Starting phenix.real_space_refine on Thu Mar 13 00:22:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yuf_34105/03_2025/7yuf_34105_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yuf_34105/03_2025/7yuf_34105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yuf_34105/03_2025/7yuf_34105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yuf_34105/03_2025/7yuf_34105.map" model { file = "/net/cci-nas-00/data/ceres_data/7yuf_34105/03_2025/7yuf_34105_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yuf_34105/03_2025/7yuf_34105_neut.cif" } resolution = 3.29 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= -0.002 sd= 0.122 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 41 5.16 5 C 5372 2.51 5 N 1409 2.21 5 O 1593 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-5624/modules/chem_data/mon_lib" Total number of atoms: 8415 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: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3183 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 12, 'TRANS': 404} Chain breaks: 2 Chain: "K" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Time building chain proxies: 5.42, per 1000 atoms: 0.64 Number of scatterers: 8415 At special positions: 0 Unit cell: (80.3, 86.9, 162.8, 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 41 16.00 O 1593 8.00 N 1409 7.00 C 5372 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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=2.04 Simple disulfide: pdb=" SG CYS L 25 " - pdb=" SG CYS L 90 " distance=2.05 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 97 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " 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: 2.26 Conformation dependent library (CDL) restraints added in 1.1 seconds 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 16 sheets defined 38.5% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'H' and resid 32 through 36 removed outlier: 4.063A pdb=" N TYR H 35 " --> pdb=" O ASN H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 69 Processing helix chain 'H' and resid 91 through 95 removed outlier: 3.754A pdb=" N ASP H 94 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR H 95 " --> pdb=" O ALA H 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 91 through 95' Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 175 through 177 No H-bonds generated for 'chain 'H' and resid 175 through 177' Processing helix chain 'H' and resid 206 through 209 Processing helix chain 'L' and resid 123 through 130 removed outlier: 3.617A pdb=" N SER L 129 " --> pdb=" O SER L 125 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY L 130 " --> pdb=" O GLN L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 190 removed outlier: 3.601A pdb=" N LYS L 190 " --> pdb=" O ALA L 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 66 removed outlier: 3.745A pdb=" N LYS N 66 " --> pdb=" O ASP N 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 63 through 66' Processing helix chain 'N' and resid 88 through 92 removed outlier: 3.995A pdb=" N THR N 92 " --> pdb=" O PRO N 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 118 Processing helix chain 'R' and resid 122 through 124 No H-bonds generated for 'chain 'R' and resid 122 through 124' Processing helix chain 'R' and resid 125 through 133 removed outlier: 3.787A pdb=" N GLN R 131 " --> pdb=" O LEU R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 141 Processing helix chain 'R' and resid 141 through 162 Proline residue: R 156 - end of helix Processing helix chain 'R' and resid 167 through 185 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 193 through 221 Proline residue: R 215 - end of helix Processing helix chain 'R' and resid 226 through 236 removed outlier: 3.761A pdb=" N MET R 230 " --> pdb=" O THR R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 257 removed outlier: 3.899A pdb=" N TYR R 246 " --> pdb=" O SER R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 264 Processing helix chain 'R' and resid 265 through 277 removed outlier: 4.205A pdb=" N LEU R 269 " --> pdb=" O VAL R 265 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR R 275 " --> pdb=" O MET R 271 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 310 removed outlier: 3.566A pdb=" N LYS R 307 " --> pdb=" O LEU R 303 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) 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: 3.511A pdb=" N PHE R 366 " --> pdb=" O ASP R 362 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY R 367 " --> pdb=" O SER R 363 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N PHE R 375 " --> pdb=" O CYS R 371 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL R 378 " --> pdb=" O GLY R 374 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA R 382 " --> pdb=" O VAL R 378 " (cutoff:3.500A) Processing helix chain 'R' and resid 394 through 412 removed outlier: 3.689A pdb=" N LEU R 398 " --> pdb=" O ARG R 394 " (cutoff:3.500A) Processing helix chain 'R' and resid 413 through 418 Processing helix chain 'R' and resid 421 through 437 removed outlier: 3.715A pdb=" N ALA R 425 " --> pdb=" O SER R 421 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE R 437 " --> pdb=" O GLU R 433 " (cutoff:3.500A) Processing helix chain 'R' and resid 438 through 441 removed outlier: 3.938A pdb=" N ALA R 441 " --> pdb=" O SER R 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 438 through 441' Processing helix chain 'R' and resid 442 through 451 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: 3.752A pdb=" N ALA R 461 " --> pdb=" O ALA R 457 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN R 463 " --> pdb=" O ALA R 459 " (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: 4.081A pdb=" N PHE R 510 " --> pdb=" O MET R 506 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE R 525 " --> pdb=" O ALA R 521 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL R 527 " --> pdb=" O ALA R 523 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER R 528 " --> pdb=" O LEU R 524 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'H' and resid 7 through 11 Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15 removed outlier: 6.454A pdb=" N GLY H 14 " --> pdb=" O THR H 129 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG H 42 " --> pdb=" O TRP H 51 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N TRP H 51 " --> pdb=" O ARG H 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 139 through 143 removed outlier: 5.926A pdb=" N TYR H 195 " --> pdb=" O ASP H 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 150 through 151 removed outlier: 5.926A pdb=" N TYR H 195 " --> pdb=" O ASP H 163 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER H 196 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL H 188 " --> pdb=" O SER H 196 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 170 through 173 Processing sheet with id=AA6, first strand: chain 'L' and resid 7 through 9 Processing sheet with id=AA7, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.266A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 12 through 14 Processing sheet with id=AA9, first strand: chain 'L' and resid 116 through 120 removed outlier: 6.428A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 156 through 157 removed outlier: 4.744A pdb=" N TRP L 150 " --> pdb=" O GLN L 157 " (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 10 through 12 removed outlier: 6.271A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ARG N 39 " --> pdb=" O GLY N 48 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLY N 48 " --> pdb=" O ARG N 39 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.271A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.215A pdb=" N GLY K 10 " --> pdb=" O THR K 118 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.215A pdb=" N GLY K 10 " --> pdb=" O THR K 118 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR K 110 " --> pdb=" O ILE K 98 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1278 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: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2665 1.35 - 1.47: 2312 1.47 - 1.59: 3575 1.59 - 1.71: 0 1.71 - 1.83: 59 Bond restraints: 8611 Sorted by residual: bond pdb=" CD1 TYR H 104 " pdb=" CE1 TYR H 104 " ideal model delta sigma weight residual 1.382 1.340 0.042 3.00e-02 1.11e+03 1.93e+00 bond pdb=" CG LEU N 82 " pdb=" CD2 LEU N 82 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.86e+00 bond pdb=" C GLY R 206 " pdb=" O GLY R 206 " ideal model delta sigma weight residual 1.234 1.249 -0.016 1.21e-02 6.83e+03 1.64e+00 bond pdb=" CB PRO R 397 " pdb=" CG PRO R 397 " ideal model delta sigma weight residual 1.492 1.430 0.062 5.00e-02 4.00e+02 1.55e+00 bond pdb=" CG TYR N 96 " pdb=" CD1 TYR N 96 " ideal model delta sigma weight residual 1.389 1.364 0.025 2.10e-02 2.27e+03 1.39e+00 ... (remaining 8606 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 10987 1.51 - 3.02: 590 3.02 - 4.53: 86 4.53 - 6.03: 34 6.03 - 7.54: 2 Bond angle restraints: 11699 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 122.17 115.44 6.73 1.54e+00 4.22e-01 1.91e+01 angle pdb=" N GLN H 105 " pdb=" CA GLN H 105 " pdb=" CB GLN H 105 " ideal model delta sigma weight residual 114.17 109.20 4.97 1.14e+00 7.69e-01 1.90e+01 angle pdb=" CA TRP R 178 " pdb=" CB TRP R 178 " pdb=" CG TRP R 178 " ideal model delta sigma weight residual 113.60 121.14 -7.54 1.90e+00 2.77e-01 1.58e+01 angle pdb=" C THR N 34 " pdb=" N LEU N 35 " pdb=" CA LEU N 35 " ideal model delta sigma weight residual 122.77 117.28 5.49 1.41e+00 5.03e-01 1.51e+01 angle pdb=" C LYS N 120 " pdb=" CA LYS N 120 " pdb=" CB LYS N 120 " ideal model delta sigma weight residual 109.02 103.04 5.98 1.68e+00 3.54e-01 1.27e+01 ... (remaining 11694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4715 17.95 - 35.90: 267 35.90 - 53.85: 38 53.85 - 71.80: 12 71.80 - 89.75: 7 Dihedral angle restraints: 5039 sinusoidal: 1876 harmonic: 3163 Sorted by residual: dihedral pdb=" CA TYR N 32 " pdb=" C TYR N 32 " pdb=" N TYR N 33 " pdb=" CA TYR N 33 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA SER L 30 " pdb=" C SER L 30 " pdb=" N VAL L 31 " pdb=" CA VAL L 31 " ideal model delta harmonic sigma weight residual 180.00 160.72 19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA HIS H 110 " pdb=" C HIS H 110 " pdb=" N ALA H 111 " pdb=" CA ALA H 111 " ideal model delta harmonic sigma weight residual 180.00 161.21 18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 5036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 789 0.037 - 0.074: 375 0.074 - 0.112: 118 0.112 - 0.149: 31 0.149 - 0.186: 4 Chirality restraints: 1317 Sorted by residual: chirality pdb=" CA TRP R 178 " pdb=" N TRP R 178 " pdb=" C TRP R 178 " pdb=" CB TRP R 178 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" CA THR N 34 " pdb=" N THR N 34 " pdb=" C THR N 34 " pdb=" CB THR N 34 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" CA HIS H 110 " pdb=" N HIS H 110 " pdb=" C HIS H 110 " pdb=" CB HIS H 110 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 1314 not shown) Planarity restraints: 1476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 167 " 0.051 5.00e-02 4.00e+02 7.82e-02 9.78e+00 pdb=" N PRO H 168 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO H 168 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO H 168 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR N 122 " -0.050 5.00e-02 4.00e+02 7.66e-02 9.38e+00 pdb=" N PRO N 123 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO N 123 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO N 123 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 203 " 0.042 5.00e-02 4.00e+02 6.42e-02 6.58e+00 pdb=" N PRO H 204 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO H 204 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 204 " 0.035 5.00e-02 4.00e+02 ... (remaining 1473 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1500 2.77 - 3.30: 7606 3.30 - 3.83: 12939 3.83 - 4.37: 14022 4.37 - 4.90: 26068 Nonbonded interactions: 62135 Sorted by model distance: nonbonded pdb=" OD1 ASN H 174 " pdb=" N ILE H 214 " model vdw 2.232 3.120 nonbonded pdb=" O PRO H 204 " pdb=" OG SER H 207 " model vdw 2.277 3.040 nonbonded pdb=" OG SER K 35 " pdb=" OH TYR K 108 " model vdw 2.338 3.040 nonbonded pdb=" OH TYR L 38 " pdb=" OE1 GLN L 91 " model vdw 2.360 3.040 nonbonded pdb=" OG SER R 314 " pdb=" OD2 ASP R 529 " model vdw 2.364 3.040 ... (remaining 62130 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.980 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 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 : 0.006 0.062 8611 Z= 0.404 Angle : 0.802 7.543 11699 Z= 0.478 Chirality : 0.048 0.186 1317 Planarity : 0.006 0.078 1476 Dihedral : 12.368 89.749 3011 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.26 (0.25), residues: 1091 helix: 0.27 (0.27), residues: 370 sheet: 0.83 (0.30), residues: 307 loop : -1.32 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 178 HIS 0.006 0.002 HIS R 468 PHE 0.022 0.002 PHE R 151 TYR 0.027 0.003 TYR N 32 ARG 0.009 0.001 ARG R 342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.824 Fit side-chains REVERT: H 23 ARG cc_start: 0.7428 (ttt90) cc_final: 0.7175 (ttm170) REVERT: L 9 SER cc_start: 0.8354 (t) cc_final: 0.7751 (m) REVERT: L 47 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8177 (mttm) REVERT: L 76 THR cc_start: 0.8877 (m) cc_final: 0.8596 (t) REVERT: L 105 LYS cc_start: 0.8522 (ttmt) cc_final: 0.8300 (tttm) REVERT: L 145 GLU cc_start: 0.7585 (mp0) cc_final: 0.7294 (mp0) REVERT: L 179 SER cc_start: 0.8736 (t) cc_final: 0.8404 (m) REVERT: R 236 PHE cc_start: 0.5965 (m-10) cc_final: 0.5538 (m-80) REVERT: R 307 LYS cc_start: 0.8047 (mttp) cc_final: 0.7832 (mttt) REVERT: R 311 ARG cc_start: 0.7549 (ttm-80) cc_final: 0.7148 (mtm110) REVERT: R 534 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7701 (mt-10) REVERT: K 47 PHE cc_start: 0.7489 (t80) cc_final: 0.7150 (t80) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2120 time to fit residues: 51.3497 Evaluate side-chains 115 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.3980 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 0.0070 chunk 98 optimal weight: 20.0000 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 7 GLN ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 126 GLN R 190 GLN K 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.215430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.168936 restraints weight = 9761.900| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 3.13 r_work: 0.3612 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8611 Z= 0.180 Angle : 0.577 7.588 11699 Z= 0.308 Chirality : 0.042 0.143 1317 Planarity : 0.005 0.056 1476 Dihedral : 4.358 20.019 1204 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.98 % Allowed : 7.37 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.47 (0.26), residues: 1091 helix: 1.37 (0.28), residues: 377 sheet: 0.87 (0.29), residues: 319 loop : -1.21 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 178 HIS 0.003 0.001 HIS H 110 PHE 0.017 0.001 PHE N 30 TYR 0.016 0.001 TYR N 32 ARG 0.004 0.000 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.821 Fit side-chains REVERT: L 9 SER cc_start: 0.8018 (t) cc_final: 0.7289 (m) REVERT: L 76 THR cc_start: 0.8906 (m) cc_final: 0.8589 (t) REVERT: L 105 LYS cc_start: 0.8160 (ttmt) cc_final: 0.7893 (ttmm) REVERT: L 145 GLU cc_start: 0.7342 (mp0) cc_final: 0.6984 (mp0) REVERT: L 179 SER cc_start: 0.8424 (t) cc_final: 0.7869 (m) REVERT: N 111 ASP cc_start: 0.7710 (t0) cc_final: 0.6799 (p0) REVERT: R 236 PHE cc_start: 0.6465 (m-10) cc_final: 0.6037 (m-80) REVERT: R 386 ARG cc_start: 0.7819 (mtm180) cc_final: 0.7537 (mtp85) REVERT: K 34 MET cc_start: 0.8454 (mmt) cc_final: 0.8189 (mmm) REVERT: K 83 MET cc_start: 0.6949 (pmm) cc_final: 0.6275 (ttt) outliers start: 18 outliers final: 13 residues processed: 126 average time/residue: 0.2188 time to fit residues: 37.6115 Evaluate side-chains 115 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 113 TRP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 210 SER Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 240 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 0.0050 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 0.0070 chunk 71 optimal weight: 0.9990 overall best weight: 1.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.214045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.165071 restraints weight = 10089.640| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 3.34 r_work: 0.3599 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8611 Z= 0.305 Angle : 0.648 11.293 11699 Z= 0.346 Chirality : 0.045 0.198 1317 Planarity : 0.005 0.058 1476 Dihedral : 4.453 24.756 1204 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.19 % Allowed : 8.91 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.42 (0.26), residues: 1091 helix: 1.28 (0.28), residues: 376 sheet: 0.81 (0.29), residues: 308 loop : -1.09 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 178 HIS 0.004 0.001 HIS H 110 PHE 0.026 0.002 PHE N 30 TYR 0.024 0.002 TYR N 96 ARG 0.005 0.001 ARG R 530 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: L 76 THR cc_start: 0.8955 (m) cc_final: 0.8607 (t) REVERT: L 105 LYS cc_start: 0.8301 (ttmt) cc_final: 0.8096 (ttmm) REVERT: L 145 GLU cc_start: 0.7168 (mp0) cc_final: 0.6900 (mp0) REVERT: L 149 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7186 (mm-40) REVERT: L 179 SER cc_start: 0.8351 (t) cc_final: 0.7784 (m) REVERT: L 209 LYS cc_start: 0.6954 (mmtp) cc_final: 0.6745 (mmmm) REVERT: R 236 PHE cc_start: 0.6443 (m-10) cc_final: 0.6075 (m-80) REVERT: R 386 ARG cc_start: 0.7869 (mtm180) cc_final: 0.7635 (ttm-80) REVERT: K 34 MET cc_start: 0.8450 (mmt) cc_final: 0.8201 (mmm) REVERT: K 47 PHE cc_start: 0.6507 (t80) cc_final: 0.6270 (t80) REVERT: K 83 MET cc_start: 0.7030 (pmm) cc_final: 0.6490 (pmm) outliers start: 29 outliers final: 20 residues processed: 117 average time/residue: 0.2078 time to fit residues: 33.4852 Evaluate side-chains 109 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 113 TRP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 210 SER Chi-restraints excluded: chain N residue 33 TYR Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 233 VAL Chi-restraints excluded: chain R residue 538 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 37 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.211790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.165170 restraints weight = 9878.715| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 3.06 r_work: 0.3553 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8611 Z= 0.229 Angle : 0.588 14.094 11699 Z= 0.306 Chirality : 0.043 0.168 1317 Planarity : 0.004 0.050 1476 Dihedral : 4.166 22.260 1204 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.97 % Allowed : 9.79 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1091 helix: 1.44 (0.28), residues: 373 sheet: 0.84 (0.29), residues: 325 loop : -0.99 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 178 HIS 0.003 0.001 HIS H 110 PHE 0.019 0.002 PHE R 498 TYR 0.020 0.001 TYR N 32 ARG 0.003 0.000 ARG R 530 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: L 76 THR cc_start: 0.8959 (m) cc_final: 0.8638 (t) REVERT: L 145 GLU cc_start: 0.7155 (mp0) cc_final: 0.6844 (mp0) REVERT: L 179 SER cc_start: 0.8473 (t) cc_final: 0.7907 (m) REVERT: R 236 PHE cc_start: 0.6579 (m-10) cc_final: 0.6265 (m-80) REVERT: K 34 MET cc_start: 0.8383 (mmt) cc_final: 0.8160 (mmm) REVERT: K 83 MET cc_start: 0.7054 (pmm) cc_final: 0.6273 (pmm) outliers start: 27 outliers final: 21 residues processed: 105 average time/residue: 0.1813 time to fit residues: 27.4082 Evaluate side-chains 102 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 113 TRP Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 210 SER Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 233 VAL Chi-restraints excluded: chain R residue 411 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 72 optimal weight: 0.0470 chunk 2 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.212716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.166210 restraints weight = 9902.292| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 3.10 r_work: 0.3558 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8611 Z= 0.192 Angle : 0.567 14.839 11699 Z= 0.292 Chirality : 0.042 0.155 1317 Planarity : 0.004 0.048 1476 Dihedral : 3.995 23.318 1204 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.52 % Allowed : 10.45 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.79 (0.26), residues: 1091 helix: 1.59 (0.28), residues: 373 sheet: 1.10 (0.29), residues: 311 loop : -0.96 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 178 HIS 0.003 0.001 HIS H 110 PHE 0.020 0.002 PHE K 47 TYR 0.019 0.001 TYR N 32 ARG 0.002 0.000 ARG R 530 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 1.041 Fit side-chains REVERT: L 76 THR cc_start: 0.8994 (m) cc_final: 0.8664 (t) REVERT: L 179 SER cc_start: 0.8481 (t) cc_final: 0.7911 (m) REVERT: R 236 PHE cc_start: 0.6623 (m-10) cc_final: 0.6341 (m-10) REVERT: R 302 TRP cc_start: 0.6729 (OUTLIER) cc_final: 0.6484 (p-90) REVERT: R 386 ARG cc_start: 0.8101 (ttm-80) cc_final: 0.7351 (ttp-170) REVERT: K 83 MET cc_start: 0.6945 (pmm) cc_final: 0.6322 (pmm) outliers start: 32 outliers final: 27 residues processed: 108 average time/residue: 0.1861 time to fit residues: 28.8215 Evaluate side-chains 113 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 113 TRP Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 210 SER Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 233 VAL Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 302 TRP Chi-restraints excluded: chain R residue 314 SER Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain K residue 17 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 40 optimal weight: 20.0000 chunk 90 optimal weight: 0.6980 chunk 96 optimal weight: 30.0000 chunk 67 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.207914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.159341 restraints weight = 9940.952| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 3.20 r_work: 0.3435 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 8611 Z= 0.367 Angle : 0.685 15.017 11699 Z= 0.358 Chirality : 0.046 0.198 1317 Planarity : 0.005 0.051 1476 Dihedral : 4.400 23.968 1204 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.62 % Allowed : 10.34 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.52 (0.26), residues: 1091 helix: 1.37 (0.28), residues: 364 sheet: 0.86 (0.29), residues: 321 loop : -1.02 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 178 HIS 0.004 0.001 HIS H 110 PHE 0.021 0.002 PHE N 30 TYR 0.029 0.002 TYR N 32 ARG 0.004 0.000 ARG R 530 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 87 time to evaluate : 0.879 Fit side-chains REVERT: L 76 THR cc_start: 0.8945 (m) cc_final: 0.8635 (t) REVERT: L 179 SER cc_start: 0.8433 (t) cc_final: 0.7869 (m) REVERT: R 236 PHE cc_start: 0.6529 (m-10) cc_final: 0.6244 (m-10) REVERT: R 302 TRP cc_start: 0.6778 (OUTLIER) cc_final: 0.6509 (p-90) REVERT: R 506 MET cc_start: 0.7916 (mmt) cc_final: 0.7638 (mmt) REVERT: K 83 MET cc_start: 0.6784 (pmm) cc_final: 0.6182 (pmm) outliers start: 42 outliers final: 35 residues processed: 115 average time/residue: 0.2206 time to fit residues: 37.6000 Evaluate side-chains 122 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 86 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 113 TRP Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 199 SER Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 210 SER Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 230 MET Chi-restraints excluded: chain R residue 233 VAL Chi-restraints excluded: chain R residue 302 TRP Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 314 SER Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain R residue 434 THR Chi-restraints excluded: chain R residue 538 ASN Chi-restraints excluded: chain K residue 17 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 0.0980 chunk 21 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 0.0020 chunk 99 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.214626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.166159 restraints weight = 9942.967| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 3.10 r_work: 0.3565 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8611 Z= 0.158 Angle : 0.546 15.472 11699 Z= 0.278 Chirality : 0.041 0.154 1317 Planarity : 0.004 0.047 1476 Dihedral : 3.958 22.115 1204 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.64 % Allowed : 12.43 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.91 (0.26), residues: 1091 helix: 1.76 (0.28), residues: 364 sheet: 1.23 (0.30), residues: 306 loop : -0.93 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP R 178 HIS 0.003 0.001 HIS R 341 PHE 0.022 0.001 PHE K 47 TYR 0.012 0.001 TYR N 32 ARG 0.002 0.000 ARG R 487 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.964 Fit side-chains REVERT: L 6 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7055 (mtp) REVERT: L 76 THR cc_start: 0.8937 (m) cc_final: 0.8555 (t) REVERT: R 236 PHE cc_start: 0.6424 (m-10) cc_final: 0.6171 (m-10) REVERT: R 302 TRP cc_start: 0.6674 (OUTLIER) cc_final: 0.6471 (p-90) REVERT: K 83 MET cc_start: 0.6969 (pmm) cc_final: 0.6349 (pmm) outliers start: 24 outliers final: 22 residues processed: 107 average time/residue: 0.1866 time to fit residues: 28.9540 Evaluate side-chains 113 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 113 TRP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 302 TRP Chi-restraints excluded: chain K residue 17 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.211278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.162706 restraints weight = 9967.440| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 3.02 r_work: 0.3509 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8611 Z= 0.245 Angle : 0.591 14.600 11699 Z= 0.307 Chirality : 0.043 0.170 1317 Planarity : 0.004 0.047 1476 Dihedral : 4.039 23.362 1204 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.41 % Allowed : 11.77 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.84 (0.26), residues: 1091 helix: 1.69 (0.28), residues: 361 sheet: 1.10 (0.30), residues: 308 loop : -0.87 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 178 HIS 0.003 0.001 HIS R 341 PHE 0.018 0.002 PHE R 498 TYR 0.023 0.001 TYR N 32 ARG 0.003 0.000 ARG R 530 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 0.809 Fit side-chains REVERT: L 76 THR cc_start: 0.8952 (m) cc_final: 0.8590 (t) REVERT: R 236 PHE cc_start: 0.6479 (m-10) cc_final: 0.6225 (m-10) REVERT: R 302 TRP cc_start: 0.6784 (OUTLIER) cc_final: 0.6550 (p-90) REVERT: K 83 MET cc_start: 0.6764 (pmm) cc_final: 0.6151 (pmm) outliers start: 31 outliers final: 28 residues processed: 105 average time/residue: 0.2147 time to fit residues: 32.4670 Evaluate side-chains 113 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 113 TRP Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 210 SER Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 302 TRP Chi-restraints excluded: chain R residue 314 SER Chi-restraints excluded: chain K residue 17 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 96 optimal weight: 30.0000 chunk 28 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.210746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.162126 restraints weight = 9986.617| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 3.19 r_work: 0.3494 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8611 Z= 0.253 Angle : 0.608 14.704 11699 Z= 0.314 Chirality : 0.043 0.171 1317 Planarity : 0.004 0.047 1476 Dihedral : 4.112 22.274 1204 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.63 % Allowed : 11.77 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.84 (0.26), residues: 1091 helix: 1.63 (0.28), residues: 360 sheet: 1.15 (0.30), residues: 300 loop : -0.81 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 178 HIS 0.004 0.001 HIS H 110 PHE 0.022 0.002 PHE K 47 TYR 0.023 0.001 TYR N 32 ARG 0.003 0.000 ARG R 530 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.816 Fit side-chains REVERT: H 124 GLN cc_start: 0.8645 (tp-100) cc_final: 0.8388 (tp-100) REVERT: L 76 THR cc_start: 0.8957 (m) cc_final: 0.8599 (t) REVERT: N 45 GLU cc_start: 0.7258 (mm-30) cc_final: 0.7017 (mm-30) REVERT: R 236 PHE cc_start: 0.6426 (m-10) cc_final: 0.6166 (m-10) REVERT: R 302 TRP cc_start: 0.6788 (OUTLIER) cc_final: 0.6577 (p-90) REVERT: R 410 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.7176 (t80) REVERT: R 517 MET cc_start: 0.7587 (mmp) cc_final: 0.7297 (mmm) REVERT: K 83 MET cc_start: 0.6751 (pmm) cc_final: 0.6124 (pmm) outliers start: 33 outliers final: 31 residues processed: 111 average time/residue: 0.1804 time to fit residues: 28.9002 Evaluate side-chains 120 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 113 TRP Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 199 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 210 SER Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 302 TRP Chi-restraints excluded: chain R residue 314 SER Chi-restraints excluded: chain R residue 410 PHE Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain K residue 17 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 80 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 61 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 18 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.211750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.164112 restraints weight = 9851.363| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 3.14 r_work: 0.3531 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8611 Z= 0.163 Angle : 0.547 14.588 11699 Z= 0.279 Chirality : 0.041 0.168 1317 Planarity : 0.004 0.047 1476 Dihedral : 3.850 22.190 1204 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.86 % Allowed : 12.98 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.27), residues: 1091 helix: 2.06 (0.29), residues: 352 sheet: 1.35 (0.31), residues: 299 loop : -0.79 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP R 178 HIS 0.003 0.001 HIS R 341 PHE 0.017 0.001 PHE R 498 TYR 0.015 0.001 TYR N 32 ARG 0.002 0.000 ARG R 532 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.814 Fit side-chains REVERT: H 105 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7780 (tt0) REVERT: H 124 GLN cc_start: 0.8583 (tp-100) cc_final: 0.8319 (tp-100) REVERT: L 76 THR cc_start: 0.8954 (m) cc_final: 0.8573 (t) REVERT: R 236 PHE cc_start: 0.6430 (m-10) cc_final: 0.6210 (m-10) REVERT: R 302 TRP cc_start: 0.6700 (OUTLIER) cc_final: 0.6482 (p-90) REVERT: R 517 MET cc_start: 0.7611 (mmp) cc_final: 0.7329 (mmm) REVERT: K 83 MET cc_start: 0.6758 (pmm) cc_final: 0.6123 (pmm) outliers start: 26 outliers final: 25 residues processed: 110 average time/residue: 0.1865 time to fit residues: 29.1904 Evaluate side-chains 117 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 113 TRP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 302 TRP Chi-restraints excluded: chain R residue 314 SER Chi-restraints excluded: chain K residue 17 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 32 optimal weight: 6.9990 chunk 55 optimal weight: 0.4980 chunk 106 optimal weight: 20.0000 chunk 43 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 98 optimal weight: 30.0000 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.213930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.165998 restraints weight = 10005.867| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 3.03 r_work: 0.3531 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8611 Z= 0.183 Angle : 0.561 13.610 11699 Z= 0.289 Chirality : 0.041 0.165 1317 Planarity : 0.004 0.047 1476 Dihedral : 3.843 21.921 1204 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.19 % Allowed : 12.76 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.27), residues: 1091 helix: 2.01 (0.29), residues: 355 sheet: 1.40 (0.31), residues: 299 loop : -0.73 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP R 178 HIS 0.003 0.001 HIS R 341 PHE 0.022 0.001 PHE K 47 TYR 0.020 0.001 TYR N 32 ARG 0.002 0.000 ARG K 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4100.99 seconds wall clock time: 72 minutes 7.74 seconds (4327.74 seconds total)