Starting phenix.real_space_refine on Fri Apr 5 20:50:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gej_29972/04_2024/8gej_29972_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gej_29972/04_2024/8gej_29972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gej_29972/04_2024/8gej_29972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gej_29972/04_2024/8gej_29972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gej_29972/04_2024/8gej_29972_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gej_29972/04_2024/8gej_29972_updated.pdb" } resolution = 4.2 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= -0.001 sd= 0.020 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 9 5.16 5 C 3368 2.51 5 N 1029 2.21 5 O 1030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5436 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 1718 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 247} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 10 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 928 Unresolved non-hydrogen angles: 1174 Unresolved non-hydrogen dihedrals: 762 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 16, 'TRP:plan': 4, 'ASP:plan': 20, 'PHE:plan': 11, 'GLU:plan': 25, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 548 Chain: "B" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 1894 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 191} Link IDs: {'PTRANS': 5, 'TRANS': 317} Chain breaks: 3 Unresolved non-hydrogen bonds: 601 Unresolved non-hydrogen angles: 757 Unresolved non-hydrogen dihedrals: 462 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 25, 'ASN:plan1': 14, 'TRP:plan': 1, 'HIS:plan': 2, 'ASN%COO:plan1': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 315 Chain: "G" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 232 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 62 Chain: "R" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1577 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 6, 'TRANS': 263} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 625 Unresolved non-hydrogen angles: 813 Unresolved non-hydrogen dihedrals: 506 Unresolved non-hydrogen chiralities: 91 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 12, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 281 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.62, per 1000 atoms: 0.67 Number of scatterers: 5436 At special positions: 0 Unit cell: (66.78, 97.52, 127.2, 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 9 16.00 O 1030 8.00 N 1029 7.00 C 3368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.3 seconds 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1816 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 8 sheets defined 46.0% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.933A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 60 Processing helix chain 'A' and resid 91 through 112 Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 145 through 155 Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.815A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 387 removed outlier: 3.767A pdb=" N GLN A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.164A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 23 Processing helix chain 'G' and resid 30 through 45 Processing helix chain 'R' and resid 32 through 60 removed outlier: 3.928A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 95 removed outlier: 3.910A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 103 through 136 removed outlier: 3.718A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA R 128 " --> pdb=" O LEU R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 144 removed outlier: 4.211A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 159 Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 182 through 186 Processing helix chain 'R' and resid 197 through 235 removed outlier: 3.559A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA R 202 " --> pdb=" O ALA R 198 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix Processing helix chain 'R' and resid 270 through 298 removed outlier: 3.763A pdb=" N ILE R 278 " --> pdb=" O THR R 274 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 305 through 326 removed outlier: 3.933A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 332 through 338 Processing sheet with id= A, first strand: chain 'A' and resid 41 through 44 Processing sheet with id= B, first strand: chain 'A' and resid 243 through 245 removed outlier: 6.744A pdb=" N SER A 286 " --> pdb=" O ILE A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 69 through 73 removed outlier: 3.918A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.506A pdb=" N CYS B 114 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.763A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP B 297 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.849A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.537A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 315 through 320 removed outlier: 6.909A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) 318 hydrogen bonds defined for protein. 939 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: 1.39 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 975 1.31 - 1.43: 1459 1.43 - 1.56: 3063 1.56 - 1.69: 1 1.69 - 1.81: 9 Bond restraints: 5507 Sorted by residual: bond pdb=" C SER R 319 " pdb=" O SER R 319 " ideal model delta sigma weight residual 1.237 1.182 0.055 1.17e-02 7.31e+03 2.22e+01 bond pdb=" CA LEU R 310 " pdb=" C LEU R 310 " ideal model delta sigma weight residual 1.524 1.479 0.046 1.28e-02 6.10e+03 1.28e+01 bond pdb=" CA ILE R 314 " pdb=" C ILE R 314 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.27e-02 6.20e+03 1.06e+01 bond pdb=" CA TYR R 316 " pdb=" C TYR R 316 " ideal model delta sigma weight residual 1.524 1.482 0.041 1.29e-02 6.01e+03 1.03e+01 bond pdb=" CA TRP R 313 " pdb=" C TRP R 313 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.34e-02 5.57e+03 9.00e+00 ... (remaining 5502 not shown) Histogram of bond angle deviations from ideal: 102.46 - 108.78: 246 108.78 - 115.10: 3017 115.10 - 121.41: 2892 121.41 - 127.73: 1415 127.73 - 134.05: 47 Bond angle restraints: 7617 Sorted by residual: angle pdb=" N ASN R 322 " pdb=" CA ASN R 322 " pdb=" C ASN R 322 " ideal model delta sigma weight residual 113.16 106.18 6.98 1.42e+00 4.96e-01 2.41e+01 angle pdb=" C ILE R 314 " pdb=" N GLY R 315 " pdb=" CA GLY R 315 " ideal model delta sigma weight residual 119.94 114.54 5.40 1.11e+00 8.12e-01 2.36e+01 angle pdb=" C ILE R 314 " pdb=" CA ILE R 314 " pdb=" CB ILE R 314 " ideal model delta sigma weight residual 112.14 105.99 6.15 1.35e+00 5.49e-01 2.07e+01 angle pdb=" C ASN R 322 " pdb=" N PRO R 323 " pdb=" CA PRO R 323 " ideal model delta sigma weight residual 119.05 123.62 -4.57 1.11e+00 8.12e-01 1.69e+01 angle pdb=" N LEU R 324 " pdb=" CA LEU R 324 " pdb=" C LEU R 324 " ideal model delta sigma weight residual 111.28 107.39 3.89 1.09e+00 8.42e-01 1.27e+01 ... (remaining 7612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.88: 2928 8.88 - 17.75: 115 17.75 - 26.62: 56 26.62 - 35.49: 19 35.49 - 44.37: 10 Dihedral angle restraints: 3128 sinusoidal: 366 harmonic: 2762 Sorted by residual: dihedral pdb=" CA SER B 74 " pdb=" C SER B 74 " pdb=" N GLN B 75 " pdb=" CA GLN B 75 " ideal model delta harmonic sigma weight residual 180.00 162.15 17.85 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 164.51 15.49 0 5.00e+00 4.00e-02 9.60e+00 dihedral pdb=" CA HIS B 54 " pdb=" C HIS B 54 " pdb=" N LEU B 55 " pdb=" CA LEU B 55 " ideal model delta harmonic sigma weight residual -180.00 -165.58 -14.42 0 5.00e+00 4.00e-02 8.32e+00 ... (remaining 3125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 720 0.042 - 0.085: 187 0.085 - 0.127: 48 0.127 - 0.170: 1 0.170 - 0.212: 1 Chirality restraints: 957 Sorted by residual: chirality pdb=" CA TYR R 316 " pdb=" N TYR R 316 " pdb=" C TYR R 316 " pdb=" CB TYR R 316 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.54 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 954 not shown) Planarity restraints: 1037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 309 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.03e+00 pdb=" C ILE R 309 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE R 309 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU R 310 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 313 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C TRP R 313 " 0.032 2.00e-02 2.50e+03 pdb=" O TRP R 313 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE R 314 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 310 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C LEU R 310 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU R 310 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU R 311 " 0.009 2.00e-02 2.50e+03 ... (remaining 1034 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 752 2.75 - 3.29: 5613 3.29 - 3.82: 8997 3.82 - 4.36: 8364 4.36 - 4.90: 14717 Nonbonded interactions: 38443 Sorted by model distance: nonbonded pdb=" OE1 GLN A 19 " pdb=" OG1 THR B 86 " model vdw 2.210 2.440 nonbonded pdb=" N SER B 147 " pdb=" O SER B 160 " model vdw 2.242 2.520 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.309 2.440 nonbonded pdb=" O ASN R 183 " pdb=" N GLU R 187 " model vdw 2.316 2.520 nonbonded pdb=" O ASP B 228 " pdb=" N ASP B 246 " model vdw 2.318 2.520 ... (remaining 38438 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.690 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: 5.750 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.870 Find NCS groups from input model: 0.210 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 0.055 5507 Z= 0.253 Angle : 0.501 6.976 7617 Z= 0.327 Chirality : 0.040 0.212 957 Planarity : 0.003 0.036 1037 Dihedral : 8.378 44.368 1309 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.29), residues: 906 helix: 2.79 (0.25), residues: 432 sheet: -0.03 (0.56), residues: 106 loop : -1.43 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 297 HIS 0.003 0.001 HIS R 296 PHE 0.010 0.001 PHE A 340 TYR 0.011 0.001 TYR A 147 ARG 0.001 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.623 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0821 time to fit residues: 5.4377 Evaluate side-chains 30 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5507 Z= 0.206 Angle : 0.407 5.313 7617 Z= 0.240 Chirality : 0.039 0.123 957 Planarity : 0.003 0.037 1037 Dihedral : 3.821 18.039 971 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.29), residues: 906 helix: 2.70 (0.25), residues: 427 sheet: -0.49 (0.53), residues: 122 loop : -1.54 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.003 0.001 HIS R 296 PHE 0.017 0.001 PHE R 208 TYR 0.010 0.001 TYR A 147 ARG 0.001 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.670 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0771 time to fit residues: 5.3165 Evaluate side-chains 30 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5507 Z= 0.118 Angle : 0.358 5.307 7617 Z= 0.206 Chirality : 0.039 0.121 957 Planarity : 0.002 0.037 1037 Dihedral : 3.436 15.566 971 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.29), residues: 906 helix: 2.76 (0.25), residues: 441 sheet: -0.40 (0.54), residues: 118 loop : -1.44 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 313 HIS 0.002 0.001 HIS B 54 PHE 0.016 0.001 PHE R 208 TYR 0.009 0.001 TYR R 219 ARG 0.001 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.663 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0750 time to fit residues: 5.0814 Evaluate side-chains 30 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5507 Z= 0.221 Angle : 0.409 5.188 7617 Z= 0.242 Chirality : 0.039 0.119 957 Planarity : 0.003 0.037 1037 Dihedral : 3.813 20.750 971 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.29), residues: 906 helix: 2.81 (0.25), residues: 426 sheet: -0.62 (0.51), residues: 127 loop : -1.54 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.003 0.001 HIS G 44 PHE 0.018 0.001 PHE R 208 TYR 0.011 0.001 TYR A 147 ARG 0.002 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.511 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0760 time to fit residues: 5.0690 Evaluate side-chains 31 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 0.1980 chunk 77 optimal weight: 0.4980 chunk 62 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 22 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.017 5507 Z= 0.089 Angle : 0.349 5.324 7617 Z= 0.199 Chirality : 0.038 0.123 957 Planarity : 0.002 0.039 1037 Dihedral : 3.275 16.763 971 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.29), residues: 906 helix: 2.87 (0.25), residues: 439 sheet: -0.62 (0.49), residues: 138 loop : -1.30 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 63 HIS 0.004 0.001 HIS R 296 PHE 0.016 0.001 PHE R 208 TYR 0.009 0.001 TYR R 219 ARG 0.001 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.610 Fit side-chains REVERT: R 136 THR cc_start: 0.8397 (t) cc_final: 0.8039 (p) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0790 time to fit residues: 5.5485 Evaluate side-chains 31 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 0.0050 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5507 Z= 0.139 Angle : 0.359 5.182 7617 Z= 0.208 Chirality : 0.039 0.122 957 Planarity : 0.002 0.038 1037 Dihedral : 3.352 18.359 971 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.29), residues: 906 helix: 2.89 (0.25), residues: 442 sheet: -0.20 (0.54), residues: 115 loop : -1.46 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.002 0.001 HIS G 44 PHE 0.020 0.001 PHE R 208 TYR 0.009 0.001 TYR R 219 ARG 0.001 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.666 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0793 time to fit residues: 5.2961 Evaluate side-chains 31 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 66 optimal weight: 0.0030 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 90 optimal weight: 0.2980 chunk 56 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 overall best weight: 1.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5507 Z= 0.146 Angle : 0.362 5.230 7617 Z= 0.209 Chirality : 0.039 0.122 957 Planarity : 0.002 0.038 1037 Dihedral : 3.384 18.156 971 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.29), residues: 906 helix: 2.81 (0.24), residues: 448 sheet: -0.28 (0.53), residues: 116 loop : -1.46 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.002 0.001 HIS R 296 PHE 0.021 0.001 PHE R 208 TYR 0.011 0.001 TYR A 360 ARG 0.001 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.689 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0790 time to fit residues: 5.3479 Evaluate side-chains 31 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 57 optimal weight: 0.0030 chunk 61 optimal weight: 0.0470 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 20.0000 chunk 71 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.5892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5507 Z= 0.142 Angle : 0.363 5.297 7617 Z= 0.210 Chirality : 0.039 0.117 957 Planarity : 0.002 0.038 1037 Dihedral : 3.363 18.162 971 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.29), residues: 906 helix: 2.83 (0.24), residues: 448 sheet: -0.30 (0.53), residues: 117 loop : -1.43 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.002 0.001 HIS R 296 PHE 0.021 0.001 PHE R 208 TYR 0.009 0.001 TYR A 360 ARG 0.001 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.658 Fit side-chains REVERT: R 136 THR cc_start: 0.8434 (t) cc_final: 0.8069 (p) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0839 time to fit residues: 5.7919 Evaluate side-chains 32 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 0.0370 chunk 25 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.017 5507 Z= 0.083 Angle : 0.336 5.327 7617 Z= 0.190 Chirality : 0.039 0.120 957 Planarity : 0.002 0.038 1037 Dihedral : 3.058 15.818 971 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.29), residues: 906 helix: 2.96 (0.24), residues: 451 sheet: -0.48 (0.50), residues: 129 loop : -1.24 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 63 HIS 0.002 0.000 HIS R 296 PHE 0.020 0.001 PHE R 208 TYR 0.011 0.001 TYR R 219 ARG 0.001 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.656 Fit side-chains REVERT: R 136 THR cc_start: 0.8349 (t) cc_final: 0.8004 (p) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0768 time to fit residues: 5.3512 Evaluate side-chains 29 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 7 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5507 Z= 0.387 Angle : 0.528 5.171 7617 Z= 0.321 Chirality : 0.041 0.121 957 Planarity : 0.003 0.036 1037 Dihedral : 4.552 21.908 971 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.29), residues: 906 helix: 2.38 (0.25), residues: 425 sheet: -0.43 (0.53), residues: 118 loop : -1.65 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 297 HIS 0.007 0.002 HIS R 172 PHE 0.020 0.002 PHE R 208 TYR 0.016 0.002 TYR A 147 ARG 0.003 0.000 ARG B 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.751 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0859 time to fit residues: 5.3108 Evaluate side-chains 29 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.062157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.055760 restraints weight = 41860.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.056500 restraints weight = 28266.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.057004 restraints weight = 20835.870| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5507 Z= 0.227 Angle : 0.427 5.158 7617 Z= 0.254 Chirality : 0.040 0.120 957 Planarity : 0.003 0.037 1037 Dihedral : 4.084 19.720 971 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.29), residues: 906 helix: 2.48 (0.25), residues: 426 sheet: -0.42 (0.54), residues: 113 loop : -1.64 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.007 0.001 HIS R 296 PHE 0.018 0.002 PHE B 278 TYR 0.015 0.001 TYR A 360 ARG 0.001 0.000 ARG B 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1151.29 seconds wall clock time: 21 minutes 33.14 seconds (1293.14 seconds total)