Starting phenix.real_space_refine on Wed Feb 14 06:45:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnm_34916/02_2024/8hnm_34916_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnm_34916/02_2024/8hnm_34916.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnm_34916/02_2024/8hnm_34916_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnm_34916/02_2024/8hnm_34916_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnm_34916/02_2024/8hnm_34916_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnm_34916/02_2024/8hnm_34916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnm_34916/02_2024/8hnm_34916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnm_34916/02_2024/8hnm_34916_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnm_34916/02_2024/8hnm_34916_updated.pdb" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 Br 1 7.06 5 S 63 5.16 5 C 5604 2.51 5 N 1504 2.21 5 O 1612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 276": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "R GLU 327": "OE1" <-> "OE2" Residue "S GLU 42": "OE1" <-> "OE2" Residue "S GLU 89": "OE1" <-> "OE2" Residue "S GLU 153": "OE1" <-> "OE2" Residue "S GLU 220": "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: 8784 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "R" Number of atoms: 2159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2159 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'4IE': 1, 'CLR': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.80, per 1000 atoms: 0.55 Number of scatterers: 8784 At special positions: 0 Unit cell: (90.95, 120.7, 129.2, 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) Br 1 34.99 S 63 16.00 O 1612 8.00 N 1504 7.00 C 5604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 124 " - pdb=" SG CYS R 203 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 3.19 Conformation dependent library (CDL) restraints added in 1.7 seconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 13 sheets defined 34.3% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 Processing helix chain 'A' and resid 47 through 50 No H-bonds generated for 'chain 'A' and resid 47 through 50' Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.081A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 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 309 Processing helix chain 'A' and resid 328 through 350 removed outlier: 4.311A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 25 removed outlier: 3.638A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.811A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'R' and resid 61 through 80 Processing helix chain 'R' and resid 88 through 114 Proline residue: R 107 - end of helix Processing helix chain 'R' and resid 122 through 154 removed outlier: 3.614A pdb=" N ALA R 139 " --> pdb=" O PHE R 135 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU R 142 " --> pdb=" O GLY R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 162 removed outlier: 3.624A pdb=" N ARG R 161 " --> pdb=" O THR R 157 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG R 162 " --> pdb=" O GLN R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 183 Processing helix chain 'R' and resid 187 through 189 No H-bonds generated for 'chain 'R' and resid 187 through 189' Processing helix chain 'R' and resid 209 through 244 removed outlier: 3.836A pdb=" N GLY R 223 " --> pdb=" O GLN R 219 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU R 226 " --> pdb=" O ALA R 222 " (cutoff:3.500A) Proline residue: R 227 - end of helix Processing helix chain 'R' and resid 249 through 283 removed outlier: 4.153A pdb=" N THR R 269 " --> pdb=" O ALA R 265 " (cutoff:3.500A) Proline residue: R 270 - end of helix Processing helix chain 'R' and resid 290 through 318 Proline residue: R 315 - end of helix Processing helix chain 'R' and resid 323 through 335 removed outlier: 3.679A pdb=" N ARG R 335 " --> pdb=" O MET R 331 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.459A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.617A 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: 7.026A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.755A 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: 7.122A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.900A 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: 6.739A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.131A 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: 7.004A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.352A 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: 6.873A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.910A 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: 6.493A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.775A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'R' and resid 190 through 193 removed outlier: 3.738A pdb=" N HIS R 202 " --> pdb=" O HIS R 193 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.721A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.689A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 155 through 160 408 hydrogen bonds defined for protein. 1179 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: 2.53 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 2868 1.36 - 1.50: 2319 1.50 - 1.63: 3689 1.63 - 1.77: 0 1.77 - 1.90: 91 Bond restraints: 8967 Sorted by residual: bond pdb=" C5 4IE R 603 " pdb=" C6 4IE R 603 " ideal model delta sigma weight residual 1.712 1.324 0.388 2.00e-02 2.50e+03 3.77e+02 bond pdb=" C7 4IE R 603 " pdb=" C8 4IE R 603 " ideal model delta sigma weight residual 1.223 1.555 -0.332 2.00e-02 2.50e+03 2.76e+02 bond pdb=" C4 4IE R 603 " pdb=" C5 4IE R 603 " ideal model delta sigma weight residual 1.709 1.504 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C3 4IE R 603 " pdb=" C8 4IE R 603 " ideal model delta sigma weight residual 1.347 1.543 -0.196 2.00e-02 2.50e+03 9.59e+01 bond pdb=" C2 4IE R 603 " pdb=" C7 4IE R 603 " ideal model delta sigma weight residual 1.648 1.572 0.076 2.00e-02 2.50e+03 1.46e+01 ... (remaining 8962 not shown) Histogram of bond angle deviations from ideal: 84.69 - 94.57: 4 94.57 - 104.46: 93 104.46 - 114.35: 5392 114.35 - 124.24: 6445 124.24 - 134.13: 227 Bond angle restraints: 12161 Sorted by residual: angle pdb=" C3 4IE R 603 " pdb=" C8 4IE R 603 " pdb=" C7 4IE R 603 " ideal model delta sigma weight residual 109.70 85.85 23.85 3.00e+00 1.11e-01 6.32e+01 angle pdb=" C16 4IE R 603 " pdb=" C19 4IE R 603 " pdb=" C24 4IE R 603 " ideal model delta sigma weight residual 113.81 125.19 -11.38 3.00e+00 1.11e-01 1.44e+01 angle pdb=" CA GLU S 246 " pdb=" C GLU S 246 " pdb=" O GLU S 246 " ideal model delta sigma weight residual 121.40 117.91 3.49 1.11e+00 8.12e-01 9.88e+00 angle pdb=" CA LEU R 283 " pdb=" C LEU R 283 " pdb=" O LEU R 283 " ideal model delta sigma weight residual 121.02 118.20 2.82 9.00e-01 1.23e+00 9.80e+00 angle pdb=" C4 4IE R 603 " pdb=" C5 4IE R 603 " pdb=" C6 4IE R 603 " ideal model delta sigma weight residual 110.67 119.85 -9.18 3.00e+00 1.11e-01 9.36e+00 ... (remaining 12156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.49: 4870 20.49 - 40.98: 433 40.98 - 61.48: 91 61.48 - 81.97: 10 81.97 - 102.46: 7 Dihedral angle restraints: 5411 sinusoidal: 2184 harmonic: 3227 Sorted by residual: dihedral pdb=" CA GLU B 215 " pdb=" C GLU B 215 " pdb=" N GLY B 216 " pdb=" CA GLY B 216 " ideal model delta harmonic sigma weight residual 180.00 158.12 21.88 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA PHE R 207 " pdb=" C PHE R 207 " pdb=" N PRO R 208 " pdb=" CA PRO R 208 " ideal model delta harmonic sigma weight residual -180.00 -158.49 -21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA SER S 208 " pdb=" C SER S 208 " pdb=" N GLY S 209 " pdb=" CA GLY S 209 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 5408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.198: 1389 1.198 - 2.397: 0 2.397 - 3.595: 0 3.595 - 4.794: 0 4.794 - 5.992: 2 Chirality restraints: 1391 Sorted by residual: chirality pdb=" C7 4IE R 603 " pdb=" C2 4IE R 603 " pdb=" C6 4IE R 603 " pdb=" C8 4IE R 603 " both_signs ideal model delta sigma weight residual False -2.70 3.29 -5.99 2.00e-01 2.50e+01 8.98e+02 chirality pdb=" C3 4IE R 603 " pdb=" C2 4IE R 603 " pdb=" C4 4IE R 603 " pdb=" C8 4IE R 603 " both_signs ideal model delta sigma weight residual False 2.72 -3.20 5.92 2.00e-01 2.50e+01 8.76e+02 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.23e-01 ... (remaining 1388 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 285 " -0.013 2.00e-02 2.50e+03 2.77e-02 7.66e+00 pdb=" C ALA R 285 " 0.048 2.00e-02 2.50e+03 pdb=" O ALA R 285 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU R 286 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO S 75 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS R 272 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C HIS R 272 " 0.031 2.00e-02 2.50e+03 pdb=" O HIS R 272 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU R 273 " -0.011 2.00e-02 2.50e+03 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1367 2.76 - 3.29: 8092 3.29 - 3.83: 14329 3.83 - 4.36: 16943 4.36 - 4.90: 30422 Nonbonded interactions: 71153 Sorted by model distance: nonbonded pdb=" NE2 GLN R 209 " pdb=" NH2 ARG R 212 " model vdw 2.223 3.200 nonbonded pdb=" O ARG R 167 " pdb=" OG1 THR R 171 " model vdw 2.238 2.440 nonbonded pdb=" NE2 GLN R 158 " pdb=" NH2 ARG R 162 " model vdw 2.255 3.200 nonbonded pdb=" NZ LYS R 125 " pdb=" O PHE R 187 " model vdw 2.298 2.520 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.298 2.440 ... (remaining 71148 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.870 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 25.810 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.388 8967 Z= 0.466 Angle : 0.686 23.848 12161 Z= 0.346 Chirality : 0.230 5.992 1391 Planarity : 0.004 0.047 1523 Dihedral : 15.919 102.460 3322 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.53 % Allowed : 19.72 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.26), residues: 1101 helix: 1.94 (0.27), residues: 378 sheet: 0.30 (0.32), residues: 257 loop : -1.23 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS R 272 PHE 0.030 0.001 PHE R 207 TYR 0.019 0.001 TYR S 235 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 1.053 Fit side-chains REVERT: R 271 TYR cc_start: 0.8080 (t80) cc_final: 0.7786 (t80) outliers start: 5 outliers final: 5 residues processed: 120 average time/residue: 1.3235 time to fit residues: 168.9435 Evaluate side-chains 109 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 191 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 0.0670 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 294 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 8967 Z= 0.193 Angle : 0.690 21.545 12161 Z= 0.301 Chirality : 0.169 4.418 1391 Planarity : 0.003 0.045 1523 Dihedral : 7.299 118.023 1364 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.92 % Allowed : 18.77 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.26), residues: 1101 helix: 2.10 (0.27), residues: 379 sheet: 0.36 (0.32), residues: 256 loop : -1.20 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS R 272 PHE 0.010 0.001 PHE R 187 TYR 0.024 0.001 TYR S 235 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 120 time to evaluate : 1.058 Fit side-chains REVERT: A 186 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: A 305 CYS cc_start: 0.7625 (p) cc_final: 0.7154 (p) REVERT: G 21 MET cc_start: 0.8689 (mmm) cc_final: 0.7934 (tmt) REVERT: R 158 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7543 (tp40) REVERT: R 309 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7805 (ptm) REVERT: S 235 TYR cc_start: 0.7469 (OUTLIER) cc_final: 0.7032 (t80) outliers start: 37 outliers final: 16 residues processed: 137 average time/residue: 1.2343 time to fit residues: 180.3298 Evaluate side-chains 128 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 309 MET Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 99 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 33 optimal weight: 0.0670 chunk 79 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 209 GLN S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8967 Z= 0.182 Angle : 0.684 20.860 12161 Z= 0.298 Chirality : 0.169 4.355 1391 Planarity : 0.003 0.043 1523 Dihedral : 6.888 119.154 1354 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.50 % Allowed : 20.47 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.58 (0.26), residues: 1101 helix: 2.21 (0.27), residues: 379 sheet: 0.43 (0.32), residues: 250 loop : -1.20 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS R 272 PHE 0.009 0.001 PHE R 187 TYR 0.022 0.001 TYR S 235 ARG 0.007 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 118 time to evaluate : 0.979 Fit side-chains REVERT: A 186 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7530 (tm-30) REVERT: A 305 CYS cc_start: 0.7661 (p) cc_final: 0.7149 (p) REVERT: G 21 MET cc_start: 0.8672 (mmm) cc_final: 0.7912 (tmt) REVERT: G 22 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7493 (mt-10) REVERT: R 124 CYS cc_start: 0.6144 (OUTLIER) cc_final: 0.5811 (t) REVERT: R 158 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7475 (tp40) REVERT: R 254 MET cc_start: 0.8162 (mtp) cc_final: 0.7958 (mtm) REVERT: R 309 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7801 (ptm) REVERT: S 235 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.6961 (t80) outliers start: 33 outliers final: 14 residues processed: 135 average time/residue: 1.2726 time to fit residues: 182.7106 Evaluate side-chains 133 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 309 MET Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 0.0470 chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8967 Z= 0.216 Angle : 0.694 20.739 12161 Z= 0.306 Chirality : 0.169 4.343 1391 Planarity : 0.003 0.045 1523 Dihedral : 6.952 119.502 1352 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.35 % Allowed : 20.57 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.26), residues: 1101 helix: 2.20 (0.27), residues: 379 sheet: 0.43 (0.32), residues: 250 loop : -1.21 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 195 PHE 0.012 0.001 PHE A 189 TYR 0.024 0.001 TYR S 235 ARG 0.007 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 117 time to evaluate : 1.083 Fit side-chains REVERT: A 305 CYS cc_start: 0.7671 (p) cc_final: 0.7140 (p) REVERT: G 21 MET cc_start: 0.8681 (mmm) cc_final: 0.7927 (tmt) REVERT: G 22 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7472 (mt-10) REVERT: R 124 CYS cc_start: 0.6164 (OUTLIER) cc_final: 0.5884 (t) REVERT: R 158 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7524 (tp40) REVERT: R 254 MET cc_start: 0.8140 (mtp) cc_final: 0.7935 (mtm) REVERT: R 309 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7788 (ptm) REVERT: S 191 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8212 (mpt-90) REVERT: S 235 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.7027 (t80) outliers start: 41 outliers final: 17 residues processed: 138 average time/residue: 1.2108 time to fit residues: 178.3157 Evaluate side-chains 132 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 309 MET Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 294 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8967 Z= 0.209 Angle : 0.697 20.696 12161 Z= 0.306 Chirality : 0.168 4.328 1391 Planarity : 0.003 0.044 1523 Dihedral : 6.952 119.683 1352 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.09 % Allowed : 20.47 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.56 (0.26), residues: 1101 helix: 2.19 (0.27), residues: 379 sheet: 0.35 (0.31), residues: 257 loop : -1.19 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 195 PHE 0.011 0.001 PHE R 187 TYR 0.023 0.001 TYR S 235 ARG 0.004 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 114 time to evaluate : 0.973 Fit side-chains REVERT: A 33 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: A 305 CYS cc_start: 0.7678 (p) cc_final: 0.7123 (p) REVERT: B 234 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8927 (m-80) REVERT: G 21 MET cc_start: 0.8715 (mmm) cc_final: 0.7909 (tmt) REVERT: G 22 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7505 (mt-10) REVERT: R 124 CYS cc_start: 0.6148 (OUTLIER) cc_final: 0.5874 (t) REVERT: R 158 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7519 (tp40) REVERT: R 309 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7823 (ptm) REVERT: S 82 GLN cc_start: 0.8739 (tp40) cc_final: 0.8463 (tp40) REVERT: S 191 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7938 (mpt-90) REVERT: S 235 TYR cc_start: 0.7479 (OUTLIER) cc_final: 0.6974 (t80) outliers start: 48 outliers final: 19 residues processed: 143 average time/residue: 1.2405 time to fit residues: 189.7687 Evaluate side-chains 136 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 309 MET Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8967 Z= 0.175 Angle : 0.686 20.700 12161 Z= 0.299 Chirality : 0.168 4.309 1391 Planarity : 0.003 0.044 1523 Dihedral : 6.886 119.760 1352 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.92 % Allowed : 21.95 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.26), residues: 1101 helix: 2.30 (0.27), residues: 379 sheet: 0.39 (0.31), residues: 256 loop : -1.17 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 272 PHE 0.010 0.001 PHE R 187 TYR 0.020 0.001 TYR S 235 ARG 0.004 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 116 time to evaluate : 1.043 Fit side-chains REVERT: A 305 CYS cc_start: 0.7665 (p) cc_final: 0.7130 (p) REVERT: B 234 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8907 (m-80) REVERT: B 259 GLN cc_start: 0.7078 (mt0) cc_final: 0.6740 (mt0) REVERT: G 21 MET cc_start: 0.8744 (mmm) cc_final: 0.7893 (tmt) REVERT: G 22 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7473 (mt-10) REVERT: R 124 CYS cc_start: 0.6105 (OUTLIER) cc_final: 0.5805 (t) REVERT: R 158 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7517 (tp40) REVERT: R 309 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7855 (ptm) REVERT: S 235 TYR cc_start: 0.7349 (OUTLIER) cc_final: 0.6860 (t80) outliers start: 37 outliers final: 17 residues processed: 136 average time/residue: 1.2050 time to fit residues: 175.1283 Evaluate side-chains 136 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 309 MET Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 0.0570 chunk 105 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8967 Z= 0.195 Angle : 0.702 20.610 12161 Z= 0.305 Chirality : 0.168 4.304 1391 Planarity : 0.003 0.046 1523 Dihedral : 6.927 119.950 1352 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.03 % Allowed : 21.95 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.61 (0.26), residues: 1101 helix: 2.23 (0.27), residues: 380 sheet: 0.33 (0.31), residues: 262 loop : -1.15 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 195 PHE 0.011 0.001 PHE R 187 TYR 0.021 0.001 TYR S 235 ARG 0.004 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 112 time to evaluate : 0.986 Fit side-chains REVERT: B 234 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8852 (m-80) REVERT: G 21 MET cc_start: 0.8723 (mmm) cc_final: 0.7903 (tmt) REVERT: G 22 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: R 124 CYS cc_start: 0.6068 (OUTLIER) cc_final: 0.5773 (t) REVERT: R 158 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7528 (tp40) REVERT: R 254 MET cc_start: 0.8174 (mtp) cc_final: 0.7944 (mtm) REVERT: R 309 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7852 (ptm) REVERT: S 235 TYR cc_start: 0.7382 (OUTLIER) cc_final: 0.6873 (t80) outliers start: 38 outliers final: 23 residues processed: 135 average time/residue: 1.1933 time to fit residues: 171.8406 Evaluate side-chains 139 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 309 MET Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8967 Z= 0.212 Angle : 0.712 20.501 12161 Z= 0.311 Chirality : 0.168 4.305 1391 Planarity : 0.003 0.046 1523 Dihedral : 6.988 120.122 1352 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.14 % Allowed : 21.74 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.58 (0.26), residues: 1101 helix: 2.19 (0.27), residues: 380 sheet: 0.34 (0.31), residues: 262 loop : -1.18 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 195 PHE 0.012 0.001 PHE R 187 TYR 0.023 0.001 TYR S 235 ARG 0.004 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 113 time to evaluate : 1.093 Fit side-chains REVERT: B 234 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8869 (m-80) REVERT: G 21 MET cc_start: 0.8718 (mmm) cc_final: 0.7868 (tmt) REVERT: G 22 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: R 124 CYS cc_start: 0.6075 (OUTLIER) cc_final: 0.5781 (t) REVERT: R 158 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7515 (tp40) REVERT: R 254 MET cc_start: 0.8195 (mtp) cc_final: 0.7964 (mtm) REVERT: R 309 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7839 (ptm) REVERT: S 235 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.6926 (t80) outliers start: 39 outliers final: 23 residues processed: 140 average time/residue: 1.1910 time to fit residues: 177.9715 Evaluate side-chains 136 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 107 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 309 MET Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 103 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8967 Z= 0.202 Angle : 0.712 20.525 12161 Z= 0.310 Chirality : 0.168 4.301 1391 Planarity : 0.003 0.045 1523 Dihedral : 6.970 120.085 1352 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.29 % Allowed : 23.12 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.58 (0.26), residues: 1101 helix: 2.20 (0.27), residues: 380 sheet: 0.39 (0.31), residues: 256 loop : -1.20 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS R 272 PHE 0.011 0.001 PHE R 187 TYR 0.022 0.001 TYR S 235 ARG 0.004 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 111 time to evaluate : 1.097 Fit side-chains REVERT: B 234 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8861 (m-80) REVERT: G 21 MET cc_start: 0.8673 (mmm) cc_final: 0.7836 (tmt) REVERT: G 22 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7425 (mt-10) REVERT: R 124 CYS cc_start: 0.6061 (OUTLIER) cc_final: 0.5769 (t) REVERT: R 158 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7528 (tp40) REVERT: R 254 MET cc_start: 0.8188 (mtp) cc_final: 0.7950 (mtm) REVERT: R 309 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.7855 (ptm) REVERT: S 235 TYR cc_start: 0.7386 (OUTLIER) cc_final: 0.6865 (t80) outliers start: 31 outliers final: 22 residues processed: 129 average time/residue: 1.2646 time to fit residues: 173.8632 Evaluate side-chains 137 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain R residue 309 MET Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 86 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8967 Z= 0.178 Angle : 0.693 20.563 12161 Z= 0.303 Chirality : 0.168 4.293 1391 Planarity : 0.003 0.045 1523 Dihedral : 6.878 120.036 1352 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.29 % Allowed : 23.22 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.60 (0.26), residues: 1101 helix: 2.22 (0.27), residues: 380 sheet: 0.38 (0.31), residues: 256 loop : -1.18 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS R 272 PHE 0.010 0.001 PHE R 187 TYR 0.019 0.001 TYR S 235 ARG 0.002 0.000 ARG A 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 117 time to evaluate : 1.080 Fit side-chains REVERT: B 234 PHE cc_start: 0.9248 (OUTLIER) cc_final: 0.8817 (m-80) REVERT: B 259 GLN cc_start: 0.7086 (mt0) cc_final: 0.6763 (mt0) REVERT: G 21 MET cc_start: 0.8617 (mmm) cc_final: 0.7789 (tmt) REVERT: R 87 SER cc_start: 0.8190 (t) cc_final: 0.7934 (t) REVERT: R 124 CYS cc_start: 0.6047 (OUTLIER) cc_final: 0.5755 (t) REVERT: R 158 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7458 (tp40) REVERT: R 254 MET cc_start: 0.8152 (mtp) cc_final: 0.7922 (mtm) REVERT: R 281 MET cc_start: 0.4907 (ttt) cc_final: 0.4642 (ttp) REVERT: R 293 GLU cc_start: 0.8720 (tp30) cc_final: 0.8494 (tp30) REVERT: R 309 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7840 (ptm) REVERT: S 82 GLN cc_start: 0.8750 (tp40) cc_final: 0.8465 (tp40) REVERT: S 235 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.6819 (t80) outliers start: 31 outliers final: 23 residues processed: 136 average time/residue: 1.2036 time to fit residues: 174.9843 Evaluate side-chains 140 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain R residue 309 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.126930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.096091 restraints weight = 11750.034| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.94 r_work: 0.3033 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 8967 Z= 0.335 Angle : 0.775 20.251 12161 Z= 0.348 Chirality : 0.169 4.320 1391 Planarity : 0.004 0.048 1523 Dihedral : 7.317 120.316 1352 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.61 % Allowed : 23.22 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.25), residues: 1101 helix: 1.90 (0.27), residues: 381 sheet: 0.27 (0.32), residues: 259 loop : -1.20 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.006 0.001 HIS R 272 PHE 0.015 0.002 PHE R 187 TYR 0.029 0.002 TYR S 235 ARG 0.002 0.000 ARG R 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3545.33 seconds wall clock time: 64 minutes 5.97 seconds (3845.97 seconds total)