Starting phenix.real_space_refine on Tue Nov 14 22:32:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/11_2023/6pza_20530_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/11_2023/6pza_20530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/11_2023/6pza_20530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/11_2023/6pza_20530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/11_2023/6pza_20530_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/11_2023/6pza_20530_neut_updated.pdb" } resolution = 3.74 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 3 5.49 5 S 34 5.16 5 Cl 1 4.86 5 C 6209 2.51 5 N 1717 2.21 5 O 1695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 16": "NH1" <-> "NH2" Residue "C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 258": "NH1" <-> "NH2" Residue "C ARG 285": "NH1" <-> "NH2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C ARG 298": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 598": "NH1" <-> "NH2" Residue "C ARG 702": "NH1" <-> "NH2" Residue "C ARG 837": "NH1" <-> "NH2" Residue "C ARG 1104": "NH1" <-> "NH2" Residue "C ARG 1218": "NH1" <-> "NH2" Residue "C ARG 1300": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 9659 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 9501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1422, 9501 Classifications: {'peptide': 1422} Incomplete info: {'truncation_to_alanine': 543} Link IDs: {'CIS': 1, 'PTRANS': 48, 'TRANS': 1372} Chain breaks: 4 Unresolved non-hydrogen bonds: 1768 Unresolved non-hydrogen angles: 2233 Unresolved non-hydrogen dihedrals: 1378 Unresolved non-hydrogen chiralities: 225 Planarities with less than four sites: {'GLN:plan1': 32, 'ASP:plan': 41, 'TYR:plan': 2, 'ASN:plan1': 21, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 44, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 833 Chain: "D" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 94 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 17} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'ATP': 1, 'GBM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.81, per 1000 atoms: 0.60 Number of scatterers: 9659 At special positions: 0 Unit cell: (96.615, 110.295, 140.22, 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) Cl 1 17.00 S 34 16.00 P 3 15.00 O 1695 8.00 N 1717 7.00 C 6209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 26 " distance=2.02 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: 3.84 Conformation dependent library (CDL) restraints added in 2.0 seconds 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2730 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 6 sheets defined 60.5% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'C' and resid 13 through 15 No H-bonds generated for 'chain 'C' and resid 13 through 15' Processing helix chain 'C' and resid 27 through 54 removed outlier: 3.885A pdb=" N VAL C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) Proline residue: C 35 - end of helix Proline residue: C 45 - end of helix Processing helix chain 'C' and resid 59 through 62 removed outlier: 4.448A pdb=" N HIS C 62 " --> pdb=" O HIS C 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 59 through 62' Processing helix chain 'C' and resid 72 through 96 Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 109 through 128 removed outlier: 3.599A pdb=" N TYR C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 159 removed outlier: 3.651A pdb=" N ILE C 137 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA C 138 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 139 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE C 141 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR C 144 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 146 " --> pdb=" O TRP C 143 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE C 147 " --> pdb=" O THR C 144 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C 149 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 150 " --> pdb=" O PHE C 147 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 155 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 193 Processing helix chain 'C' and resid 208 through 211 No H-bonds generated for 'chain 'C' and resid 208 through 211' Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 255 through 257 No H-bonds generated for 'chain 'C' and resid 255 through 257' Processing helix chain 'C' and resid 259 through 276 Processing helix chain 'C' and resid 284 through 327 removed outlier: 5.732A pdb=" N ARG C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ARG C 298 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) Proline residue: C 317 - end of helix Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 348 through 352 Processing helix chain 'C' and resid 356 through 397 removed outlier: 3.505A pdb=" N LEU C 368 " --> pdb=" O LEU C 364 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLN C 374 " --> pdb=" O ARG C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 433 removed outlier: 3.554A pdb=" N ASP C 424 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR C 425 " --> pdb=" O VAL C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 455 removed outlier: 3.822A pdb=" N TRP C 439 " --> pdb=" O CYS C 435 " (cutoff:3.500A) Proline residue: C 442 - end of helix Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 471 through 503 removed outlier: 4.128A pdb=" N GLU C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 511 Processing helix chain 'C' and resid 516 through 563 removed outlier: 4.277A pdb=" N THR C 525 " --> pdb=" O ARG C 521 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER C 543 " --> pdb=" O TYR C 539 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 544 " --> pdb=" O THR C 540 " (cutoff:3.500A) Proline residue: C 551 - end of helix Processing helix chain 'C' and resid 573 through 614 Proline residue: C 589 - end of helix removed outlier: 3.972A pdb=" N LEU C 592 " --> pdb=" O THR C 588 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 594 " --> pdb=" O LEU C 590 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 595 " --> pdb=" O PHE C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 726 Processing helix chain 'C' and resid 786 through 789 No H-bonds generated for 'chain 'C' and resid 786 through 789' Processing helix chain 'C' and resid 796 through 805 Processing helix chain 'C' and resid 809 through 814 Processing helix chain 'C' and resid 832 through 845 Processing helix chain 'C' and resid 863 through 878 Processing helix chain 'C' and resid 914 through 917 No H-bonds generated for 'chain 'C' and resid 914 through 917' Processing helix chain 'C' and resid 997 through 1008 Processing helix chain 'C' and resid 1010 through 1042 removed outlier: 4.494A pdb=" N LEU C1015 " --> pdb=" O LEU C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1061 through 1106 removed outlier: 3.906A pdb=" N LEU C1074 " --> pdb=" O LEU C1070 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU C1087 " --> pdb=" O SER C1083 " (cutoff:3.500A) Processing helix chain 'C' and resid 1110 through 1115 Processing helix chain 'C' and resid 1118 through 1134 removed outlier: 4.733A pdb=" N ASP C1128 " --> pdb=" O ARG C1124 " (cutoff:3.500A) Processing helix chain 'C' and resid 1136 through 1160 removed outlier: 4.000A pdb=" N LEU C1148 " --> pdb=" O SER C1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 1164 through 1209 Proline residue: C1170 - end of helix removed outlier: 3.720A pdb=" N ASP C1188 " --> pdb=" O VAL C1184 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C1196 " --> pdb=" O LEU C1192 " (cutoff:3.500A) Proline residue: C1199 - end of helix removed outlier: 3.587A pdb=" N VAL C1208 " --> pdb=" O PHE C1204 " (cutoff:3.500A) Processing helix chain 'C' and resid 1211 through 1216 Processing helix chain 'C' and resid 1220 through 1272 removed outlier: 3.666A pdb=" N ALA C1237 " --> pdb=" O SER C1233 " (cutoff:3.500A) Processing helix chain 'C' and resid 1279 through 1291 removed outlier: 3.914A pdb=" N TYR C1287 " --> pdb=" O LEU C1283 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET C1290 " --> pdb=" O THR C1286 " (cutoff:3.500A) Processing helix chain 'C' and resid 1295 through 1319 removed outlier: 3.806A pdb=" N ALA C1311 " --> pdb=" O ILE C1307 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL C1312 " --> pdb=" O GLN C1308 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE C1315 " --> pdb=" O ALA C1311 " (cutoff:3.500A) Processing helix chain 'C' and resid 1386 through 1393 removed outlier: 4.668A pdb=" N PHE C1393 " --> pdb=" O SER C1389 " (cutoff:3.500A) Processing helix chain 'C' and resid 1415 through 1418 No H-bonds generated for 'chain 'C' and resid 1415 through 1418' Processing helix chain 'C' and resid 1436 through 1441 Processing helix chain 'C' and resid 1448 through 1457 Processing helix chain 'C' and resid 1461 through 1464 No H-bonds generated for 'chain 'C' and resid 1461 through 1464' Processing helix chain 'C' and resid 1485 through 1497 Processing helix chain 'C' and resid 1513 through 1529 Processing helix chain 'C' and resid 1540 through 1542 No H-bonds generated for 'chain 'C' and resid 1540 through 1542' Processing helix chain 'C' and resid 1565 through 1569 Processing helix chain 'C' and resid 1572 through 1577 Processing sheet with id= A, first strand: chain 'C' and resid 338 through 340 removed outlier: 4.227A pdb=" N THR C 338 " --> pdb=" O PHE C 345 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 679 through 681 Processing sheet with id= C, first strand: chain 'C' and resid 708 through 711 removed outlier: 6.611A pdb=" N VAL C 884 " --> pdb=" O THR C 709 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE C 711 " --> pdb=" O VAL C 884 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 886 " --> pdb=" O ILE C 711 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 1346 through 1348 Processing sheet with id= E, first strand: chain 'C' and resid 1422 through 1424 removed outlier: 6.435A pdb=" N ILE C1502 " --> pdb=" O SER C1423 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 1549 through 1551 616 hydrogen bonds defined for protein. 1791 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1543 1.31 - 1.43: 2702 1.43 - 1.56: 5567 1.56 - 1.68: 7 1.68 - 1.81: 53 Bond restraints: 9872 Sorted by residual: bond pdb=" O5 GBM C1601 " pdb=" S2 GBM C1601 " ideal model delta sigma weight residual 1.448 1.648 -0.200 2.00e-02 2.50e+03 9.97e+01 bond pdb=" O4 GBM C1601 " pdb=" S2 GBM C1601 " ideal model delta sigma weight residual 1.453 1.647 -0.194 2.00e-02 2.50e+03 9.43e+01 bond pdb=" C4 ATP C1602 " pdb=" C5 ATP C1602 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.26e+01 bond pdb=" C5 ATP C1602 " pdb=" C6 ATP C1602 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.31e+01 bond pdb=" C17 GBM C1601 " pdb=" N8 GBM C1601 " ideal model delta sigma weight residual 1.340 1.443 -0.103 2.00e-02 2.50e+03 2.65e+01 ... (remaining 9867 not shown) Histogram of bond angle deviations from ideal: 98.60 - 106.00: 216 106.00 - 113.41: 5478 113.41 - 120.81: 4781 120.81 - 128.22: 3000 128.22 - 135.62: 101 Bond angle restraints: 13576 Sorted by residual: angle pdb=" PB ATP C1602 " pdb=" O3B ATP C1602 " pdb=" PG ATP C1602 " ideal model delta sigma weight residual 139.87 117.67 22.20 1.00e+00 1.00e+00 4.93e+02 angle pdb=" PA ATP C1602 " pdb=" O3A ATP C1602 " pdb=" PB ATP C1602 " ideal model delta sigma weight residual 136.83 117.58 19.25 1.00e+00 1.00e+00 3.70e+02 angle pdb=" C5 ATP C1602 " pdb=" C4 ATP C1602 " pdb=" N3 ATP C1602 " ideal model delta sigma weight residual 126.80 119.13 7.67 1.00e+00 1.00e+00 5.88e+01 angle pdb=" C LEU C 571 " pdb=" N SER C 572 " pdb=" CA SER C 572 " ideal model delta sigma weight residual 121.70 134.37 -12.67 1.80e+00 3.09e-01 4.95e+01 angle pdb=" N3 ATP C1602 " pdb=" C4 ATP C1602 " pdb=" N9 ATP C1602 " ideal model delta sigma weight residual 127.04 135.10 -8.06 1.15e+00 7.59e-01 4.93e+01 ... (remaining 13571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 5424 16.79 - 33.58: 206 33.58 - 50.37: 45 50.37 - 67.16: 4 67.16 - 83.95: 3 Dihedral angle restraints: 5682 sinusoidal: 1482 harmonic: 4200 Sorted by residual: dihedral pdb=" CA LYS C 252 " pdb=" C LYS C 252 " pdb=" N LEU C 253 " pdb=" CA LEU C 253 " ideal model delta harmonic sigma weight residual 180.00 132.03 47.97 0 5.00e+00 4.00e-02 9.20e+01 dihedral pdb=" CA ILE C 996 " pdb=" C ILE C 996 " pdb=" N PRO C 997 " pdb=" CA PRO C 997 " ideal model delta harmonic sigma weight residual -180.00 -137.86 -42.14 0 5.00e+00 4.00e-02 7.10e+01 dihedral pdb=" CA LYS C1562 " pdb=" C LYS C1562 " pdb=" N PRO C1563 " pdb=" CA PRO C1563 " ideal model delta harmonic sigma weight residual 180.00 151.85 28.15 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 5679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1144 0.056 - 0.111: 416 0.111 - 0.167: 75 0.167 - 0.222: 7 0.222 - 0.278: 4 Chirality restraints: 1646 Sorted by residual: chirality pdb=" CG LEU C1248 " pdb=" CB LEU C1248 " pdb=" CD1 LEU C1248 " pdb=" CD2 LEU C1248 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA LEU C 175 " pdb=" N LEU C 175 " pdb=" C LEU C 175 " pdb=" CB LEU C 175 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C1' ATP C1602 " pdb=" C2' ATP C1602 " pdb=" N9 ATP C1602 " pdb=" O4' ATP C1602 " both_signs ideal model delta sigma weight residual False 2.41 2.64 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1643 not shown) Planarity restraints: 1752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 420 " -0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C LEU C 420 " 0.058 2.00e-02 2.50e+03 pdb=" O LEU C 420 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL C 421 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET C 441 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO C 442 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 442 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 442 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1037 " 0.023 2.00e-02 2.50e+03 1.62e-02 6.53e+00 pdb=" CG TRP C1037 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP C1037 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP C1037 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C1037 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C1037 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C1037 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1037 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1037 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C1037 " 0.000 2.00e-02 2.50e+03 ... (remaining 1749 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2266 2.78 - 3.31: 9221 3.31 - 3.84: 15515 3.84 - 4.37: 16416 4.37 - 4.90: 28420 Nonbonded interactions: 71838 Sorted by model distance: nonbonded pdb=" OH TYR C 123 " pdb=" O LEU C 135 " model vdw 2.252 2.440 nonbonded pdb=" OD2 ASP C1128 " pdb=" NH1 ARG C1314 " model vdw 2.271 2.520 nonbonded pdb=" O GLU C 791 " pdb=" OH TYR C1219 " model vdw 2.287 2.440 nonbonded pdb=" OG1 THR C 338 " pdb=" O PHE C 345 " model vdw 2.291 2.440 nonbonded pdb=" O THR C 789 " pdb=" OG SER C 792 " model vdw 2.308 2.440 ... (remaining 71833 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 2.720 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.550 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5080 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 : 0.008 0.200 9872 Z= 0.530 Angle : 1.063 22.204 13576 Z= 0.612 Chirality : 0.058 0.278 1646 Planarity : 0.008 0.065 1752 Dihedral : 10.716 83.951 2949 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % Twisted General : 0.07 % 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: -4.29 (0.17), residues: 1429 helix: -2.33 (0.12), residues: 915 sheet: -3.78 (0.52), residues: 60 loop : -3.46 (0.26), residues: 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 0.937 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.2168 time to fit residues: 67.0910 Evaluate side-chains 140 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 50.0000 chunk 108 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 73 optimal weight: 0.1980 chunk 57 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 83 optimal weight: 50.0000 chunk 129 optimal weight: 50.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 160 HIS C 219 GLN C 262 ASN C 374 GLN ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 707 GLN ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5543 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9872 Z= 0.203 Angle : 0.686 9.821 13576 Z= 0.352 Chirality : 0.044 0.219 1646 Planarity : 0.005 0.048 1752 Dihedral : 5.537 49.886 1522 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.03 % Allowed : 12.25 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % Twisted General : 0.07 % 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: -1.89 (0.21), residues: 1429 helix: -0.17 (0.16), residues: 912 sheet: -3.56 (0.54), residues: 60 loop : -3.11 (0.28), residues: 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 191 average time/residue: 0.1969 time to fit residues: 53.9157 Evaluate side-chains 156 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0894 time to fit residues: 3.5649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 130 optimal weight: 0.0060 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 129 optimal weight: 40.0000 chunk 44 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS C 125 HIS ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1197 GLN C1245 ASN C1301 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9872 Z= 0.221 Angle : 0.682 12.485 13576 Z= 0.344 Chirality : 0.045 0.218 1646 Planarity : 0.005 0.064 1752 Dihedral : 5.109 58.186 1522 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.61 % Allowed : 15.56 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.22), residues: 1429 helix: 0.73 (0.17), residues: 922 sheet: -3.06 (0.58), residues: 60 loop : -2.99 (0.28), residues: 447 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 193 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 213 average time/residue: 0.1937 time to fit residues: 60.3385 Evaluate side-chains 172 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0907 time to fit residues: 4.0424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 40.0000 chunk 97 optimal weight: 10.0000 chunk 67 optimal weight: 50.0000 chunk 14 optimal weight: 0.0670 chunk 62 optimal weight: 30.0000 chunk 87 optimal weight: 8.9990 chunk 130 optimal weight: 40.0000 chunk 138 optimal weight: 50.0000 chunk 68 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 overall best weight: 6.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 HIS C 72 ASN ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 HIS ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 547 ASN ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1316 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.8731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 9872 Z= 0.431 Angle : 0.833 10.834 13576 Z= 0.432 Chirality : 0.052 0.271 1646 Planarity : 0.006 0.061 1752 Dihedral : 5.627 55.907 1522 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 7.06 % Allowed : 18.30 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: -1.20 (0.21), residues: 1429 helix: 0.42 (0.16), residues: 907 sheet: -3.53 (0.59), residues: 45 loop : -2.93 (0.26), residues: 477 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 199 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 27 residues processed: 226 average time/residue: 0.1938 time to fit residues: 63.7796 Evaluate side-chains 175 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 1.059 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.0909 time to fit residues: 6.0187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 4.9990 chunk 78 optimal weight: 50.0000 chunk 2 optimal weight: 0.0970 chunk 102 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 95 optimal weight: 0.0000 chunk 0 optimal weight: 8.9990 chunk 70 optimal weight: 20.0000 chunk 124 optimal weight: 50.0000 chunk 34 optimal weight: 8.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 HIS C 397 ASN ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1191 GLN C1316 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.9192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9872 Z= 0.240 Angle : 0.639 12.720 13576 Z= 0.325 Chirality : 0.043 0.156 1646 Planarity : 0.005 0.057 1752 Dihedral : 5.171 63.010 1522 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.60 % Allowed : 26.66 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -0.37 (0.23), residues: 1429 helix: 1.11 (0.17), residues: 910 sheet: -3.10 (0.63), residues: 55 loop : -2.72 (0.28), residues: 464 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 182 average time/residue: 0.1811 time to fit residues: 49.5392 Evaluate side-chains 159 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 147 time to evaluate : 1.016 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0966 time to fit residues: 3.5985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 9.9990 chunk 124 optimal weight: 50.0000 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 50.0000 chunk 34 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 HIS ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS C 547 ASN C 896 HIS ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1203 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.9622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9872 Z= 0.228 Angle : 0.628 9.071 13576 Z= 0.320 Chirality : 0.043 0.138 1646 Planarity : 0.004 0.053 1752 Dihedral : 4.985 61.378 1522 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.47 % Allowed : 26.95 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.03 (0.23), residues: 1429 helix: 1.40 (0.17), residues: 908 sheet: -3.03 (0.65), residues: 55 loop : -2.47 (0.29), residues: 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 155 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 168 average time/residue: 0.1773 time to fit residues: 44.7862 Evaluate side-chains 166 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0961 time to fit residues: 4.4856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 30.0000 chunk 101 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 77 optimal weight: 30.0000 chunk 137 optimal weight: 9.9990 chunk 86 optimal weight: 30.0000 chunk 84 optimal weight: 0.0060 chunk 63 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 overall best weight: 4.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 1.0202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9872 Z= 0.304 Angle : 0.672 11.560 13576 Z= 0.342 Chirality : 0.045 0.147 1646 Planarity : 0.004 0.051 1752 Dihedral : 5.026 63.770 1522 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.74 % Allowed : 27.95 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.04 (0.23), residues: 1429 helix: 1.41 (0.17), residues: 907 sheet: -3.45 (0.66), residues: 46 loop : -2.44 (0.29), residues: 476 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 155 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 162 average time/residue: 0.1953 time to fit residues: 47.2639 Evaluate side-chains 159 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1024 time to fit residues: 4.1539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 68 optimal weight: 0.0770 chunk 12 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 125 optimal weight: 0.0270 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 1.0369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9872 Z= 0.166 Angle : 0.616 11.009 13576 Z= 0.307 Chirality : 0.042 0.155 1646 Planarity : 0.004 0.056 1752 Dihedral : 4.827 59.210 1522 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.01 % Allowed : 29.83 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.24), residues: 1429 helix: 1.70 (0.17), residues: 912 sheet: -3.18 (0.65), residues: 55 loop : -2.28 (0.30), residues: 462 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 155 average time/residue: 0.1807 time to fit residues: 42.1045 Evaluate side-chains 148 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1008 time to fit residues: 2.2575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 50.0000 chunk 120 optimal weight: 50.0000 chunk 128 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 121 optimal weight: 30.0000 chunk 127 optimal weight: 30.0000 chunk 84 optimal weight: 0.0570 overall best weight: 6.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 HIS C 293 HIS ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 1.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 9872 Z= 0.383 Angle : 0.711 10.074 13576 Z= 0.367 Chirality : 0.047 0.171 1646 Planarity : 0.005 0.049 1752 Dihedral : 5.117 63.817 1522 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.02 % Allowed : 30.55 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: 0.10 (0.23), residues: 1429 helix: 1.49 (0.17), residues: 900 sheet: -3.54 (0.66), residues: 46 loop : -2.41 (0.28), residues: 483 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 151 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 158 average time/residue: 0.1951 time to fit residues: 45.5030 Evaluate side-chains 150 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 143 time to evaluate : 1.076 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0963 time to fit residues: 2.6712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 50.0000 chunk 82 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 142 optimal weight: 0.4980 chunk 131 optimal weight: 40.0000 chunk 113 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 1.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9872 Z= 0.204 Angle : 0.636 10.984 13576 Z= 0.319 Chirality : 0.043 0.221 1646 Planarity : 0.004 0.050 1752 Dihedral : 4.894 60.954 1522 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.72 % Allowed : 31.70 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.39 (0.24), residues: 1429 helix: 1.70 (0.17), residues: 903 sheet: -3.49 (0.69), residues: 46 loop : -2.28 (0.29), residues: 480 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 153 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 154 average time/residue: 0.1880 time to fit residues: 43.1673 Evaluate side-chains 151 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1161 time to fit residues: 2.0498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 116 optimal weight: 30.0000 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 0.0030 chunk 99 optimal weight: 0.9980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 ASN C 293 HIS ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.132914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107399 restraints weight = 18583.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.110037 restraints weight = 9253.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.111736 restraints weight = 5746.792| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 1.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9872 Z= 0.161 Angle : 0.609 10.141 13576 Z= 0.303 Chirality : 0.041 0.136 1646 Planarity : 0.004 0.049 1752 Dihedral : 4.665 57.595 1522 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.29 % Allowed : 33.43 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.24), residues: 1429 helix: 2.03 (0.17), residues: 904 sheet: -3.44 (0.69), residues: 46 loop : -2.14 (0.30), residues: 479 =============================================================================== Job complete usr+sys time: 1904.98 seconds wall clock time: 35 minutes 15.99 seconds (2115.99 seconds total)