 Evaluate side-chains 162 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 205 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 65 optimal weight: 0.0570 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8953 Z= 0.137 Angle : 0.455 7.157 12133 Z= 0.247 Chirality : 0.040 0.220 1369 Planarity : 0.003 0.037 1537 Dihedral : 3.841 18.710 1218 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.34 % Allowed : 15.11 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.25), residues: 1112 helix: 3.04 (0.26), residues: 383 sheet: 0.26 (0.28), residues: 296 loop : -0.19 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP R 325 HIS 0.004 0.001 HIS E 35 PHE 0.016 0.001 PHE R 203 TYR 0.011 0.001 TYR E 60 ARG 0.006 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 1.105 Fit side-chains REVERT: A 253 ILE cc_start: 0.8981 (tp) cc_final: 0.8692 (tp) REVERT: B 325 MET cc_start: 0.8160 (tpp) cc_final: 0.7913 (tpp) REVERT: E 82 GLN cc_start: 0.7803 (tp-100) cc_final: 0.7456 (tp-100) REVERT: R 117 TRP cc_start: 0.7695 (t60) cc_final: 0.7434 (t60) REVERT: R 276 ARG cc_start: 0.6527 (mmm-85) cc_final: 0.5863 (mtt-85) outliers start: 22 outliers final: 16 residues processed: 158 average time/residue: 0.2677 time to fit residues: 55.4285 Evaluate side-chains 154 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 194 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 0.0570 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8953 Z= 0.186 Angle : 0.481 7.234 12133 Z= 0.259 Chirality : 0.041 0.226 1369 Planarity : 0.003 0.040 1537 Dihedral : 3.872 18.472 1218 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.77 % Allowed : 15.43 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.25), residues: 1112 helix: 3.00 (0.26), residues: 383 sheet: 0.27 (0.29), residues: 296 loop : -0.21 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 325 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE R 203 TYR 0.009 0.001 TYR E 60 ARG 0.005 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 0.934 Fit side-chains REVERT: A 253 ILE cc_start: 0.8990 (tp) cc_final: 0.8694 (tp) REVERT: E 43 LYS cc_start: 0.8848 (mmmm) cc_final: 0.8637 (mmmm) REVERT: E 82 GLN cc_start: 0.7786 (tp-100) cc_final: 0.7451 (tp-100) REVERT: R 117 TRP cc_start: 0.7685 (t60) cc_final: 0.7426 (t60) REVERT: R 276 ARG cc_start: 0.6604 (mmm-85) cc_final: 0.6012 (mtt-85) outliers start: 26 outliers final: 22 residues processed: 153 average time/residue: 0.2633 time to fit residues: 52.5104 Evaluate side-chains 161 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 205 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 78 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8953 Z= 0.152 Angle : 0.465 7.218 12133 Z= 0.250 Chirality : 0.041 0.229 1369 Planarity : 0.003 0.038 1537 Dihedral : 3.808 18.547 1218 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.23 % Allowed : 15.96 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.25), residues: 1112 helix: 3.07 (0.26), residues: 381 sheet: 0.29 (0.29), residues: 296 loop : -0.24 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP R 325 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE R 203 TYR 0.009 0.001 TYR E 60 ARG 0.008 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 1.072 Fit side-chains REVERT: A 253 ILE cc_start: 0.8974 (tp) cc_final: 0.8684 (tp) REVERT: B 45 MET cc_start: 0.9106 (mtt) cc_final: 0.8762 (mmt) REVERT: E 43 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8655 (mmmm) REVERT: E 82 GLN cc_start: 0.7762 (tp-100) cc_final: 0.7435 (tp-100) REVERT: R 117 TRP cc_start: 0.7672 (t60) cc_final: 0.7409 (t60) REVERT: R 276 ARG cc_start: 0.6638 (mmm-85) cc_final: 0.6088 (mtt-85) outliers start: 21 outliers final: 18 residues processed: 152 average time/residue: 0.2767 time to fit residues: 54.4581 Evaluate side-chains 155 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 194 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 176 GLN B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8953 Z= 0.164 Angle : 0.479 7.221 12133 Z= 0.256 Chirality : 0.041 0.237 1369 Planarity : 0.003 0.039 1537 Dihedral : 3.824 18.424 1218 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.13 % Allowed : 16.17 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.25), residues: 1112 helix: 3.08 (0.26), residues: 380 sheet: 0.29 (0.29), residues: 296 loop : -0.20 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP R 325 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE R 203 TYR 0.009 0.001 TYR E 60 ARG 0.008 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 143 time to evaluate : 0.920 Fit side-chains REVERT: A 253 ILE cc_start: 0.8977 (tp) cc_final: 0.8682 (tp) REVERT: B 45 MET cc_start: 0.9100 (mtt) cc_final: 0.8759 (mmt) REVERT: E 43 LYS cc_start: 0.8832 (mmmm) cc_final: 0.8624 (mmmm) REVERT: E 82 GLN cc_start: 0.7757 (tp-100) cc_final: 0.7430 (tp-100) REVERT: R 117 TRP cc_start: 0.7676 (t60) cc_final: 0.7411 (t60) REVERT: R 276 ARG cc_start: 0.6656 (mmm-85) cc_final: 0.6108 (mtt-85) outliers start: 20 outliers final: 19 residues processed: 155 average time/residue: 0.2814 time to fit residues: 56.1761 Evaluate side-chains 160 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 205 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 9.9990 chunk 13 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 63 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.175509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.130163 restraints weight = 10261.827| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.71 r_work: 0.3124 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8953 Z= 0.194 Angle : 0.495 7.336 12133 Z= 0.265 Chirality : 0.041 0.234 1369 Planarity : 0.003 0.037 1537 Dihedral : 3.896 19.639 1218 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.34 % Allowed : 16.17 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.25), residues: 1112 helix: 3.02 (0.26), residues: 382 sheet: 0.25 (0.28), residues: 296 loop : -0.20 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP R 325 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE R 203 TYR 0.008 0.001 TYR R 220 ARG 0.005 0.000 ARG B 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2336.80 seconds wall clock time: 43 minutes 9.82 seconds (2589.82 seconds total)