Starting phenix.real_space_refine on Thu Feb 15 22:29:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5k_29747/02_2024/8g5k_29747.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5k_29747/02_2024/8g5k_29747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5k_29747/02_2024/8g5k_29747.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5k_29747/02_2024/8g5k_29747.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5k_29747/02_2024/8g5k_29747.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5k_29747/02_2024/8g5k_29747.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 37 5.49 5 S 78 5.16 5 C 8572 2.51 5 N 2391 2.21 5 O 2551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 124": "OE1" <-> "OE2" Residue "A ARG 309": "NH1" <-> "NH2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13629 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7079 Classifications: {'peptide': 905} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 60, 'TRANS': 844} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 103 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2934 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain breaks: 2 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2855 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 18, 'TRANS': 345} Chain breaks: 3 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "P" Number of atoms: 394 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 18, 373 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Conformer: "B" Number of residues, atoms: 18, 373 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} bond proxies already assigned to first conformer: 395 Chain: "T" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 367 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A DA P 27 " occ=0.50 ... (40 atoms not shown) pdb=" C4 B DA P 27 " occ=0.50 Time building chain proxies: 7.67, per 1000 atoms: 0.56 Number of scatterers: 13629 At special positions: 0 Unit cell: (91.686, 101.598, 139.594, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 37 15.00 O 2551 8.00 N 2391 7.00 C 8572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 5.56 Conformation dependent library (CDL) restraints added in 2.3 seconds 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3046 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 9 sheets defined 34.5% alpha, 10.1% beta 17 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'A' and resid 99 through 109 removed outlier: 4.096A pdb=" N LYS A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 146 removed outlier: 3.773A pdb=" N GLN A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 160 Processing helix chain 'A' and resid 223 through 227 removed outlier: 4.408A pdb=" N GLN A 226 " --> pdb=" O TRP A 223 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 227 " --> pdb=" O CYS A 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 227' Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 305 through 315 Processing helix chain 'A' and resid 345 through 351 removed outlier: 3.649A pdb=" N ASP A 349 " --> pdb=" O TRP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 removed outlier: 3.694A pdb=" N LEU A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 381 through 387 Processing helix chain 'A' and resid 388 through 418 removed outlier: 3.703A pdb=" N LEU A 392 " --> pdb=" O ASN A 388 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 432 removed outlier: 4.135A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 472 Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 570 through 576 Processing helix chain 'A' and resid 793 through 809 removed outlier: 4.699A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 904 Processing helix chain 'A' and resid 914 through 919 Processing helix chain 'A' and resid 933 through 940 Processing helix chain 'A' and resid 945 through 955 Processing helix chain 'A' and resid 958 through 968 removed outlier: 3.667A pdb=" N GLN A 968 " --> pdb=" O ARG A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 980 Processing helix chain 'A' and resid 982 through 989 removed outlier: 3.959A pdb=" N TYR A 986 " --> pdb=" O ALA A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1067 Processing helix chain 'A' and resid 1093 through 1115 removed outlier: 3.921A pdb=" N VAL A1097 " --> pdb=" O MET A1093 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A1115 " --> pdb=" O LEU A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1169 Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 100 through 105 removed outlier: 4.184A pdb=" N GLU B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 119 Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 192 through 197 removed outlier: 3.564A pdb=" N LEU B 197 " --> pdb=" O TYR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 265 removed outlier: 3.760A pdb=" N ASP B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.507A pdb=" N HIS B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 353 Processing helix chain 'B' and resid 394 through 407 removed outlier: 3.881A pdb=" N VAL B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 445 through 450 removed outlier: 3.618A pdb=" N GLU B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 485 Processing helix chain 'C' and resid 100 through 120 removed outlier: 4.120A pdb=" N SER C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL C 118 " --> pdb=" O TRP C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 192 removed outlier: 3.959A pdb=" N ALA C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 200 removed outlier: 3.695A pdb=" N VAL C 200 " --> pdb=" O CYS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.088A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 402 through 406 Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 427 through 435 removed outlier: 3.808A pdb=" N ASP C 433 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU C 434 " --> pdb=" O SER C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 485 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 215 removed outlier: 3.769A pdb=" N VAL A 213 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP A 198 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA3, first strand: chain 'A' and resid 1130 through 1132 Processing sheet with id=AA4, first strand: chain 'B' and resid 126 through 127 removed outlier: 6.600A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 301 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA6, first strand: chain 'B' and resid 413 through 415 removed outlier: 7.076A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.308A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.308A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LYS C 297 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE C 293 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU C 301 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 325 through 326 422 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 5.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4176 1.34 - 1.46: 2886 1.46 - 1.58: 6790 1.58 - 1.70: 72 1.70 - 1.82: 123 Bond restraints: 14047 Sorted by residual: bond pdb=" CG PRO A 241 " pdb=" CD PRO A 241 " ideal model delta sigma weight residual 1.503 1.360 0.143 3.40e-02 8.65e+02 1.77e+01 bond pdb=" N VAL A 353 " pdb=" CA VAL A 353 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.29e-02 6.01e+03 9.61e+00 bond pdb=" N GLU B 282 " pdb=" CA GLU B 282 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.74e+00 bond pdb=" N ILE A 313 " pdb=" CA ILE A 313 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.18e-02 7.18e+03 7.39e+00 bond pdb=" C3' DA P 10 " pdb=" O3' DA P 10 " ideal model delta sigma weight residual 1.422 1.499 -0.077 3.00e-02 1.11e+03 6.55e+00 ... (remaining 14042 not shown) Histogram of bond angle deviations from ideal: 82.00 - 93.44: 5 93.44 - 104.88: 426 104.88 - 116.32: 9215 116.32 - 127.75: 9288 127.75 - 139.19: 290 Bond angle restraints: 19224 Sorted by residual: angle pdb=" C3' DG P 24 " pdb=" O3' DG P 24 " pdb=" P DC P 25 " ideal model delta sigma weight residual 120.20 106.52 13.68 1.50e+00 4.44e-01 8.32e+01 angle pdb=" O3' DA P 10 " pdb=" P DG P 11 " pdb=" OP2 DG P 11 " ideal model delta sigma weight residual 108.00 82.00 26.00 3.00e+00 1.11e-01 7.51e+01 angle pdb=" N PRO A 241 " pdb=" CD PRO A 241 " pdb=" CG PRO A 241 " ideal model delta sigma weight residual 103.20 90.30 12.90 1.50e+00 4.44e-01 7.40e+01 angle pdb=" N PRO A 241 " pdb=" CA PRO A 241 " pdb=" CB PRO A 241 " ideal model delta sigma weight residual 103.25 94.97 8.28 1.05e+00 9.07e-01 6.22e+01 angle pdb=" O3' DA P 10 " pdb=" P DG P 11 " pdb=" OP1 DG P 11 " ideal model delta sigma weight residual 108.00 84.73 23.27 3.00e+00 1.11e-01 6.01e+01 ... (remaining 19219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 8017 35.44 - 70.88: 209 70.88 - 106.32: 12 106.32 - 141.76: 2 141.76 - 177.20: 3 Dihedral angle restraints: 8243 sinusoidal: 3527 harmonic: 4716 Sorted by residual: dihedral pdb=" CD ARG A 309 " pdb=" NE ARG A 309 " pdb=" CZ ARG A 309 " pdb=" NH1 ARG A 309 " ideal model delta sinusoidal sigma weight residual 0.00 74.98 -74.98 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" CA LEU B 106 " pdb=" C LEU B 106 " pdb=" N ARG B 107 " pdb=" CA ARG B 107 " ideal model delta harmonic sigma weight residual 180.00 154.04 25.96 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA PHE B 78 " pdb=" C PHE B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 8240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.416: 2091 0.416 - 0.831: 5 0.831 - 1.247: 0 1.247 - 1.662: 0 1.662 - 2.078: 1 Chirality restraints: 2097 Sorted by residual: chirality pdb=" P DG P 11 " pdb=" OP1 DG P 11 " pdb=" OP2 DG P 11 " pdb=" O5' DG P 11 " both_signs ideal model delta sigma weight residual True 2.35 0.27 2.08 2.00e-01 2.50e+01 1.08e+02 chirality pdb=" P DG T 4 " pdb=" OP1 DG T 4 " pdb=" OP2 DG T 4 " pdb=" O5' DG T 4 " both_signs ideal model delta sigma weight residual True 2.35 2.98 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P DG P 24 " pdb=" OP1 DG P 24 " pdb=" OP2 DG P 24 " pdb=" O5' DG P 24 " both_signs ideal model delta sigma weight residual True 2.35 -2.82 -0.48 2.00e-01 2.50e+01 5.73e+00 ... (remaining 2094 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 309 " -1.061 9.50e-02 1.11e+02 4.76e-01 1.36e+02 pdb=" NE ARG A 309 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 309 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 309 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 309 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 315 " 0.055 5.00e-02 4.00e+02 8.42e-02 1.13e+01 pdb=" N PRO C 316 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO C 316 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 316 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 782 " -0.051 5.00e-02 4.00e+02 7.40e-02 8.76e+00 pdb=" N PRO A 783 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 783 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 783 " -0.041 5.00e-02 4.00e+02 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1523 2.76 - 3.29: 13100 3.29 - 3.83: 22253 3.83 - 4.36: 25644 4.36 - 4.90: 43282 Nonbonded interactions: 105802 Sorted by model distance: nonbonded pdb=" O GLU C 113 " pdb=" OG1 THR C 116 " model vdw 2.223 2.440 nonbonded pdb=" OG1 THR A 885 " pdb=" O ASP A1186 " model vdw 2.248 2.440 nonbonded pdb=" OG1 THR A 586 " pdb=" OG SER A 590 " model vdw 2.287 2.440 nonbonded pdb=" OG SER B 457 " pdb=" O THR B 460 " model vdw 2.298 2.440 nonbonded pdb=" O PRO C 380 " pdb=" OG SER C 412 " model vdw 2.313 2.440 ... (remaining 105797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 68 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 77 or (resid 78 and (name N or nam \ e CA or name C or name O or name CB )) or resid 79 through 83 or (resid 84 and ( \ name N or name CA or name C or name O or name CB )) or resid 85 through 219 or ( \ resid 220 through 221 and (name N or name CA or name C or name O or name CB )) o \ r resid 228 through 327 or (resid 328 and (name N or name CA or name C or name O \ or name CB )) or resid 329 through 353 or (resid 354 and (name N or name CA or \ name C or name O or name CB )) or resid 355 through 357 or resid 372 or (resid 3 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 374 through \ 384 or (resid 385 and (name N or name CA or name C or name O or name CB )) or r \ esid 386 through 388 or (resid 389 and (name N or name CA or name C or name O or \ name CB )) or resid 390 through 428 or (resid 429 and (name N or name CA or nam \ e C or name O or name CB )) or resid 430 through 433 or (resid 434 through 435 a \ nd (name N or name CA or name C or name O or name CB )) or resid 436 through 444 \ or (resid 445 and (name N or name CA or name C or name O or name CB )) or resid \ 446 through 454 or (resid 455 and (name N or name CA or name C or name O or nam \ e CB )) or resid 456 through 485)) selection = (chain 'C' and (resid 68 through 122 or (resid 123 through 124 and (name N or na \ me CA or name C or name O or name CB )) or resid 125 or (resid 126 and (name N o \ r name CA or name C or name O or name CB )) or resid 127 through 133 or resid 17 \ 9 or (resid 180 and (name N or name CA or name C or name O or name CB )) or resi \ d 181 through 200 or (resid 201 and (name N or name CA or name C or name O or na \ me CB )) or resid 202 through 221 or (resid 228 and (name N or name CA or name C \ or name O or name CB )) or resid 229 through 245 or (resid 246 and (name N or n \ ame CA or name C or name O or name CB )) or resid 247 through 485)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 7.180 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 40.660 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 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 : 0.005 0.143 14047 Z= 0.295 Angle : 1.073 25.995 19224 Z= 0.550 Chirality : 0.075 2.078 2097 Planarity : 0.012 0.476 2340 Dihedral : 15.614 177.202 5197 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.63 % Favored : 91.31 % Rotamer: Outliers : 0.29 % Allowed : 1.03 % Favored : 98.68 % 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: -1.76 (0.20), residues: 1611 helix: -0.02 (0.22), residues: 545 sheet: -0.32 (0.37), residues: 177 loop : -2.18 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 607 HIS 0.011 0.001 HIS C 309 PHE 0.030 0.002 PHE A 197 TYR 0.027 0.001 TYR C 417 ARG 0.007 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 263 time to evaluate : 1.511 Fit side-chains REVERT: A 207 THR cc_start: 0.7723 (p) cc_final: 0.7482 (p) REVERT: A 416 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6380 (tp30) REVERT: A 544 MET cc_start: 0.6746 (mmm) cc_final: 0.6337 (mmm) REVERT: A 1097 VAL cc_start: 0.6574 (m) cc_final: 0.6254 (p) REVERT: A 1102 GLN cc_start: 0.7216 (mt0) cc_final: 0.6886 (mt0) REVERT: A 1156 THR cc_start: 0.7953 (m) cc_final: 0.7272 (p) REVERT: B 458 ARG cc_start: 0.8022 (ttp-170) cc_final: 0.7389 (ttp-170) REVERT: C 300 ILE cc_start: 0.8106 (mm) cc_final: 0.7787 (mt) outliers start: 4 outliers final: 0 residues processed: 266 average time/residue: 1.1047 time to fit residues: 325.1149 Evaluate side-chains 220 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 128 optimal weight: 0.1980 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 360 HIS ** A 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN A 811 GLN A 906 HIS A 932 HIS A 968 GLN A 970 ASN ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS B 249 ASN B 292 ASN B 323 HIS B 404 ASN C 133 HIS C 422 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14047 Z= 0.218 Angle : 0.734 26.505 19224 Z= 0.349 Chirality : 0.061 1.989 2097 Planarity : 0.005 0.059 2340 Dihedral : 16.786 176.793 2149 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.69 % Favored : 91.25 % Rotamer: Outliers : 2.49 % Allowed : 10.05 % Favored : 87.45 % 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 (0.20), residues: 1611 helix: 0.49 (0.23), residues: 526 sheet: -0.17 (0.38), residues: 165 loop : -1.98 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 607 HIS 0.006 0.001 HIS C 258 PHE 0.025 0.002 PHE A 749 TYR 0.025 0.001 TYR B 206 ARG 0.007 0.001 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 243 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7377 (mmp80) cc_final: 0.7096 (mtm110) REVERT: A 375 GLU cc_start: 0.5701 (mm-30) cc_final: 0.5456 (mm-30) REVERT: A 434 TYR cc_start: 0.7723 (t80) cc_final: 0.6888 (t80) REVERT: A 465 ASP cc_start: 0.6773 (m-30) cc_final: 0.6550 (m-30) REVERT: A 544 MET cc_start: 0.6709 (mmm) cc_final: 0.6383 (mmm) REVERT: A 953 ARG cc_start: 0.5529 (OUTLIER) cc_final: 0.5168 (mtm110) REVERT: A 1057 MET cc_start: 0.3408 (mmm) cc_final: 0.1356 (ptm) REVERT: A 1107 ASP cc_start: 0.6753 (m-30) cc_final: 0.6479 (m-30) REVERT: B 182 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7485 (ptt180) REVERT: B 260 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7307 (mt) REVERT: B 276 SER cc_start: 0.8158 (m) cc_final: 0.7806 (p) REVERT: C 300 ILE cc_start: 0.8250 (mm) cc_final: 0.7980 (mt) outliers start: 34 outliers final: 11 residues processed: 253 average time/residue: 1.1625 time to fit residues: 324.0928 Evaluate side-chains 234 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 220 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1167 LYS Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 411 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 132 optimal weight: 0.2980 chunk 147 optimal weight: 7.9990 chunk 50 optimal weight: 0.0020 chunk 119 optimal weight: 2.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS A 404 HIS ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS A1102 GLN ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 HIS ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 HIS ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14047 Z= 0.261 Angle : 0.739 25.883 19224 Z= 0.358 Chirality : 0.062 2.001 2097 Planarity : 0.005 0.049 2340 Dihedral : 16.836 177.916 2149 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.06 % Favored : 89.88 % Rotamer: Outliers : 3.37 % Allowed : 13.21 % Favored : 83.42 % 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: -1.41 (0.20), residues: 1611 helix: 0.28 (0.22), residues: 543 sheet: -0.02 (0.37), residues: 174 loop : -1.99 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 607 HIS 0.009 0.002 HIS A 805 PHE 0.026 0.002 PHE A 749 TYR 0.031 0.002 TYR B 206 ARG 0.009 0.001 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 230 time to evaluate : 1.447 Fit side-chains REVERT: A 141 LEU cc_start: 0.7377 (mm) cc_final: 0.7109 (mm) REVERT: A 283 LEU cc_start: 0.6688 (mp) cc_final: 0.6467 (mp) REVERT: A 297 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6728 (mtt) REVERT: A 375 GLU cc_start: 0.5816 (mm-30) cc_final: 0.5492 (mm-30) REVERT: A 478 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7106 (ttp80) REVERT: A 544 MET cc_start: 0.6650 (mmm) cc_final: 0.6300 (mmm) REVERT: A 877 MET cc_start: 0.6717 (mtm) cc_final: 0.6462 (mpp) REVERT: A 953 ARG cc_start: 0.5523 (OUTLIER) cc_final: 0.5106 (mtm110) REVERT: A 1107 ASP cc_start: 0.6830 (m-30) cc_final: 0.6562 (m-30) REVERT: B 182 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7488 (ptt180) REVERT: B 458 ARG cc_start: 0.8076 (ttp-170) cc_final: 0.7768 (ttp-170) REVERT: C 300 ILE cc_start: 0.8414 (mm) cc_final: 0.8190 (mt) REVERT: C 346 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.5740 (mtp) REVERT: C 382 LYS cc_start: 0.5125 (OUTLIER) cc_final: 0.4861 (mppt) outliers start: 46 outliers final: 17 residues processed: 251 average time/residue: 1.1246 time to fit residues: 311.7257 Evaluate side-chains 241 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 218 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 411 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 158 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 HIS ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS C 249 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14047 Z= 0.277 Angle : 0.734 26.015 19224 Z= 0.356 Chirality : 0.062 1.991 2097 Planarity : 0.005 0.044 2340 Dihedral : 16.841 177.746 2149 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.93 % Favored : 89.94 % Rotamer: Outliers : 3.15 % Allowed : 15.48 % Favored : 81.36 % 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: -1.46 (0.20), residues: 1611 helix: 0.22 (0.22), residues: 545 sheet: 0.12 (0.38), residues: 171 loop : -2.05 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 607 HIS 0.024 0.002 HIS A 404 PHE 0.027 0.002 PHE A 749 TYR 0.028 0.002 TYR B 206 ARG 0.007 0.001 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 228 time to evaluate : 1.549 Fit side-chains REVERT: A 299 MET cc_start: 0.6922 (mmm) cc_final: 0.6619 (tpt) REVERT: A 375 GLU cc_start: 0.5894 (mm-30) cc_final: 0.5606 (mm-30) REVERT: A 390 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.6423 (tm-30) REVERT: A 478 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7291 (ttp80) REVERT: A 544 MET cc_start: 0.6676 (mmm) cc_final: 0.6415 (mmm) REVERT: A 597 ARG cc_start: 0.7614 (mmm-85) cc_final: 0.7334 (mtt180) REVERT: A 877 MET cc_start: 0.6904 (mtm) cc_final: 0.6680 (mpp) REVERT: A 953 ARG cc_start: 0.5483 (OUTLIER) cc_final: 0.4996 (mtm110) REVERT: A 969 PHE cc_start: 0.6956 (m-10) cc_final: 0.6683 (m-10) REVERT: A 1057 MET cc_start: 0.3326 (mmm) cc_final: 0.0122 (pp-130) REVERT: A 1072 THR cc_start: 0.6298 (m) cc_final: 0.6006 (m) REVERT: A 1107 ASP cc_start: 0.6893 (m-30) cc_final: 0.6627 (m-30) REVERT: B 182 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7432 (ptt180) REVERT: B 276 SER cc_start: 0.8282 (m) cc_final: 0.8022 (p) REVERT: C 300 ILE cc_start: 0.8413 (mm) cc_final: 0.8173 (mt) REVERT: C 346 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.5743 (mtp) outliers start: 43 outliers final: 19 residues processed: 242 average time/residue: 1.1062 time to fit residues: 296.9527 Evaluate side-chains 247 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 223 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 346 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 0.0270 chunk 89 optimal weight: 3.9990 chunk 2 optimal weight: 0.0000 chunk 118 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 40 optimal weight: 0.0170 overall best weight: 0.2680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 354 ASN A1102 GLN ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 HIS ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14047 Z= 0.175 Angle : 0.679 25.980 19224 Z= 0.327 Chirality : 0.060 1.993 2097 Planarity : 0.004 0.045 2340 Dihedral : 16.708 177.666 2149 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.56 % Favored : 90.32 % Rotamer: Outliers : 2.71 % Allowed : 17.31 % 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: -1.36 (0.21), residues: 1611 helix: 0.38 (0.23), residues: 550 sheet: 0.22 (0.42), residues: 143 loop : -2.00 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 486 HIS 0.004 0.001 HIS B 77 PHE 0.022 0.001 PHE A 749 TYR 0.024 0.001 TYR B 206 ARG 0.004 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 221 time to evaluate : 1.365 Fit side-chains REVERT: A 299 MET cc_start: 0.6762 (mmm) cc_final: 0.6516 (tpt) REVERT: A 390 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6392 (tm-30) REVERT: A 478 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7023 (ttp80) REVERT: A 544 MET cc_start: 0.6653 (mmm) cc_final: 0.6380 (mmm) REVERT: A 597 ARG cc_start: 0.7555 (mmm-85) cc_final: 0.7301 (mtt180) REVERT: A 904 ASP cc_start: 0.5148 (p0) cc_final: 0.4841 (m-30) REVERT: A 953 ARG cc_start: 0.5402 (OUTLIER) cc_final: 0.5065 (ttp80) REVERT: A 969 PHE cc_start: 0.7021 (m-10) cc_final: 0.6694 (m-10) REVERT: A 1107 ASP cc_start: 0.6805 (m-30) cc_final: 0.6528 (m-30) REVERT: A 1111 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7635 (tp) REVERT: B 182 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7406 (ptt180) REVERT: B 276 SER cc_start: 0.8295 (m) cc_final: 0.8063 (p) REVERT: C 300 ILE cc_start: 0.8361 (mm) cc_final: 0.8095 (mt) REVERT: C 346 MET cc_start: 0.6666 (OUTLIER) cc_final: 0.5547 (mtp) outliers start: 37 outliers final: 17 residues processed: 230 average time/residue: 1.1246 time to fit residues: 285.7316 Evaluate side-chains 237 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 214 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 411 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 277 HIS A1102 GLN ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN C 133 HIS C 305 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14047 Z= 0.291 Angle : 0.747 25.985 19224 Z= 0.364 Chirality : 0.062 1.996 2097 Planarity : 0.005 0.045 2340 Dihedral : 16.798 177.722 2149 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.86 % Favored : 89.01 % Rotamer: Outliers : 3.45 % Allowed : 17.39 % Favored : 79.16 % 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 (0.20), residues: 1611 helix: 0.15 (0.22), residues: 551 sheet: 0.08 (0.39), residues: 169 loop : -2.01 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 607 HIS 0.009 0.001 HIS B 77 PHE 0.030 0.002 PHE A 749 TYR 0.031 0.002 TYR B 206 ARG 0.009 0.001 ARG A1187 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 228 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6590 (mt-10) REVERT: A 478 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7181 (ttp80) REVERT: A 877 MET cc_start: 0.7133 (mtm) cc_final: 0.6846 (mpp) REVERT: A 953 ARG cc_start: 0.5520 (OUTLIER) cc_final: 0.5047 (mtm110) REVERT: A 1057 MET cc_start: 0.1812 (mmp) cc_final: 0.0283 (pp-130) REVERT: A 1107 ASP cc_start: 0.6919 (m-30) cc_final: 0.6693 (m-30) REVERT: B 132 HIS cc_start: 0.6533 (OUTLIER) cc_final: 0.4767 (t-170) REVERT: B 182 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7398 (ptt180) REVERT: C 300 ILE cc_start: 0.8391 (mm) cc_final: 0.8180 (mt) REVERT: C 346 MET cc_start: 0.6787 (OUTLIER) cc_final: 0.5808 (mtp) REVERT: C 462 MET cc_start: 0.4424 (pp-130) cc_final: 0.4114 (pp-130) outliers start: 47 outliers final: 22 residues processed: 251 average time/residue: 1.0602 time to fit residues: 295.4195 Evaluate side-chains 246 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 219 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 346 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 133 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 158 optimal weight: 0.0050 chunk 98 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A1102 GLN ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14047 Z= 0.207 Angle : 0.712 25.987 19224 Z= 0.344 Chirality : 0.061 1.993 2097 Planarity : 0.004 0.048 2340 Dihedral : 16.692 177.248 2149 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.18 % Favored : 89.70 % Rotamer: Outliers : 2.86 % Allowed : 18.93 % Favored : 78.21 % 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: -1.41 (0.21), residues: 1611 helix: 0.25 (0.23), residues: 557 sheet: 0.12 (0.41), residues: 153 loop : -1.99 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 347 HIS 0.007 0.001 HIS B 77 PHE 0.027 0.001 PHE A 749 TYR 0.028 0.001 TYR B 206 ARG 0.007 0.000 ARG A1187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 223 time to evaluate : 1.514 Fit side-chains revert: symmetry clash REVERT: A 299 MET cc_start: 0.7082 (mmm) cc_final: 0.6669 (tpt) REVERT: A 478 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7102 (ttp80) REVERT: A 544 MET cc_start: 0.6778 (mmm) cc_final: 0.6561 (mmm) REVERT: A 953 ARG cc_start: 0.5404 (OUTLIER) cc_final: 0.5101 (ttp80) REVERT: A 1057 MET cc_start: 0.1738 (mmp) cc_final: 0.0227 (pp-130) REVERT: A 1107 ASP cc_start: 0.6860 (m-30) cc_final: 0.6593 (m-30) REVERT: B 132 HIS cc_start: 0.6523 (OUTLIER) cc_final: 0.4724 (t-170) REVERT: B 182 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7393 (ptt180) REVERT: B 408 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7288 (pm20) REVERT: C 300 ILE cc_start: 0.8360 (mm) cc_final: 0.8128 (mt) REVERT: C 462 MET cc_start: 0.4472 (pp-130) cc_final: 0.4039 (pp-130) outliers start: 39 outliers final: 21 residues processed: 239 average time/residue: 1.0664 time to fit residues: 282.8588 Evaluate side-chains 244 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 218 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 904 ASP Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 298 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 100 optimal weight: 0.0870 chunk 107 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 811 GLN A1102 GLN ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14047 Z= 0.209 Angle : 0.736 26.003 19224 Z= 0.350 Chirality : 0.062 1.991 2097 Planarity : 0.005 0.048 2340 Dihedral : 16.651 177.195 2149 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.74 % Favored : 89.20 % Rotamer: Outliers : 2.86 % Allowed : 19.74 % Favored : 77.40 % 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: -1.38 (0.21), residues: 1611 helix: 0.33 (0.23), residues: 555 sheet: 0.15 (0.41), residues: 154 loop : -2.02 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 347 HIS 0.007 0.001 HIS B 77 PHE 0.033 0.002 PHE A 273 TYR 0.027 0.001 TYR B 206 ARG 0.007 0.000 ARG A1187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 216 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6980 (mmm) cc_final: 0.6739 (tpt) REVERT: A 405 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6510 (mt-10) REVERT: A 478 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.6991 (ttp80) REVERT: A 592 LEU cc_start: 0.6876 (tp) cc_final: 0.6595 (mt) REVERT: A 1057 MET cc_start: 0.1740 (mmp) cc_final: 0.0212 (pp-130) REVERT: A 1102 GLN cc_start: 0.7314 (mt0) cc_final: 0.6764 (mt0) REVERT: A 1107 ASP cc_start: 0.6843 (m-30) cc_final: 0.6599 (m-30) REVERT: B 132 HIS cc_start: 0.6500 (OUTLIER) cc_final: 0.4688 (t-170) REVERT: B 182 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7391 (ptt180) REVERT: C 300 ILE cc_start: 0.8405 (mm) cc_final: 0.8192 (mt) outliers start: 39 outliers final: 23 residues processed: 232 average time/residue: 1.0748 time to fit residues: 277.5095 Evaluate side-chains 237 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 211 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 298 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 0.0060 chunk 151 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A1089 GLN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14047 Z= 0.244 Angle : 0.752 25.982 19224 Z= 0.361 Chirality : 0.062 1.993 2097 Planarity : 0.005 0.046 2340 Dihedral : 16.683 177.019 2149 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.92 % Favored : 89.01 % Rotamer: Outliers : 2.64 % Allowed : 20.32 % Favored : 77.04 % 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: -1.50 (0.21), residues: 1611 helix: 0.22 (0.23), residues: 559 sheet: 0.10 (0.41), residues: 153 loop : -2.10 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 607 HIS 0.006 0.001 HIS B 77 PHE 0.028 0.002 PHE A 749 TYR 0.029 0.002 TYR B 206 ARG 0.011 0.001 ARG A 953 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 221 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.6966 (mmm) cc_final: 0.6700 (tpt) REVERT: A 405 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6482 (mt-10) REVERT: A 478 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6907 (ttp80) REVERT: A 592 LEU cc_start: 0.6980 (tp) cc_final: 0.6708 (mt) REVERT: A 916 PHE cc_start: 0.6433 (t80) cc_final: 0.6189 (t80) REVERT: A 1057 MET cc_start: 0.1796 (mmp) cc_final: 0.0403 (pp-130) REVERT: A 1107 ASP cc_start: 0.6852 (m-30) cc_final: 0.6618 (m-30) REVERT: B 132 HIS cc_start: 0.6535 (OUTLIER) cc_final: 0.4739 (t-170) REVERT: B 182 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7416 (ptt180) REVERT: C 300 ILE cc_start: 0.8398 (mm) cc_final: 0.8177 (mt) outliers start: 36 outliers final: 25 residues processed: 237 average time/residue: 1.0869 time to fit residues: 284.9430 Evaluate side-chains 249 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 221 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 298 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 0.5980 chunk 155 optimal weight: 0.9980 chunk 95 optimal weight: 0.2980 chunk 73 optimal weight: 0.0870 chunk 108 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 740 ASN A1102 GLN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14047 Z= 0.224 Angle : 0.753 25.972 19224 Z= 0.358 Chirality : 0.062 1.992 2097 Planarity : 0.005 0.046 2340 Dihedral : 16.637 176.805 2149 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.92 % Favored : 89.01 % Rotamer: Outliers : 2.35 % Allowed : 20.91 % Favored : 76.74 % 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 (0.21), residues: 1611 helix: 0.31 (0.23), residues: 553 sheet: 0.12 (0.41), residues: 154 loop : -2.11 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 347 HIS 0.007 0.001 HIS B 77 PHE 0.035 0.002 PHE A 273 TYR 0.028 0.001 TYR B 206 ARG 0.007 0.000 ARG A1187 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 219 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: A 299 MET cc_start: 0.6949 (mmm) cc_final: 0.6671 (tpt) REVERT: A 405 GLU cc_start: 0.6752 (mt-10) cc_final: 0.6390 (mt-10) REVERT: A 478 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6857 (ttp80) REVERT: A 592 LEU cc_start: 0.6891 (tp) cc_final: 0.6634 (mt) REVERT: A 916 PHE cc_start: 0.6415 (t80) cc_final: 0.6173 (t80) REVERT: A 1057 MET cc_start: 0.1866 (mmp) cc_final: 0.0401 (pp-130) REVERT: A 1107 ASP cc_start: 0.6823 (m-30) cc_final: 0.6583 (m-30) REVERT: B 132 HIS cc_start: 0.6510 (OUTLIER) cc_final: 0.4718 (t-170) REVERT: B 182 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7408 (ptt180) outliers start: 32 outliers final: 23 residues processed: 235 average time/residue: 1.0501 time to fit residues: 273.9138 Evaluate side-chains 244 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 218 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 298 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 1.9990 chunk 138 optimal weight: 0.0670 chunk 39 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A1102 GLN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.199319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.177385 restraints weight = 19467.077| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 2.14 r_work: 0.4099 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3960 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3965 r_free = 0.3965 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3965 r_free = 0.3965 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 14047 Z= 0.249 Angle : 0.958 59.199 19224 Z= 0.517 Chirality : 0.062 1.992 2097 Planarity : 0.005 0.057 2340 Dihedral : 16.640 176.795 2149 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.11 % Favored : 88.83 % Rotamer: Outliers : 2.20 % Allowed : 21.06 % Favored : 76.74 % Cbeta Deviations : 0.07 % 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: -1.48 (0.21), residues: 1611 helix: 0.31 (0.23), residues: 553 sheet: 0.11 (0.41), residues: 154 loop : -2.12 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 347 HIS 0.006 0.001 HIS B 77 PHE 0.026 0.002 PHE A 749 TYR 0.027 0.001 TYR B 206 ARG 0.006 0.000 ARG A1187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5363.38 seconds wall clock time: 95 minutes 34.03 seconds (5734.03 seconds total)