Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 22:51:15 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/12_2021/6pza_20530_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/12_2021/6pza_20530.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/12_2021/6pza_20530_neut_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/12_2021/6pza_20530_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/12_2021/6pza_20530_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/12_2021/6pza_20530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/12_2021/6pza_20530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/12_2021/6pza_20530_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/12_2021/6pza_20530_neut_updated.pdb" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/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: {'PTRANS': 48, 'CIS': 1, '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: {'GBM': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.04, per 1000 atoms: 0.63 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 Amimo 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: 4.01 Conformation dependent library (CDL) restraints added in 1.6 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: 2.13 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: 3.45 Time building geometry restraints manager: 4.36 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=" O4 GBM C1601 " pdb=" S2 GBM C1601 " ideal model delta sigma weight residual 1.464 1.647 -0.183 2.00e-02 2.50e+03 8.39e+01 bond pdb=" O5 GBM C1601 " pdb=" S2 GBM C1601 " ideal model delta sigma weight residual 1.465 1.648 -0.183 2.00e-02 2.50e+03 8.35e+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=" C5 ATP C1602 " pdb=" N7 ATP C1602 " ideal model delta sigma weight residual 1.387 1.340 0.047 1.00e-02 1.00e+04 2.23e+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=" 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 angle pdb=" N1 ATP C1602 " pdb=" C2 ATP C1602 " pdb=" N3 ATP C1602 " ideal model delta sigma weight residual 128.69 123.68 5.01 1.00e+00 1.00e+00 2.51e+01 ... (remaining 13571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 5424 16.79 - 33.58: 204 33.58 - 50.37: 46 50.37 - 67.16: 5 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: 1145 0.056 - 0.111: 415 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 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. 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 Write .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.100 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.080 Process input model: 28.510 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.250 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 35.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5010 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 : 0.007 0.183 9872 Z= 0.509 Angle : 1.052 22.204 13576 Z= 0.608 Chirality : 0.058 0.278 1646 Planarity : 0.008 0.065 1752 Dihedral : 10.781 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 % 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 : 1.018 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.2235 time to fit residues: 70.4903 Evaluate side-chains 140 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.072 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5057 ------------------------------------------------------------------------------- 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: 3.9990 chunk 73 optimal weight: 0.1980 chunk 57 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 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: 2.0386 ------------------------------------------------------------------------------- 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 C1245 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5765 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.104 9872 Z= 0.294 Angle : 0.772 16.919 13576 Z= 0.391 Chirality : 0.045 0.242 1646 Planarity : 0.006 0.070 1752 Dihedral : 5.627 51.734 1522 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer Outliers : 4.76 % 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: -2.16 (0.21), residues: 1429 helix: -0.42 (0.16), residues: 919 sheet: -3.60 (0.54), residues: 60 loop : -3.17 (0.28), residues: 450 *********************** 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 219 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 186 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 18 residues processed: 207 average time/residue: 0.1949 time to fit residues: 58.2006 Evaluate side-chains 171 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 153 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0899 time to fit residues: 4.5241 ------------------------------------------------------------------------------- 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: 0.6980 chunk 40 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 130 optimal weight: 0.0010 chunk 140 optimal weight: 0.5980 chunk 115 optimal weight: 9.9990 chunk 129 optimal weight: 50.0000 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 HIS C 397 ASN C 896 HIS ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1224 GLN ** C1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1301 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5928 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.097 9872 Z= 0.194 Angle : 0.650 14.432 13576 Z= 0.322 Chirality : 0.042 0.177 1646 Planarity : 0.005 0.072 1752 Dihedral : 5.233 51.066 1522 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 3.75 % 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: -1.01 (0.22), residues: 1429 helix: 0.57 (0.17), residues: 925 sheet: -3.34 (0.57), residues: 60 loop : -2.96 (0.28), residues: 444 *********************** 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 196 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 184 average time/residue: 0.1777 time to fit residues: 49.5732 Evaluate side-chains 164 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 1.108 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0946 time to fit residues: 4.2552 ------------------------------------------------------------------------------- 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: 20.0000 chunk 97 optimal weight: 6.9990 chunk 67 optimal weight: 50.0000 chunk 14 optimal weight: 8.9990 chunk 62 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 130 optimal weight: 40.0000 chunk 138 optimal weight: 50.0000 chunk 68 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 ASN C 105 HIS ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN C1224 GLN ** C1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.8300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.087 9872 Z= 0.444 Angle : 0.910 23.666 13576 Z= 0.467 Chirality : 0.051 0.238 1646 Planarity : 0.006 0.071 1752 Dihedral : 6.055 63.248 1522 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer Outliers : 6.48 % 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: -1.43 (0.21), residues: 1429 helix: 0.19 (0.16), residues: 911 sheet: -3.67 (0.58), residues: 45 loop : -2.95 (0.27), residues: 473 *********************** 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 245 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 200 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 22 residues processed: 225 average time/residue: 0.1578 time to fit residues: 51.9405 Evaluate side-chains 174 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 152 time to evaluate : 0.793 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.0692 time to fit residues: 3.9519 ------------------------------------------------------------------------------- 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: 7.9990 chunk 78 optimal weight: 50.0000 chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 30.0000 chunk 124 optimal weight: 50.0000 chunk 34 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS C 547 ASN ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1203 HIS ** C1224 GLN ** 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: 0.7066 moved from start: 0.9147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 9872 Z= 0.329 Angle : 0.742 18.034 13576 Z= 0.376 Chirality : 0.045 0.176 1646 Planarity : 0.005 0.092 1752 Dihedral : 5.488 50.371 1522 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer Outliers : 4.90 % 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: -0.72 (0.22), residues: 1429 helix: 0.82 (0.17), residues: 909 sheet: -3.23 (0.63), residues: 55 loop : -2.81 (0.28), residues: 465 *********************** 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 198 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 164 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 20 residues processed: 185 average time/residue: 0.1762 time to fit residues: 49.0724 Evaluate side-chains 165 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 1.162 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0953 time to fit residues: 5.0175 ------------------------------------------------------------------------------- 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: 4.9990 chunk 81 optimal weight: 30.0000 chunk 34 optimal weight: 9.9990 chunk 138 optimal weight: 50.0000 chunk 114 optimal weight: 5.9990 chunk 64 optimal weight: 30.0000 chunk 11 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 397 ASN C 491 HIS ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1224 GLN ** C1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 1.0036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.123 9872 Z= 0.391 Angle : 0.740 15.378 13576 Z= 0.382 Chirality : 0.046 0.154 1646 Planarity : 0.006 0.102 1752 Dihedral : 5.497 58.111 1522 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer Outliers : 4.76 % 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: -0.57 (0.23), residues: 1429 helix: 0.97 (0.17), residues: 904 sheet: -3.46 (0.67), residues: 45 loop : -2.77 (0.28), residues: 480 *********************** 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 194 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 161 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 21 residues processed: 181 average time/residue: 0.2004 time to fit residues: 52.5014 Evaluate side-chains 158 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1138 time to fit residues: 5.4448 ------------------------------------------------------------------------------- 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: 7.9990 chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 40.0000 chunk 101 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 77 optimal weight: 30.0000 chunk 137 optimal weight: 20.0000 chunk 86 optimal weight: 30.0000 chunk 84 optimal weight: 0.0770 chunk 63 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 overall best weight: 4.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 HIS C 397 ASN C 485 GLN C 491 HIS ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 1.0495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 9872 Z= 0.310 Angle : 0.671 15.448 13576 Z= 0.341 Chirality : 0.044 0.150 1646 Planarity : 0.005 0.062 1752 Dihedral : 5.326 55.035 1522 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer Outliers : 3.31 % 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: -0.28 (0.23), residues: 1429 helix: 1.22 (0.17), residues: 902 sheet: -3.51 (0.67), residues: 45 loop : -2.67 (0.28), residues: 482 *********************** 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 175 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 165 average time/residue: 0.1870 time to fit residues: 45.9795 Evaluate side-chains 159 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 147 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1037 time to fit residues: 3.6895 ------------------------------------------------------------------------------- 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: 40.0000 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 0.0770 chunk 108 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 397 ASN ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 1.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 9872 Z= 0.198 Angle : 0.628 15.075 13576 Z= 0.310 Chirality : 0.042 0.141 1646 Planarity : 0.004 0.057 1752 Dihedral : 4.971 51.116 1522 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer Outliers : 0.86 % 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: 0.15 (0.24), residues: 1429 helix: 1.56 (0.18), residues: 905 sheet: -3.55 (0.68), residues: 45 loop : -2.51 (0.29), residues: 479 *********************** 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 165 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 159 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 159 average time/residue: 0.1892 time to fit residues: 44.7194 Evaluate side-chains 150 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 1.102 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1114 time to fit residues: 2.2681 ------------------------------------------------------------------------------- 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: 9.9990 chunk 128 optimal weight: 40.0000 chunk 77 optimal weight: 30.0000 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 20.0000 chunk 121 optimal weight: 30.0000 chunk 127 optimal weight: 20.0000 chunk 84 optimal weight: 0.0670 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 HIS ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 1.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.286 9872 Z= 0.269 Angle : 0.688 18.654 13576 Z= 0.357 Chirality : 0.043 0.145 1646 Planarity : 0.005 0.073 1752 Dihedral : 4.941 51.804 1522 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer Outliers : 1.59 % 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: 0.19 (0.24), residues: 1429 helix: 1.60 (0.17), residues: 904 sheet: -3.54 (0.69), residues: 45 loop : -2.51 (0.29), residues: 480 *********************** 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 161 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 150 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 155 average time/residue: 0.1747 time to fit residues: 41.1124 Evaluate side-chains 149 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 time to evaluate : 1.113 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0963 time to fit residues: 2.7344 ------------------------------------------------------------------------------- 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: 40.0000 chunk 82 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 142 optimal weight: 50.0000 chunk 131 optimal weight: 50.0000 chunk 113 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 1.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.482 9872 Z= 0.405 Angle : 0.826 27.081 13576 Z= 0.434 Chirality : 0.047 0.185 1646 Planarity : 0.005 0.084 1752 Dihedral : 5.323 57.400 1522 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer Outliers : 1.01 % 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: -0.23 (0.23), residues: 1429 helix: 1.23 (0.17), residues: 903 sheet: -3.66 (0.68), residues: 46 loop : -2.58 (0.28), 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 153 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 146 average time/residue: 0.1910 time to fit residues: 42.0680 Evaluate side-chains 143 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1098 time to fit residues: 2.5373 ------------------------------------------------------------------------------- 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: 30.0000 chunk 34 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 116 optimal weight: 30.0000 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 HIS ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.129865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.103879 restraints weight = 19570.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.106418 restraints weight = 9835.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.108069 restraints weight = 6172.368| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 1.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.709 9872 Z= 0.707 Angle : 1.052 46.553 13576 Z= 0.564 Chirality : 0.043 0.150 1646 Planarity : 0.006 0.105 1752 Dihedral : 5.070 53.229 1522 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.07 % 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: 0.19 (0.24), residues: 1429 helix: 1.63 (0.17), residues: 896 sheet: -3.64 (0.69), residues: 46 loop : -2.47 (0.29), residues: 487 =============================================================================== Job complete usr+sys time: 1723.99 seconds wall clock time: 37 minutes 12.48 seconds (2232.48 seconds total)