Starting phenix.real_space_refine on Thu Jul 2 07:34:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yub_34103/07_2026/7yub_34103_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yub_34103/07_2026/7yub_34103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yub_34103/07_2026/7yub_34103_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yub_34103/07_2026/7yub_34103_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yub_34103/07_2026/7yub_34103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yub_34103/07_2026/7yub_34103.map" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.140 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 37 5.16 5 C 4873 2.51 5 N 1271 2.21 5 O 1428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7610 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1732 Classifications: {'peptide': 229} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 217} Chain: "L" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1619 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain: "N" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 959 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "R" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3275 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 13, 'TRANS': 415} Chain breaks: 2 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'S1P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.65, per 1000 atoms: 0.22 Number of scatterers: 7610 At special positions: 0 Unit cell: (78.1, 88, 154, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 P 1 15.00 O 1428 8.00 N 1271 7.00 C 4873 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 26 " - pdb=" SG CYS H 100 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 215 " distance=2.03 Simple disulfide: pdb=" SG CYS L 25 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 97 " distance=2.03 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: 0.47 Conformation dependent library (CDL) restraints added in 328.7 milliseconds 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1816 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 42.1% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'H' and resid 32 through 35 removed outlier: 3.551A pdb=" N TYR H 35 " --> pdb=" O ASN H 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 32 through 35' Processing helix chain 'H' and resid 91 through 95 removed outlier: 3.903A pdb=" N THR H 95 " --> pdb=" O ALA H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 111 removed outlier: 4.040A pdb=" N HIS H 110 " --> pdb=" O TYR H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'L' and resid 123 through 129 removed outlier: 3.800A pdb=" N SER L 129 " --> pdb=" O SER L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 190 Processing helix chain 'N' and resid 88 through 92 removed outlier: 3.885A pdb=" N THR N 92 " --> pdb=" O PRO N 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 118 removed outlier: 5.547A pdb=" N ARG R 99 " --> pdb=" O ALA R 95 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLY R 102 " --> pdb=" O GLY R 98 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 125 removed outlier: 3.583A pdb=" N GLY R 124 " --> pdb=" O TYR R 120 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL R 125 " --> pdb=" O THR R 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 120 through 125' Processing helix chain 'R' and resid 125 through 134 Processing helix chain 'R' and resid 138 through 140 No H-bonds generated for 'chain 'R' and resid 138 through 140' Processing helix chain 'R' and resid 141 through 162 removed outlier: 3.575A pdb=" N SER R 145 " --> pdb=" O GLY R 141 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE R 147 " --> pdb=" O LEU R 143 " (cutoff:3.500A) Proline residue: R 156 - end of helix Processing helix chain 'R' and resid 166 through 185 removed outlier: 3.691A pdb=" N ILE R 170 " --> pdb=" O ASN R 166 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL R 181 " --> pdb=" O PHE R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 188 No H-bonds generated for 'chain 'R' and resid 186 through 188' Processing helix chain 'R' and resid 192 through 221 removed outlier: 3.959A pdb=" N LEU R 196 " --> pdb=" O TYR R 192 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER R 209 " --> pdb=" O ILE R 205 " (cutoff:3.500A) Proline residue: R 215 - end of helix Processing helix chain 'R' and resid 226 through 236 Processing helix chain 'R' and resid 237 through 257 removed outlier: 3.867A pdb=" N TYR R 246 " --> pdb=" O SER R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 264 Processing helix chain 'R' and resid 265 through 281 removed outlier: 3.946A pdb=" N LEU R 269 " --> pdb=" O VAL R 265 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE R 272 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR R 275 " --> pdb=" O MET R 271 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU R 278 " --> pdb=" O GLY R 274 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE R 279 " --> pdb=" O THR R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 310 Processing helix chain 'R' and resid 312 through 347 Proline residue: R 337 - end of helix Processing helix chain 'R' and resid 361 through 389 removed outlier: 3.814A pdb=" N PHE R 372 " --> pdb=" O ALA R 368 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE R 375 " --> pdb=" O CYS R 371 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL R 378 " --> pdb=" O GLY R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 394 through 413 removed outlier: 3.695A pdb=" N LEU R 398 " --> pdb=" O ARG R 394 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE R 409 " --> pdb=" O LEU R 405 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE R 410 " --> pdb=" O GLY R 406 " (cutoff:3.500A) Processing helix chain 'R' and resid 413 through 418 Processing helix chain 'R' and resid 421 through 437 removed outlier: 4.033A pdb=" N ALA R 425 " --> pdb=" O SER R 421 " (cutoff:3.500A) Processing helix chain 'R' and resid 442 through 450 removed outlier: 3.781A pdb=" N VAL R 450 " --> pdb=" O ILE R 446 " (cutoff:3.500A) Processing helix chain 'R' and resid 452 through 454 No H-bonds generated for 'chain 'R' and resid 452 through 454' Processing helix chain 'R' and resid 455 through 470 removed outlier: 3.595A pdb=" N ALA R 461 " --> pdb=" O ALA R 457 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN R 463 " --> pdb=" O ALA R 459 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE R 465 " --> pdb=" O ALA R 461 " (cutoff:3.500A) Processing helix chain 'R' and resid 474 through 488 Processing helix chain 'R' and resid 493 through 505 Processing helix chain 'R' and resid 506 through 541 removed outlier: 4.479A pdb=" N PHE R 510 " --> pdb=" O MET R 506 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE R 525 " --> pdb=" O ALA R 521 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N VAL R 527 " --> pdb=" O ALA R 523 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER R 528 " --> pdb=" O LEU R 524 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 7 through 11 removed outlier: 3.675A pdb=" N ALA H 83 " --> pdb=" O CYS H 26 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR H 82 " --> pdb=" O ASP H 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 16 removed outlier: 3.534A pdb=" N ALA H 96 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE H 38 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYR H 54 " --> pdb=" O ILE H 38 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TRP H 40 " --> pdb=" O VAL H 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 139 through 140 removed outlier: 6.044A pdb=" N TYR H 195 " --> pdb=" O ASP H 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 139 through 140 removed outlier: 6.044A pdb=" N TYR H 195 " --> pdb=" O ASP H 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 170 through 173 removed outlier: 3.918A pdb=" N TYR H 213 " --> pdb=" O VAL H 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 7 through 9 removed outlier: 3.598A pdb=" N THR L 7 " --> pdb=" O ARG L 26 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR L 24 " --> pdb=" O SER L 9 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 12 through 14 Processing sheet with id=AA8, first strand: chain 'L' and resid 55 through 56 removed outlier: 6.850A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 116 through 120 removed outlier: 3.691A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER L 178 " --> pdb=" O SER L 164 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER L 164 " --> pdb=" O SER L 178 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 155 through 156 removed outlier: 3.538A pdb=" N VAL L 198 " --> pdb=" O VAL L 207 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL L 207 " --> pdb=" O VAL L 198 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AB3, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.515A pdb=" N TYR N 95 " --> pdb=" O THR N 122 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP N 37 " --> pdb=" O VAL N 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.515A pdb=" N TYR N 95 " --> pdb=" O THR N 122 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1146 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: 0.90 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2382 1.34 - 1.46: 1906 1.46 - 1.58: 3445 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 7787 Sorted by residual: bond pdb=" O1 S1P R 601 " pdb=" P22 S1P R 601 " ideal model delta sigma weight residual 1.677 1.816 -0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" C1 S1P R 601 " pdb=" O1 S1P R 601 " ideal model delta sigma weight residual 1.421 1.342 0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" N ILE R 175 " pdb=" CA ILE R 175 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.69e+00 bond pdb=" N TYR H 104 " pdb=" CA TYR H 104 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.42e-02 4.96e+03 7.05e+00 bond pdb=" C3 S1P R 601 " pdb=" O3 S1P R 601 " ideal model delta sigma weight residual 1.445 1.394 0.051 2.00e-02 2.50e+03 6.48e+00 ... (remaining 7782 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 10325 2.17 - 4.35: 217 4.35 - 6.52: 30 6.52 - 8.69: 4 8.69 - 10.87: 1 Bond angle restraints: 10577 Sorted by residual: angle pdb=" C TYR H 114 " pdb=" N TRP H 115 " pdb=" CA TRP H 115 " ideal model delta sigma weight residual 122.17 115.00 7.17 1.54e+00 4.22e-01 2.17e+01 angle pdb=" N THR N 34 " pdb=" CA THR N 34 " pdb=" C THR N 34 " ideal model delta sigma weight residual 112.03 117.86 -5.83 1.31e+00 5.83e-01 1.98e+01 angle pdb=" C THR H 184 " pdb=" N PHE H 185 " pdb=" CA PHE H 185 " ideal model delta sigma weight residual 120.68 127.41 -6.73 1.52e+00 4.33e-01 1.96e+01 angle pdb=" N SER L 32 " pdb=" CA SER L 32 " pdb=" CB SER L 32 " ideal model delta sigma weight residual 114.17 109.35 4.82 1.14e+00 7.69e-01 1.79e+01 angle pdb=" N SER L 94 " pdb=" CA SER L 94 " pdb=" C SER L 94 " ideal model delta sigma weight residual 111.71 116.13 -4.42 1.15e+00 7.56e-01 1.48e+01 ... (remaining 10572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.36: 4419 27.36 - 54.71: 130 54.71 - 82.07: 15 82.07 - 109.42: 6 109.42 - 136.78: 3 Dihedral angle restraints: 4573 sinusoidal: 1719 harmonic: 2854 Sorted by residual: dihedral pdb=" N2 S1P R 601 " pdb=" C1 S1P R 601 " pdb=" C2 S1P R 601 " pdb=" O1 S1P R 601 " ideal model delta sinusoidal sigma weight residual -73.93 62.85 -136.78 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" C3 S1P R 601 " pdb=" C1 S1P R 601 " pdb=" C2 S1P R 601 " pdb=" O1 S1P R 601 " ideal model delta sinusoidal sigma weight residual 52.36 -174.56 -133.08 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" C2 S1P R 601 " pdb=" C1 S1P R 601 " pdb=" O1 S1P R 601 " pdb=" P22 S1P R 601 " ideal model delta sinusoidal sigma weight residual 262.13 138.86 123.27 1 3.00e+01 1.11e-03 1.65e+01 ... (remaining 4570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1010 0.058 - 0.117: 156 0.117 - 0.175: 25 0.175 - 0.234: 7 0.234 - 0.292: 1 Chirality restraints: 1199 Sorted by residual: chirality pdb=" CA SER H 112 " pdb=" N SER H 112 " pdb=" C SER H 112 " pdb=" CB SER H 112 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA PHE R 236 " pdb=" N PHE R 236 " pdb=" C PHE R 236 " pdb=" CB PHE R 236 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C2 S1P R 601 " pdb=" C1 S1P R 601 " pdb=" C3 S1P R 601 " pdb=" N2 S1P R 601 " both_signs ideal model delta sigma weight residual False -2.43 -2.64 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1196 not shown) Planarity restraints: 1325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA R 214 " 0.054 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO R 215 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO R 215 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 215 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA N 41 " 0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO N 42 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO N 42 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO N 42 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 526 " 0.019 2.00e-02 2.50e+03 1.47e-02 3.76e+00 pdb=" CG PHE R 526 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE R 526 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE R 526 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 526 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 526 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE R 526 " 0.006 2.00e-02 2.50e+03 ... (remaining 1322 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 107 2.68 - 3.24: 6845 3.24 - 3.79: 10645 3.79 - 4.35: 14265 4.35 - 4.90: 24925 Nonbonded interactions: 56787 Sorted by model distance: nonbonded pdb=" O TRP H 113 " pdb=" OG SER L 33 " model vdw 2.127 3.040 nonbonded pdb=" OH TYR R 116 " pdb=" O3 S1P R 601 " model vdw 2.199 3.040 nonbonded pdb=" OG SER R 314 " pdb=" OD2 ASP R 529 " model vdw 2.295 3.040 nonbonded pdb=" O TRP R 496 " pdb=" OG SER R 500 " model vdw 2.339 3.040 nonbonded pdb=" O PHE R 236 " pdb=" CG PHE R 236 " model vdw 2.371 3.260 ... (remaining 56782 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.720 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 0.139 7792 Z= 0.235 Angle : 0.762 10.865 10587 Z= 0.448 Chirality : 0.047 0.292 1199 Planarity : 0.005 0.080 1325 Dihedral : 13.922 136.780 2742 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.27), residues: 985 helix: 0.49 (0.28), residues: 376 sheet: 0.76 (0.35), residues: 225 loop : -1.30 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 530 TYR 0.017 0.001 TYR H 54 PHE 0.033 0.002 PHE R 526 TRP 0.027 0.002 TRP R 496 HIS 0.007 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.24 ( 7787) covalent geometry : angle 0.76227 / 0.45 (10577) SS BOND : bond 0.00274 / 0.14 ( 5) SS BOND : angle 0.96070 / 0.57 ( 10) hydrogen bonds : bond 0.19515 / 13.31 ( 401) hydrogen bonds : angle 6.83745 / 4.59 ( 1146) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.276 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1109 time to fit residues: 11.8245 Evaluate side-chains 70 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 92 GLN N 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.195240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.141950 restraints weight = 8179.834| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.97 r_work: 0.3167 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7792 Z= 0.136 Angle : 0.579 7.381 10587 Z= 0.309 Chirality : 0.043 0.159 1199 Planarity : 0.005 0.050 1325 Dihedral : 9.940 124.157 1107 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.85 % Allowed : 4.50 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.28), residues: 985 helix: 1.15 (0.29), residues: 373 sheet: 0.95 (0.35), residues: 233 loop : -1.00 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 164 TYR 0.014 0.001 TYR N 32 PHE 0.024 0.002 PHE R 236 TRP 0.023 0.002 TRP H 113 HIS 0.006 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 7787) covalent geometry : angle 0.57856 / 0.31 (10577) SS BOND : bond 0.00375 / 0.19 ( 5) SS BOND : angle 0.99147 / 0.56 ( 10) hydrogen bonds : bond 0.05945 / 3.99 ( 401) hydrogen bonds : angle 4.95351 / 3.36 ( 1146) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.280 Fit side-chains REVERT: H 104 TYR cc_start: 0.8949 (OUTLIER) cc_final: 0.8714 (m-80) REVERT: R 164 ARG cc_start: 0.6768 (mmt90) cc_final: 0.6445 (mmt90) REVERT: R 306 MET cc_start: 0.6859 (mmt) cc_final: 0.6652 (mmm) outliers start: 7 outliers final: 5 residues processed: 80 average time/residue: 0.1101 time to fit residues: 11.6282 Evaluate side-chains 79 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 45 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 14 optimal weight: 30.0000 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 105 GLN L 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.192596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.138887 restraints weight = 8248.230| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.30 r_work: 0.3102 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7792 Z= 0.159 Angle : 0.591 8.067 10587 Z= 0.315 Chirality : 0.043 0.178 1199 Planarity : 0.005 0.046 1325 Dihedral : 9.319 111.010 1107 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.58 % Allowed : 6.45 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.28), residues: 985 helix: 1.38 (0.29), residues: 374 sheet: 1.25 (0.35), residues: 221 loop : -0.95 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 46 TYR 0.015 0.002 TYR N 32 PHE 0.018 0.002 PHE R 526 TRP 0.028 0.002 TRP R 178 HIS 0.008 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 7787) covalent geometry : angle 0.59054 / 0.32 (10577) SS BOND : bond 0.00295 / 0.15 ( 5) SS BOND : angle 0.81573 / 0.45 ( 10) hydrogen bonds : bond 0.06295 / 4.19 ( 401) hydrogen bonds : angle 4.67624 / 3.18 ( 1146) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.331 Fit side-chains REVERT: H 54 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.7493 (t80) REVERT: L 84 ASP cc_start: 0.6640 (m-30) cc_final: 0.6397 (m-30) REVERT: N 107 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.5825 (tpt) REVERT: R 164 ARG cc_start: 0.6770 (mmt90) cc_final: 0.6420 (mmt90) outliers start: 13 outliers final: 8 residues processed: 81 average time/residue: 0.1081 time to fit residues: 11.6744 Evaluate side-chains 81 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 71 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 30.0000 chunk 26 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.193098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.139845 restraints weight = 8310.739| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.07 r_work: 0.3134 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7792 Z= 0.147 Angle : 0.570 7.738 10587 Z= 0.302 Chirality : 0.042 0.179 1199 Planarity : 0.004 0.043 1325 Dihedral : 8.918 108.769 1107 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.82 % Allowed : 7.18 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.28), residues: 985 helix: 1.67 (0.29), residues: 367 sheet: 1.29 (0.35), residues: 226 loop : -0.81 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 46 TYR 0.016 0.001 TYR N 32 PHE 0.027 0.002 PHE R 236 TRP 0.028 0.002 TRP R 178 HIS 0.007 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 7787) covalent geometry : angle 0.56991 / 0.30 (10577) SS BOND : bond 0.00285 / 0.15 ( 5) SS BOND : angle 0.71801 / 0.39 ( 10) hydrogen bonds : bond 0.05884 / 3.92 ( 401) hydrogen bonds : angle 4.47080 / 3.04 ( 1146) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.260 Fit side-chains REVERT: H 16 VAL cc_start: 0.7687 (t) cc_final: 0.7446 (m) REVERT: H 54 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.7460 (t80) REVERT: R 164 ARG cc_start: 0.6705 (mmt90) cc_final: 0.6350 (mmt90) outliers start: 15 outliers final: 12 residues processed: 82 average time/residue: 0.0995 time to fit residues: 10.9989 Evaluate side-chains 86 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain R residue 236 PHE Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.190970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.135332 restraints weight = 8224.390| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.86 r_work: 0.3170 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7792 Z= 0.150 Angle : 0.567 7.861 10587 Z= 0.301 Chirality : 0.042 0.183 1199 Planarity : 0.004 0.042 1325 Dihedral : 8.570 106.768 1107 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.82 % Allowed : 8.39 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.28), residues: 985 helix: 1.75 (0.29), residues: 367 sheet: 1.33 (0.35), residues: 221 loop : -0.76 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 46 TYR 0.016 0.001 TYR N 32 PHE 0.029 0.002 PHE R 236 TRP 0.029 0.002 TRP R 178 HIS 0.006 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 7787) covalent geometry : angle 0.56701 / 0.30 (10577) SS BOND : bond 0.00292 / 0.15 ( 5) SS BOND : angle 0.69152 / 0.38 ( 10) hydrogen bonds : bond 0.05929 / 3.94 ( 401) hydrogen bonds : angle 4.39035 / 2.99 ( 1146) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.301 Fit side-chains REVERT: H 16 VAL cc_start: 0.7650 (t) cc_final: 0.7443 (m) REVERT: H 54 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.7578 (t80) REVERT: N 107 MET cc_start: 0.6733 (OUTLIER) cc_final: 0.5561 (tpp) outliers start: 15 outliers final: 12 residues processed: 84 average time/residue: 0.0930 time to fit residues: 10.7086 Evaluate side-chains 89 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 21 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 0.0670 chunk 76 optimal weight: 0.6980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.192516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.136605 restraints weight = 8208.825| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.78 r_work: 0.3160 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7792 Z= 0.132 Angle : 0.540 7.715 10587 Z= 0.286 Chirality : 0.042 0.174 1199 Planarity : 0.004 0.039 1325 Dihedral : 8.328 104.993 1107 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.19 % Allowed : 8.52 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.28), residues: 985 helix: 1.88 (0.29), residues: 367 sheet: 1.27 (0.35), residues: 226 loop : -0.70 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 46 TYR 0.015 0.001 TYR N 32 PHE 0.022 0.001 PHE R 236 TRP 0.030 0.001 TRP R 178 HIS 0.006 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 7787) covalent geometry : angle 0.53997 / 0.29 (10577) SS BOND : bond 0.00278 / 0.14 ( 5) SS BOND : angle 0.62707 / 0.35 ( 10) hydrogen bonds : bond 0.05419 / 3.61 ( 401) hydrogen bonds : angle 4.26728 / 2.91 ( 1146) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.283 Fit side-chains REVERT: H 54 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.7533 (t80) REVERT: N 107 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.5530 (tpp) REVERT: R 334 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6326 (ttt) outliers start: 18 outliers final: 13 residues processed: 79 average time/residue: 0.0930 time to fit residues: 10.0506 Evaluate side-chains 82 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain R residue 236 PHE Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 334 MET Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 5 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 6 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.190342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.134130 restraints weight = 8245.031| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.85 r_work: 0.3117 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7792 Z= 0.164 Angle : 0.580 7.994 10587 Z= 0.306 Chirality : 0.043 0.189 1199 Planarity : 0.004 0.041 1325 Dihedral : 7.214 100.299 1107 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.07 % Allowed : 9.37 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.28), residues: 985 helix: 1.78 (0.29), residues: 367 sheet: 1.20 (0.35), residues: 227 loop : -0.76 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 46 TYR 0.018 0.002 TYR N 32 PHE 0.022 0.002 PHE R 236 TRP 0.029 0.002 TRP R 178 HIS 0.006 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 7787) covalent geometry : angle 0.57981 / 0.31 (10577) SS BOND : bond 0.00302 / 0.16 ( 5) SS BOND : angle 0.68604 / 0.38 ( 10) hydrogen bonds : bond 0.06160 / 4.08 ( 401) hydrogen bonds : angle 4.36172 / 2.98 ( 1146) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.347 Fit side-chains REVERT: H 54 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.7498 (t80) REVERT: N 107 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.5562 (tpp) REVERT: R 334 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6691 (ttt) outliers start: 17 outliers final: 13 residues processed: 79 average time/residue: 0.1059 time to fit residues: 11.2011 Evaluate side-chains 88 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain R residue 236 PHE Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 334 MET Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 80 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 85 optimal weight: 0.0370 chunk 25 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 40 optimal weight: 0.0870 chunk 5 optimal weight: 4.9990 chunk 58 optimal weight: 0.0970 overall best weight: 0.8438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.192316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.136398 restraints weight = 8255.181| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.83 r_work: 0.3150 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7792 Z= 0.132 Angle : 0.538 7.640 10587 Z= 0.284 Chirality : 0.041 0.176 1199 Planarity : 0.004 0.039 1325 Dihedral : 7.010 97.069 1107 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.58 % Allowed : 9.85 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.28), residues: 985 helix: 1.90 (0.29), residues: 368 sheet: 1.21 (0.35), residues: 232 loop : -0.63 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 164 TYR 0.015 0.001 TYR N 32 PHE 0.022 0.001 PHE R 236 TRP 0.030 0.001 TRP R 178 HIS 0.006 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 7787) covalent geometry : angle 0.53792 / 0.28 (10577) SS BOND : bond 0.00265 / 0.14 ( 5) SS BOND : angle 0.58817 / 0.32 ( 10) hydrogen bonds : bond 0.05390 / 3.59 ( 401) hydrogen bonds : angle 4.22971 / 2.89 ( 1146) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.277 Fit side-chains REVERT: N 107 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.5536 (tpp) REVERT: R 334 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6465 (ttt) outliers start: 13 outliers final: 11 residues processed: 76 average time/residue: 0.0896 time to fit residues: 9.2684 Evaluate side-chains 83 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain R residue 236 PHE Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 334 MET Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 36 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 89 optimal weight: 0.2980 chunk 84 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.190135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.133790 restraints weight = 8203.496| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.88 r_work: 0.3151 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7792 Z= 0.165 Angle : 0.578 8.011 10587 Z= 0.305 Chirality : 0.042 0.193 1199 Planarity : 0.004 0.039 1325 Dihedral : 7.129 97.463 1107 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.82 % Allowed : 9.98 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.28), residues: 985 helix: 1.82 (0.29), residues: 367 sheet: 1.15 (0.35), residues: 232 loop : -0.70 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 46 TYR 0.018 0.002 TYR N 32 PHE 0.022 0.002 PHE R 236 TRP 0.029 0.002 TRP R 178 HIS 0.007 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 7787) covalent geometry : angle 0.57841 / 0.30 (10577) SS BOND : bond 0.00303 / 0.16 ( 5) SS BOND : angle 0.64481 / 0.36 ( 10) hydrogen bonds : bond 0.06155 / 4.08 ( 401) hydrogen bonds : angle 4.33288 / 2.96 ( 1146) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.328 Fit side-chains REVERT: H 54 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.7654 (t80) REVERT: N 107 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.5572 (tpp) REVERT: R 334 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6707 (ttt) outliers start: 15 outliers final: 12 residues processed: 79 average time/residue: 0.0931 time to fit residues: 9.9816 Evaluate side-chains 87 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain R residue 236 PHE Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 334 MET Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.191242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.135131 restraints weight = 8220.640| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.90 r_work: 0.3170 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7792 Z= 0.143 Angle : 0.554 7.833 10587 Z= 0.291 Chirality : 0.042 0.182 1199 Planarity : 0.004 0.038 1325 Dihedral : 7.043 97.331 1107 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.82 % Allowed : 9.73 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.28), residues: 985 helix: 1.89 (0.29), residues: 367 sheet: 1.18 (0.35), residues: 232 loop : -0.62 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 164 TYR 0.014 0.001 TYR N 32 PHE 0.022 0.001 PHE R 236 TRP 0.030 0.001 TRP R 178 HIS 0.006 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 7787) covalent geometry : angle 0.55389 / 0.29 (10577) SS BOND : bond 0.00284 / 0.15 ( 5) SS BOND : angle 0.59506 / 0.33 ( 10) hydrogen bonds : bond 0.05708 / 3.80 ( 401) hydrogen bonds : angle 4.25830 / 2.91 ( 1146) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.336 Fit side-chains REVERT: H 54 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.7598 (t80) REVERT: N 107 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.5548 (tpp) REVERT: R 334 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6567 (ttt) outliers start: 15 outliers final: 12 residues processed: 79 average time/residue: 0.0998 time to fit residues: 10.7106 Evaluate side-chains 87 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain R residue 236 PHE Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 334 MET Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 62 optimal weight: 3.9990 chunk 44 optimal weight: 0.1980 chunk 80 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 20 optimal weight: 0.0770 overall best weight: 0.5140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.195896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.140131 restraints weight = 8260.153| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.14 r_work: 0.3229 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7792 Z= 0.107 Angle : 0.499 7.860 10587 Z= 0.261 Chirality : 0.040 0.151 1199 Planarity : 0.004 0.037 1325 Dihedral : 6.689 96.020 1107 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.58 % Allowed : 10.34 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.29), residues: 985 helix: 2.11 (0.29), residues: 366 sheet: 1.24 (0.35), residues: 234 loop : -0.46 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 164 TYR 0.011 0.001 TYR N 32 PHE 0.022 0.001 PHE R 236 TRP 0.032 0.001 TRP R 178 HIS 0.005 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 ( 7787) covalent geometry : angle 0.49884 / 0.26 (10577) SS BOND : bond 0.00243 / 0.12 ( 5) SS BOND : angle 0.51938 / 0.29 ( 10) hydrogen bonds : bond 0.04507 / 3.02 ( 401) hydrogen bonds : angle 4.06200 / 2.77 ( 1146) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2188.99 seconds wall clock time: 38 minutes 15.53 seconds (2295.53 seconds total)