Starting phenix.real_space_refine on Fri Nov 15 08:04:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh0_39278/11_2024/8yh0_39278.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh0_39278/11_2024/8yh0_39278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh0_39278/11_2024/8yh0_39278.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh0_39278/11_2024/8yh0_39278.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh0_39278/11_2024/8yh0_39278.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh0_39278/11_2024/8yh0_39278.cif" } resolution = 2.86 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= -0.004 sd= 1.047 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 66 5.16 5 C 5561 2.51 5 N 1463 2.21 5 O 1603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8693 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2198 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1700 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 208} 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: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NEC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.46, per 1000 atoms: 0.63 Number of scatterers: 8693 At special positions: 0 Unit cell: (90.37, 123.936, 123.936, 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 66 16.00 O 1603 8.00 N 1463 7.00 C 5561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 83 " - pdb=" SG CYS R 165 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.09 Conformation dependent library (CDL) restraints added in 979.3 milliseconds 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2066 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 37.8% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'R' and resid 9 through 40 Processing helix chain 'R' and resid 41 through 44 Processing helix chain 'R' and resid 45 through 64 Processing helix chain 'R' and resid 64 through 75 Processing helix chain 'R' and resid 79 through 115 removed outlier: 3.534A pdb=" N CYS R 83 " --> pdb=" O HIS R 79 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR R 115 " --> pdb=" O ARG R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 122 Processing helix chain 'R' and resid 123 through 144 Processing helix chain 'R' and resid 145 through 148 Processing helix chain 'R' and resid 150 through 154 Processing helix chain 'R' and resid 166 through 171 removed outlier: 3.533A pdb=" N VAL R 170 " --> pdb=" O ARG R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 179 Processing helix chain 'R' and resid 179 through 185 Processing helix chain 'R' and resid 185 through 207 Processing helix chain 'R' and resid 225 through 254 Proline residue: R 244 - end of helix Processing helix chain 'R' and resid 259 through 282 removed outlier: 3.688A pdb=" N MET R 275 " --> pdb=" O HIS R 271 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 285 through 295 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.880A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.572A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.817A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 349 Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.705A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.847A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.025A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.955A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.910A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.635A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.138A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.815A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.028A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.409A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.472A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.278A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 130 removed outlier: 3.555A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.189A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1212 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: 2.69 Time building geometry restraints manager: 2.39 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: 1389 1.31 - 1.44: 2459 1.44 - 1.56: 4930 1.56 - 1.69: 0 1.69 - 1.82: 98 Bond restraints: 8876 Sorted by residual: bond pdb=" C5 NEC R 801 " pdb=" N7 NEC R 801 " ideal model delta sigma weight residual 1.370 1.524 -0.154 2.00e-02 2.50e+03 5.89e+01 bond pdb=" C6 NEC R 801 " pdb=" N6 NEC R 801 " ideal model delta sigma weight residual 1.334 1.451 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C5' NEC R 801 " pdb=" N5' NEC R 801 " ideal model delta sigma weight residual 1.335 1.451 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C8 NEC R 801 " pdb=" N9 NEC R 801 " ideal model delta sigma weight residual 1.370 1.254 0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C4 NEC R 801 " pdb=" C5 NEC R 801 " ideal model delta sigma weight residual 1.385 1.479 -0.094 2.00e-02 2.50e+03 2.22e+01 ... (remaining 8871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 11957 3.00 - 6.00: 49 6.00 - 9.00: 7 9.00 - 11.99: 7 11.99 - 14.99: 1 Bond angle restraints: 12021 Sorted by residual: angle pdb=" N PRO G 53 " pdb=" CA PRO G 53 " pdb=" C PRO G 53 " ideal model delta sigma weight residual 111.14 121.41 -10.27 1.56e+00 4.11e-01 4.34e+01 angle pdb=" C4 NEC R 801 " pdb=" N9 NEC R 801 " pdb=" C8 NEC R 801 " ideal model delta sigma weight residual 106.36 121.35 -14.99 3.00e+00 1.11e-01 2.50e+01 angle pdb=" N LYS A 349 " pdb=" CA LYS A 349 " pdb=" C LYS A 349 " ideal model delta sigma weight residual 113.19 108.87 4.32 1.19e+00 7.06e-01 1.32e+01 angle pdb=" N ILE R 185 " pdb=" CA ILE R 185 " pdb=" C ILE R 185 " ideal model delta sigma weight residual 111.62 108.77 2.85 7.90e-01 1.60e+00 1.30e+01 angle pdb=" N VAL R 121 " pdb=" CA VAL R 121 " pdb=" C VAL R 121 " ideal model delta sigma weight residual 112.96 109.38 3.58 1.00e+00 1.00e+00 1.28e+01 ... (remaining 12016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 4673 15.55 - 31.10: 478 31.10 - 46.65: 104 46.65 - 62.20: 14 62.20 - 77.75: 5 Dihedral angle restraints: 5274 sinusoidal: 2072 harmonic: 3202 Sorted by residual: dihedral pdb=" CA TYR S 178 " pdb=" C TYR S 178 " pdb=" N ARG S 179 " pdb=" CA ARG S 179 " ideal model delta harmonic sigma weight residual 180.00 155.88 24.12 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 132.98 -39.98 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CA PHE A 267 " pdb=" C PHE A 267 " pdb=" N LEU A 268 " pdb=" CA LEU A 268 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 5271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.339: 1374 0.339 - 0.679: 1 0.679 - 1.018: 0 1.018 - 1.357: 0 1.357 - 1.697: 1 Chirality restraints: 1376 Sorted by residual: chirality pdb=" CG LEU A 227 " pdb=" CB LEU A 227 " pdb=" CD1 LEU A 227 " pdb=" CD2 LEU A 227 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.20e+01 chirality pdb=" CA PRO G 53 " pdb=" N PRO G 53 " pdb=" C PRO G 53 " pdb=" CB PRO G 53 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" C2' NEC R 801 " pdb=" C1' NEC R 801 " pdb=" C3' NEC R 801 " pdb=" O2' NEC R 801 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1373 not shown) Planarity restraints: 1499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 258 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO R 259 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO R 259 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 259 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 277 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO R 278 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO R 278 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 278 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 14 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C LEU B 14 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU B 14 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS B 15 " 0.011 2.00e-02 2.50e+03 ... (remaining 1496 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 122 2.64 - 3.20: 8071 3.20 - 3.77: 13311 3.77 - 4.33: 19282 4.33 - 4.90: 31789 Nonbonded interactions: 72575 Sorted by model distance: nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.070 3.040 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.085 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.098 3.040 nonbonded pdb=" OE2 GLU A 14 " pdb=" OG1 THR S 57 " model vdw 2.103 3.040 nonbonded pdb=" OE1 GLN S 130 " pdb=" OG1 THR S 231 " model vdw 2.121 3.040 ... (remaining 72570 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.250 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.140 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 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 : 0.004 0.154 8876 Z= 0.289 Angle : 0.656 14.994 12021 Z= 0.361 Chirality : 0.063 1.697 1376 Planarity : 0.004 0.050 1499 Dihedral : 13.132 77.755 3199 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1085 helix: 1.45 (0.28), residues: 363 sheet: -0.82 (0.29), residues: 293 loop : -0.57 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.018 0.001 PHE B 234 TYR 0.012 0.001 TYR S 178 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 LEU cc_start: 0.8608 (mt) cc_final: 0.8191 (mt) outliers start: 0 outliers final: 1 residues processed: 226 average time/residue: 1.3958 time to fit residues: 333.7289 Evaluate side-chains 130 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 0.0770 chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 30 ASN R 79 HIS ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS A 255 ASN A 294 ASN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 295 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 8876 Z= 0.323 Angle : 0.734 11.181 12021 Z= 0.375 Chirality : 0.046 0.233 1376 Planarity : 0.005 0.069 1499 Dihedral : 5.088 51.720 1219 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.41 % Favored : 96.50 % Rotamer: Outliers : 3.15 % Allowed : 12.80 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.00 (0.26), residues: 1085 helix: 1.38 (0.27), residues: 370 sheet: -0.66 (0.29), residues: 297 loop : -0.63 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 184 HIS 0.007 0.001 HIS A 322 PHE 0.017 0.002 PHE B 199 TYR 0.017 0.002 TYR A 302 ARG 0.007 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 336 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7771 (mp) outliers start: 30 outliers final: 12 residues processed: 166 average time/residue: 1.3247 time to fit residues: 233.1046 Evaluate side-chains 125 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 146 MET Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 57 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.0370 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 322 HIS B 155 ASN B 266 HIS S 130 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8876 Z= 0.196 Angle : 0.668 12.884 12021 Z= 0.341 Chirality : 0.044 0.250 1376 Planarity : 0.004 0.049 1499 Dihedral : 4.728 51.236 1219 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.59 % Rotamer: Outliers : 3.46 % Allowed : 16.89 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.20 (0.27), residues: 1085 helix: 1.46 (0.28), residues: 378 sheet: -0.34 (0.30), residues: 284 loop : -0.65 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 184 HIS 0.003 0.001 HIS A 322 PHE 0.014 0.001 PHE B 253 TYR 0.015 0.001 TYR A 287 ARG 0.007 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 243 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7503 (mt) REVERT: B 217 MET cc_start: 0.6106 (OUTLIER) cc_final: 0.5702 (pp-130) outliers start: 33 outliers final: 14 residues processed: 158 average time/residue: 1.2349 time to fit residues: 207.8001 Evaluate side-chains 124 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 145 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 105 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 204 GLN S 39 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 8876 Z= 0.293 Angle : 0.692 13.221 12021 Z= 0.351 Chirality : 0.045 0.239 1376 Planarity : 0.005 0.054 1499 Dihedral : 4.753 49.732 1219 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.31 % Rotamer: Outliers : 3.57 % Allowed : 19.73 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.27), residues: 1085 helix: 1.64 (0.28), residues: 366 sheet: -0.38 (0.30), residues: 289 loop : -0.68 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP R 184 HIS 0.004 0.001 HIS B 225 PHE 0.014 0.002 PHE B 199 TYR 0.024 0.002 TYR A 302 ARG 0.007 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 LEU cc_start: 0.8713 (mt) cc_final: 0.8464 (mt) REVERT: B 217 MET cc_start: 0.6218 (OUTLIER) cc_final: 0.5810 (pp-130) outliers start: 34 outliers final: 18 residues processed: 150 average time/residue: 1.2990 time to fit residues: 207.3420 Evaluate side-chains 129 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 0 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8876 Z= 0.257 Angle : 0.690 12.247 12021 Z= 0.349 Chirality : 0.044 0.215 1376 Planarity : 0.005 0.072 1499 Dihedral : 4.470 20.640 1217 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.59 % Rotamer: Outliers : 3.78 % Allowed : 19.41 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.19 (0.26), residues: 1085 helix: 1.63 (0.28), residues: 365 sheet: -0.36 (0.30), residues: 288 loop : -0.77 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP R 184 HIS 0.005 0.001 HIS B 225 PHE 0.014 0.001 PHE B 199 TYR 0.023 0.001 TYR A 302 ARG 0.007 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 146 MET cc_start: 0.6682 (OUTLIER) cc_final: 0.6219 (mmm) REVERT: R 243 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7593 (mt) REVERT: A 255 ASN cc_start: 0.5076 (m-40) cc_final: 0.4763 (m-40) REVERT: B 211 TRP cc_start: 0.5629 (OUTLIER) cc_final: 0.3781 (m-10) REVERT: B 217 MET cc_start: 0.6258 (OUTLIER) cc_final: 0.5796 (pp-130) outliers start: 36 outliers final: 17 residues processed: 142 average time/residue: 1.3073 time to fit residues: 198.2272 Evaluate side-chains 130 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 146 MET Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 244 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8876 Z= 0.211 Angle : 0.692 12.807 12021 Z= 0.345 Chirality : 0.044 0.185 1376 Planarity : 0.004 0.052 1499 Dihedral : 4.334 20.456 1217 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.59 % Rotamer: Outliers : 3.15 % Allowed : 21.09 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.19 (0.26), residues: 1085 helix: 1.54 (0.28), residues: 376 sheet: -0.33 (0.30), residues: 284 loop : -0.75 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP R 184 HIS 0.005 0.001 HIS B 225 PHE 0.013 0.001 PHE B 253 TYR 0.033 0.001 TYR A 302 ARG 0.007 0.001 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 192 MET cc_start: 0.6807 (mtm) cc_final: 0.6573 (mtp) REVERT: R 243 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7580 (mt) REVERT: A 255 ASN cc_start: 0.4961 (m-40) cc_final: 0.4620 (m-40) REVERT: B 211 TRP cc_start: 0.5532 (OUTLIER) cc_final: 0.3738 (m-10) REVERT: B 217 MET cc_start: 0.6221 (OUTLIER) cc_final: 0.5744 (pp-130) outliers start: 30 outliers final: 14 residues processed: 146 average time/residue: 1.2652 time to fit residues: 196.9843 Evaluate side-chains 128 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 244 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8876 Z= 0.213 Angle : 0.725 13.606 12021 Z= 0.358 Chirality : 0.044 0.206 1376 Planarity : 0.004 0.053 1499 Dihedral : 4.338 20.070 1217 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 3.46 % Allowed : 22.46 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.22 (0.26), residues: 1085 helix: 1.62 (0.28), residues: 370 sheet: -0.33 (0.31), residues: 282 loop : -0.75 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP R 184 HIS 0.004 0.001 HIS B 225 PHE 0.013 0.001 PHE B 253 TYR 0.020 0.001 TYR A 302 ARG 0.008 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 243 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7555 (mt) REVERT: A 255 ASN cc_start: 0.4969 (m-40) cc_final: 0.4654 (m-40) REVERT: B 211 TRP cc_start: 0.5511 (OUTLIER) cc_final: 0.3736 (m-10) REVERT: B 217 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.5713 (pp-130) outliers start: 33 outliers final: 12 residues processed: 151 average time/residue: 1.3131 time to fit residues: 210.5843 Evaluate side-chains 131 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 235 LEU 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: 7.9990 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8876 Z= 0.266 Angle : 0.773 14.457 12021 Z= 0.385 Chirality : 0.046 0.296 1376 Planarity : 0.004 0.050 1499 Dihedral : 4.378 20.215 1217 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.13 % Rotamer: Outliers : 2.83 % Allowed : 24.13 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1085 helix: 1.57 (0.28), residues: 370 sheet: -0.37 (0.31), residues: 282 loop : -0.77 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP R 184 HIS 0.013 0.001 HIS B 225 PHE 0.013 0.001 PHE B 199 TYR 0.018 0.001 TYR A 302 ARG 0.009 0.001 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 192 MET cc_start: 0.6868 (mtm) cc_final: 0.6615 (mtp) REVERT: R 243 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7627 (mt) REVERT: B 211 TRP cc_start: 0.5601 (OUTLIER) cc_final: 0.3782 (m-10) REVERT: B 217 MET cc_start: 0.6307 (OUTLIER) cc_final: 0.5800 (pp-130) outliers start: 27 outliers final: 12 residues processed: 143 average time/residue: 1.3785 time to fit residues: 208.9376 Evaluate side-chains 127 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 92 optimal weight: 0.0770 chunk 64 optimal weight: 6.9990 chunk 103 optimal weight: 0.2980 chunk 63 optimal weight: 0.6980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 244 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8876 Z= 0.227 Angle : 0.797 14.491 12021 Z= 0.396 Chirality : 0.045 0.204 1376 Planarity : 0.005 0.064 1499 Dihedral : 4.312 21.384 1217 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.13 % Rotamer: Outliers : 2.10 % Allowed : 25.92 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.15 (0.26), residues: 1085 helix: 1.60 (0.28), residues: 372 sheet: -0.32 (0.31), residues: 282 loop : -0.89 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP R 184 HIS 0.009 0.001 HIS B 225 PHE 0.027 0.001 PHE R 48 TYR 0.013 0.001 TYR S 178 ARG 0.012 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 192 MET cc_start: 0.6779 (mtm) cc_final: 0.6501 (mtp) REVERT: R 243 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7538 (mt) REVERT: B 211 TRP cc_start: 0.5483 (OUTLIER) cc_final: 0.3710 (m-10) REVERT: B 217 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.5548 (pp-130) outliers start: 20 outliers final: 12 residues processed: 136 average time/residue: 1.2973 time to fit residues: 187.7860 Evaluate side-chains 131 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 0.1980 chunk 99 optimal weight: 20.0000 chunk 86 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 271 HIS A 22 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8876 Z= 0.220 Angle : 0.809 14.861 12021 Z= 0.402 Chirality : 0.047 0.370 1376 Planarity : 0.005 0.049 1499 Dihedral : 4.277 25.402 1217 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.31 % Rotamer: Outliers : 1.89 % Allowed : 27.07 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1085 helix: 1.45 (0.28), residues: 379 sheet: -0.35 (0.30), residues: 284 loop : -1.01 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP R 184 HIS 0.007 0.001 HIS B 225 PHE 0.021 0.001 PHE R 48 TYR 0.027 0.001 TYR B 59 ARG 0.010 0.001 ARG S 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 173 MET cc_start: 0.7190 (mmm) cc_final: 0.6915 (mmp) REVERT: R 192 MET cc_start: 0.6756 (mtm) cc_final: 0.6473 (mtp) REVERT: R 243 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7493 (mt) REVERT: B 211 TRP cc_start: 0.5454 (OUTLIER) cc_final: 0.3730 (m-10) REVERT: B 217 MET cc_start: 0.6030 (OUTLIER) cc_final: 0.5520 (pp-130) outliers start: 18 outliers final: 10 residues processed: 137 average time/residue: 1.2896 time to fit residues: 188.0643 Evaluate side-chains 128 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 244 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.107482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.084712 restraints weight = 20857.211| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.47 r_work: 0.3414 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8876 Z= 0.232 Angle : 0.826 17.048 12021 Z= 0.409 Chirality : 0.047 0.483 1376 Planarity : 0.005 0.071 1499 Dihedral : 4.215 21.232 1217 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.94 % Rotamer: Outliers : 1.99 % Allowed : 27.07 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.26), residues: 1085 helix: 1.40 (0.28), residues: 379 sheet: -0.34 (0.30), residues: 284 loop : -0.99 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP R 184 HIS 0.008 0.001 HIS B 225 PHE 0.024 0.001 PHE R 48 TYR 0.021 0.001 TYR B 59 ARG 0.010 0.001 ARG S 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3908.98 seconds wall clock time: 70 minutes 55.53 seconds (4255.53 seconds total)