Starting phenix.real_space_refine on Sat Mar 16 02:45:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td2_25821/03_2024/7td2_25821_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td2_25821/03_2024/7td2_25821.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td2_25821/03_2024/7td2_25821_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td2_25821/03_2024/7td2_25821_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td2_25821/03_2024/7td2_25821_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td2_25821/03_2024/7td2_25821.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td2_25821/03_2024/7td2_25821.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td2_25821/03_2024/7td2_25821_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td2_25821/03_2024/7td2_25821_trim_updated.pdb" } resolution = 3.11 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= 1.055 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 60 5.16 5 C 4416 2.51 5 N 1156 2.21 5 O 1263 1.98 5 H 6632 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 226": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 63": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13528 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 4482 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 7, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 4863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 4863 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 80 Chain: "A" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3394 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 760 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'NKP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.98, per 1000 atoms: 0.44 Number of scatterers: 13528 At special positions: 0 Unit cell: (94.696, 95.76, 128.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 1 15.00 O 1263 8.00 N 1156 7.00 C 4416 6.00 H 6632 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 24 " - pdb=" SG CYS R 190 " distance=2.03 Simple disulfide: pdb=" SG CYS R 188 " - pdb=" SG CYS R 195 " distance=1.95 Simple disulfide: pdb=" SG CYS R 284 " - pdb=" SG CYS R 287 " 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: 9.63 Conformation dependent library (CDL) restraints added in 1.1 seconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1714 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 8 sheets defined 40.2% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'R' and resid 30 through 36 Processing helix chain 'R' and resid 47 through 76 Processing helix chain 'R' and resid 83 through 105 Processing helix chain 'R' and resid 110 through 114 Processing helix chain 'R' and resid 118 through 150 removed outlier: 3.652A pdb=" N ILE R 128 " --> pdb=" O ARG R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 181 Processing helix chain 'R' and resid 204 through 237 Processing helix chain 'R' and resid 252 through 283 removed outlier: 3.621A pdb=" N PHE R 267 " --> pdb=" O VAL R 263 " (cutoff:3.500A) Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 293 through 311 removed outlier: 3.983A pdb=" N SER R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA R 305 " --> pdb=" O GLU R 301 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 316 through 321 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'A' and resid 11 through 31 Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.331A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.871A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 42 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.775A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.530A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 150 removed outlier: 6.957A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.081A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.042A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.886A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.755A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.496A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 990 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: 4.52 Time building geometry restraints manager: 10.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6607 1.03 - 1.23: 30 1.23 - 1.42: 2949 1.42 - 1.62: 3989 1.62 - 1.82: 90 Bond restraints: 13665 Sorted by residual: bond pdb=" C LYS A 349 " pdb=" O LYS A 349 " ideal model delta sigma weight residual 1.236 1.196 0.041 1.26e-02 6.30e+03 1.04e+01 bond pdb=" C LEU A 348 " pdb=" N LYS A 349 " ideal model delta sigma weight residual 1.335 1.293 0.042 1.38e-02 5.25e+03 9.26e+00 bond pdb=" N LYS A 349 " pdb=" H LYS A 349 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.43e+00 bond pdb=" N PHE A 354 " pdb=" H PHE A 354 " ideal model delta sigma weight residual 0.860 0.907 -0.047 2.00e-02 2.50e+03 5.47e+00 bond pdb=" C LYS A 349 " pdb=" N ASP A 350 " ideal model delta sigma weight residual 1.334 1.305 0.029 1.46e-02 4.69e+03 4.00e+00 ... (remaining 13660 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.12: 183 107.12 - 113.84: 16084 113.84 - 120.56: 4530 120.56 - 127.27: 3693 127.27 - 133.99: 70 Bond angle restraints: 24560 Sorted by residual: angle pdb=" C LEU A 353 " pdb=" N PHE A 354 " pdb=" CA PHE A 354 " ideal model delta sigma weight residual 121.70 128.74 -7.04 1.80e+00 3.09e-01 1.53e+01 angle pdb=" N LYS A 349 " pdb=" CA LYS A 349 " pdb=" C LYS A 349 " ideal model delta sigma weight residual 111.82 108.03 3.79 1.16e+00 7.43e-01 1.07e+01 angle pdb=" CA GLY A 292 " pdb=" C GLY A 292 " pdb=" N SER A 293 " ideal model delta sigma weight residual 114.58 116.74 -2.16 8.60e-01 1.35e+00 6.32e+00 angle pdb=" N VAL R 289 " pdb=" CA VAL R 289 " pdb=" C VAL R 289 " ideal model delta sigma weight residual 112.96 110.48 2.48 1.00e+00 1.00e+00 6.15e+00 angle pdb=" CA LEU A 353 " pdb=" C LEU A 353 " pdb=" N PHE A 354 " ideal model delta sigma weight residual 116.76 112.93 3.83 1.58e+00 4.01e-01 5.89e+00 ... (remaining 24555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 6021 17.17 - 34.33: 364 34.33 - 51.50: 75 51.50 - 68.67: 25 68.67 - 85.84: 4 Dihedral angle restraints: 6489 sinusoidal: 3345 harmonic: 3144 Sorted by residual: dihedral pdb=" CA CYS R 284 " pdb=" C CYS R 284 " pdb=" N PRO R 285 " pdb=" CA PRO R 285 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CB GLU B 226 " pdb=" CG GLU B 226 " pdb=" CD GLU B 226 " pdb=" OE1 GLU B 226 " ideal model delta sinusoidal sigma weight residual 0.00 -85.84 85.84 1 3.00e+01 1.11e-03 9.89e+00 dihedral pdb=" CA ASP R 204 " pdb=" CB ASP R 204 " pdb=" CG ASP R 204 " pdb=" OD1 ASP R 204 " ideal model delta sinusoidal sigma weight residual -30.00 -83.23 53.23 1 2.00e+01 2.50e-03 9.63e+00 ... (remaining 6486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 705 0.027 - 0.053: 269 0.053 - 0.080: 83 0.080 - 0.106: 37 0.106 - 0.133: 27 Chirality restraints: 1121 Sorted by residual: 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 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA LYS A 349 " pdb=" N LYS A 349 " pdb=" C LYS A 349 " pdb=" CB LYS A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 ... (remaining 1118 not shown) Planarity restraints: 2076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 348 " -0.012 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" N LYS A 349 " 0.037 2.00e-02 2.50e+03 pdb=" CA LYS A 349 " -0.010 2.00e-02 2.50e+03 pdb=" H LYS A 349 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 353 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C LEU A 353 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU A 353 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE A 354 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 348 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" C LEU A 348 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU A 348 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS A 349 " -0.009 2.00e-02 2.50e+03 ... (remaining 2073 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 738 2.22 - 2.81: 28428 2.81 - 3.41: 34929 3.41 - 4.00: 46723 4.00 - 4.60: 72992 Nonbonded interactions: 183810 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" HG SER B 316 " model vdw 1.619 1.850 nonbonded pdb=" O ASP B 298 " pdb=" H ALA B 302 " model vdw 1.631 1.850 nonbonded pdb=" O ILE R 63 " pdb="HD22 ASN R 67 " model vdw 1.635 1.850 nonbonded pdb=" HA ASP R 315 " pdb=" HE2 PHE A 354 " model vdw 1.638 2.270 nonbonded pdb=" OG SER B 201 " pdb=" HE1 TRP B 211 " model vdw 1.642 1.850 ... (remaining 183805 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 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: 0.190 Extract box with map and model: 1.330 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 42.930 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 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 : 0.002 0.042 7033 Z= 0.141 Angle : 0.411 7.043 9551 Z= 0.246 Chirality : 0.037 0.133 1121 Planarity : 0.002 0.020 1197 Dihedral : 11.886 85.837 2425 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.42 % Allowed : 5.64 % Favored : 93.94 % 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: -0.58 (0.27), residues: 890 helix: 0.95 (0.25), residues: 382 sheet: -1.03 (0.36), residues: 177 loop : -1.54 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.005 0.001 PHE A 189 TYR 0.011 0.001 TYR R 231 ARG 0.001 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 191 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 ILE cc_start: 0.9097 (mm) cc_final: 0.8832 (mt) REVERT: B 186 ASP cc_start: 0.8580 (m-30) cc_final: 0.8020 (m-30) REVERT: B 220 GLN cc_start: 0.8020 (mt0) cc_final: 0.7799 (mt0) REVERT: A 207 GLU cc_start: 0.7001 (tp30) cc_final: 0.6737 (tp30) REVERT: G 21 MET cc_start: 0.3344 (mmm) cc_final: 0.3061 (mmt) outliers start: 3 outliers final: 1 residues processed: 192 average time/residue: 0.4085 time to fit residues: 103.6984 Evaluate side-chains 158 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN A 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 7033 Z= 0.362 Angle : 0.512 5.247 9551 Z= 0.286 Chirality : 0.041 0.153 1121 Planarity : 0.004 0.051 1197 Dihedral : 5.297 56.746 983 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.55 % Allowed : 12.13 % Favored : 86.32 % 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: 0.33 (0.28), residues: 890 helix: 1.67 (0.26), residues: 390 sheet: -0.53 (0.38), residues: 175 loop : -1.10 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 322 PHE 0.013 0.002 PHE A 196 TYR 0.017 0.002 TYR R 231 ARG 0.004 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 172 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 MET cc_start: 0.7002 (mmp) cc_final: 0.6586 (mmp) REVERT: B 123 ILE cc_start: 0.9113 (mm) cc_final: 0.8909 (mt) REVERT: B 186 ASP cc_start: 0.8662 (m-30) cc_final: 0.8147 (m-30) REVERT: B 220 GLN cc_start: 0.8268 (mt0) cc_final: 0.8060 (mt0) REVERT: B 323 ASP cc_start: 0.7231 (t0) cc_final: 0.6987 (t0) REVERT: A 24 ARG cc_start: 0.7637 (mtm110) cc_final: 0.7352 (mtm110) REVERT: A 308 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8046 (mt-10) REVERT: A 318 GLU cc_start: 0.8267 (tt0) cc_final: 0.7733 (tt0) outliers start: 11 outliers final: 8 residues processed: 177 average time/residue: 0.3526 time to fit residues: 85.1368 Evaluate side-chains 168 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7033 Z= 0.244 Angle : 0.449 4.622 9551 Z= 0.247 Chirality : 0.039 0.136 1121 Planarity : 0.003 0.031 1197 Dihedral : 5.258 50.592 983 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.54 % Allowed : 13.82 % Favored : 83.64 % 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: 0.78 (0.29), residues: 890 helix: 2.20 (0.26), residues: 380 sheet: -0.36 (0.37), residues: 180 loop : -0.97 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 PHE 0.010 0.001 PHE A 196 TYR 0.011 0.001 TYR R 231 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 167 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 MET cc_start: 0.7332 (mmp) cc_final: 0.6857 (mmt) REVERT: B 186 ASP cc_start: 0.8644 (m-30) cc_final: 0.8102 (m-30) REVERT: B 220 GLN cc_start: 0.8219 (mt0) cc_final: 0.7984 (mt0) REVERT: A 24 ARG cc_start: 0.7695 (mtm110) cc_final: 0.7458 (mtm110) REVERT: A 308 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7945 (mt-10) REVERT: G 21 MET cc_start: 0.3479 (mmm) cc_final: 0.3215 (mmt) outliers start: 18 outliers final: 15 residues processed: 177 average time/residue: 0.3671 time to fit residues: 87.6624 Evaluate side-chains 173 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 272 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 22 optimal weight: 0.0870 chunk 70 optimal weight: 3.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 67 ASN R 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7033 Z= 0.215 Angle : 0.438 4.583 9551 Z= 0.241 Chirality : 0.038 0.147 1121 Planarity : 0.003 0.032 1197 Dihedral : 5.245 54.057 983 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.12 % Allowed : 15.37 % Favored : 82.51 % 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: 1.12 (0.29), residues: 890 helix: 2.52 (0.26), residues: 380 sheet: -0.18 (0.38), residues: 180 loop : -0.84 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.008 0.001 PHE B 278 TYR 0.011 0.001 TYR R 231 ARG 0.002 0.000 ARG R 238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 161 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ASP cc_start: 0.8621 (m-30) cc_final: 0.8071 (m-30) REVERT: B 268 ASN cc_start: 0.8378 (t0) cc_final: 0.8105 (t0) REVERT: A 24 ARG cc_start: 0.7746 (mtm110) cc_final: 0.7359 (mtm110) outliers start: 15 outliers final: 13 residues processed: 172 average time/residue: 0.3730 time to fit residues: 87.3235 Evaluate side-chains 170 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 157 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 76 optimal weight: 0.5980 chunk 21 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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: 0.7635 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7033 Z= 0.247 Angle : 0.446 4.633 9551 Z= 0.246 Chirality : 0.038 0.139 1121 Planarity : 0.003 0.033 1197 Dihedral : 5.327 55.189 983 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.54 % Allowed : 15.23 % Favored : 82.23 % 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: 890 helix: 2.63 (0.26), residues: 380 sheet: -0.13 (0.38), residues: 180 loop : -0.78 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 322 PHE 0.014 0.001 PHE G 61 TYR 0.011 0.001 TYR R 231 ARG 0.005 0.000 ARG R 235 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ASP cc_start: 0.8602 (m-30) cc_final: 0.8063 (m-30) REVERT: B 268 ASN cc_start: 0.8402 (t0) cc_final: 0.8118 (t0) REVERT: A 24 ARG cc_start: 0.7775 (mtm110) cc_final: 0.7422 (mtm110) REVERT: A 229 ASP cc_start: 0.8657 (p0) cc_final: 0.8428 (p0) outliers start: 18 outliers final: 17 residues processed: 180 average time/residue: 0.3518 time to fit residues: 86.5502 Evaluate side-chains 179 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 162 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 272 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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: 0.7613 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7033 Z= 0.160 Angle : 0.417 4.431 9551 Z= 0.228 Chirality : 0.038 0.136 1121 Planarity : 0.003 0.033 1197 Dihedral : 5.143 54.936 983 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.54 % Allowed : 16.36 % Favored : 81.10 % 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: 1.47 (0.29), residues: 890 helix: 2.86 (0.26), residues: 380 sheet: -0.09 (0.39), residues: 180 loop : -0.68 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.000 HIS A 188 PHE 0.010 0.001 PHE G 61 TYR 0.008 0.001 TYR B 59 ARG 0.004 0.000 ARG R 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 165 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ASP cc_start: 0.8585 (m-30) cc_final: 0.8006 (m-30) REVERT: B 268 ASN cc_start: 0.8399 (t0) cc_final: 0.8115 (t0) REVERT: A 24 ARG cc_start: 0.7741 (mtm110) cc_final: 0.7416 (mtm110) REVERT: A 229 ASP cc_start: 0.8670 (p0) cc_final: 0.8404 (p0) REVERT: A 256 ASN cc_start: 0.8693 (t0) cc_final: 0.8409 (t0) outliers start: 18 outliers final: 16 residues processed: 177 average time/residue: 0.3681 time to fit residues: 89.3808 Evaluate side-chains 178 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 272 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.7624 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7033 Z= 0.199 Angle : 0.430 4.551 9551 Z= 0.235 Chirality : 0.038 0.138 1121 Planarity : 0.003 0.033 1197 Dihedral : 5.195 55.835 983 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.26 % Allowed : 16.93 % Favored : 80.82 % 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: 1.52 (0.29), residues: 890 helix: 2.90 (0.26), residues: 380 sheet: -0.10 (0.39), residues: 180 loop : -0.64 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 225 PHE 0.012 0.001 PHE G 61 TYR 0.010 0.001 TYR R 231 ARG 0.002 0.000 ARG R 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ASP cc_start: 0.8551 (m-30) cc_final: 0.7990 (m-30) REVERT: B 268 ASN cc_start: 0.8414 (t0) cc_final: 0.8123 (t0) REVERT: A 24 ARG cc_start: 0.7749 (mtm110) cc_final: 0.7408 (mtm110) REVERT: A 229 ASP cc_start: 0.8698 (p0) cc_final: 0.8486 (p0) REVERT: A 256 ASN cc_start: 0.8716 (t0) cc_final: 0.8428 (t0) REVERT: A 261 ASP cc_start: 0.8361 (p0) cc_final: 0.8074 (p0) REVERT: G 21 MET cc_start: 0.3418 (mmm) cc_final: 0.3135 (mmt) outliers start: 16 outliers final: 16 residues processed: 176 average time/residue: 0.3540 time to fit residues: 84.5802 Evaluate side-chains 174 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 158 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 272 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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: 0.7624 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7033 Z= 0.195 Angle : 0.431 4.518 9551 Z= 0.236 Chirality : 0.038 0.156 1121 Planarity : 0.003 0.033 1197 Dihedral : 5.226 56.574 983 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.26 % Allowed : 17.21 % Favored : 80.54 % 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: 1.60 (0.29), residues: 890 helix: 2.98 (0.26), residues: 380 sheet: -0.09 (0.39), residues: 179 loop : -0.57 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.000 HIS A 322 PHE 0.011 0.001 PHE G 61 TYR 0.009 0.001 TYR R 231 ARG 0.004 0.000 ARG R 235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ASP cc_start: 0.8536 (m-30) cc_final: 0.7972 (m-30) REVERT: B 268 ASN cc_start: 0.8424 (t0) cc_final: 0.8137 (t0) REVERT: A 24 ARG cc_start: 0.7729 (mtm110) cc_final: 0.7414 (mtm110) REVERT: A 229 ASP cc_start: 0.8719 (p0) cc_final: 0.8471 (p0) REVERT: A 256 ASN cc_start: 0.8721 (t0) cc_final: 0.8441 (t0) REVERT: A 261 ASP cc_start: 0.8346 (p0) cc_final: 0.8051 (p0) REVERT: G 21 MET cc_start: 0.3494 (mmm) cc_final: 0.3176 (mmt) outliers start: 16 outliers final: 16 residues processed: 173 average time/residue: 0.3540 time to fit residues: 83.7304 Evaluate side-chains 173 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 272 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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: 0.7653 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7033 Z= 0.297 Angle : 0.476 4.738 9551 Z= 0.261 Chirality : 0.039 0.142 1121 Planarity : 0.003 0.033 1197 Dihedral : 5.530 59.047 983 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.26 % Allowed : 17.49 % Favored : 80.25 % 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: 1.39 (0.29), residues: 890 helix: 2.75 (0.26), residues: 379 sheet: -0.07 (0.39), residues: 174 loop : -0.67 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 322 PHE 0.014 0.001 PHE G 61 TYR 0.014 0.001 TYR R 231 ARG 0.005 0.000 ARG R 235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 ARG cc_start: 0.8102 (mmt-90) cc_final: 0.7800 (mmt90) REVERT: B 186 ASP cc_start: 0.8534 (m-30) cc_final: 0.7985 (m-30) REVERT: B 268 ASN cc_start: 0.8499 (t0) cc_final: 0.8198 (t0) REVERT: A 24 ARG cc_start: 0.7697 (mtm110) cc_final: 0.7390 (mtm110) REVERT: A 229 ASP cc_start: 0.8712 (p0) cc_final: 0.8505 (p0) REVERT: A 256 ASN cc_start: 0.8741 (t0) cc_final: 0.8452 (t0) REVERT: A 261 ASP cc_start: 0.8386 (p0) cc_final: 0.8102 (p0) REVERT: G 21 MET cc_start: 0.3466 (mmm) cc_final: 0.3150 (mmt) outliers start: 16 outliers final: 16 residues processed: 174 average time/residue: 0.3583 time to fit residues: 84.6586 Evaluate side-chains 176 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 160 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 272 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 87 optimal weight: 0.0980 chunk 80 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7598 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7033 Z= 0.112 Angle : 0.412 4.404 9551 Z= 0.222 Chirality : 0.038 0.144 1121 Planarity : 0.003 0.032 1197 Dihedral : 5.218 57.303 983 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.83 % Allowed : 17.77 % Favored : 80.39 % 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: 1.84 (0.30), residues: 890 helix: 3.19 (0.27), residues: 379 sheet: 0.13 (0.40), residues: 170 loop : -0.51 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.000 HIS B 91 PHE 0.009 0.001 PHE G 61 TYR 0.007 0.001 TYR B 59 ARG 0.005 0.000 ARG R 235 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 159 is missing expected H atoms. Skipping. Residue MET 237 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 316 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 163 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 ARG cc_start: 0.7967 (mmt-90) cc_final: 0.7567 (mmt90) REVERT: B 83 ASP cc_start: 0.8547 (t0) cc_final: 0.8333 (t0) REVERT: B 268 ASN cc_start: 0.8464 (t0) cc_final: 0.8180 (t0) REVERT: A 24 ARG cc_start: 0.7707 (mtm110) cc_final: 0.7402 (mtm110) REVERT: A 229 ASP cc_start: 0.8675 (p0) cc_final: 0.8464 (p0) REVERT: A 256 ASN cc_start: 0.8679 (t0) cc_final: 0.8429 (t0) REVERT: A 261 ASP cc_start: 0.8278 (p0) cc_final: 0.8039 (p0) REVERT: G 21 MET cc_start: 0.3542 (mmm) cc_final: 0.3218 (mmt) outliers start: 13 outliers final: 13 residues processed: 173 average time/residue: 0.4004 time to fit residues: 94.7155 Evaluate side-chains 173 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 272 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 8 optimal weight: 0.0870 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.137200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.107975 restraints weight = 24604.820| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.39 r_work: 0.3015 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7033 Z= 0.219 Angle : 0.440 4.602 9551 Z= 0.240 Chirality : 0.038 0.137 1121 Planarity : 0.003 0.034 1197 Dihedral : 5.366 59.528 983 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.12 % Allowed : 17.91 % Favored : 79.97 % 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: 1.74 (0.30), residues: 890 helix: 3.08 (0.26), residues: 379 sheet: 0.02 (0.40), residues: 174 loop : -0.49 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS A 322 PHE 0.012 0.001 PHE G 61 TYR 0.011 0.001 TYR R 231 ARG 0.005 0.000 ARG R 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3594.86 seconds wall clock time: 63 minutes 51.25 seconds (3831.25 seconds total)