Starting phenix.real_space_refine on Tue Mar 3 19:11:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pzi_20535/03_2026/6pzi_20535_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pzi_20535/03_2026/6pzi_20535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pzi_20535/03_2026/6pzi_20535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pzi_20535/03_2026/6pzi_20535.map" model { file = "/net/cci-nas-00/data/ceres_data/6pzi_20535/03_2026/6pzi_20535_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pzi_20535/03_2026/6pzi_20535_neut.cif" } resolution = 4.5 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 Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 3 5.16 5 C 4968 2.51 5 N 1514 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7985 Number of models: 1 Model: "" Number of chains: 2 Chain: "G" Number of atoms: 7954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1412, 7954 Classifications: {'peptide': 1412} Incomplete info: {'truncation_to_alanine': 991} Link IDs: {'PTRANS': 48, 'TRANS': 1363} Chain breaks: 5 Unresolved non-hydrogen bonds: 3286 Unresolved non-hydrogen angles: 4184 Unresolved non-hydrogen dihedrals: 2582 Unresolved non-hydrogen chiralities: 452 Planarities with less than four sites: {'GLU:plan': 56, 'ASP:plan': 51, 'GLN:plan1': 57, 'ASN:plan1': 37, 'PHE:plan': 51, 'HIS:plan': 13, 'ARG:plan': 63, 'TYR:plan': 8, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 1512 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.24, per 1000 atoms: 0.28 Number of scatterers: 7985 At special positions: 0 Unit cell: (97.47, 112.86, 141.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 3 16.00 P 3 15.00 O 1497 8.00 N 1514 7.00 C 4968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 26 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.73 Conformation dependent library (CDL) restraints added in 389.3 milliseconds 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2674 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 7 sheets defined 68.8% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'G' and resid 26 through 52 Proline residue: G 35 - end of helix Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 71 through 99 removed outlier: 3.865A pdb=" N THR G 99 " --> pdb=" O SER G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 130 removed outlier: 3.859A pdb=" N SER G 130 " --> pdb=" O ASN G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 135 Processing helix chain 'G' and resid 136 through 160 removed outlier: 3.584A pdb=" N LEU G 145 " --> pdb=" O ILE G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 194 removed outlier: 3.987A pdb=" N CYS G 170 " --> pdb=" O GLN G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 212 Processing helix chain 'G' and resid 223 through 230 Processing helix chain 'G' and resid 231 through 240 removed outlier: 4.232A pdb=" N ALA G 235 " --> pdb=" O TRP G 231 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE G 236 " --> pdb=" O TRP G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 257 Processing helix chain 'G' and resid 258 through 277 Processing helix chain 'G' and resid 283 through 315 removed outlier: 5.451A pdb=" N ARG G 297 " --> pdb=" O HIS G 293 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ARG G 298 " --> pdb=" O ALA G 294 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU G 301 " --> pdb=" O ARG G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 329 Processing helix chain 'G' and resid 347 through 352 Processing helix chain 'G' and resid 355 through 400 removed outlier: 4.435A pdb=" N THR G 371 " --> pdb=" O LEU G 367 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLN G 374 " --> pdb=" O ARG G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 435 Processing helix chain 'G' and resid 436 through 456 Proline residue: G 442 - end of helix Processing helix chain 'G' and resid 457 through 469 Processing helix chain 'G' and resid 470 through 505 removed outlier: 3.667A pdb=" N GLN G 474 " --> pdb=" O LEU G 470 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU G 494 " --> pdb=" O GLU G 490 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY G 505 " --> pdb=" O GLU G 501 " (cutoff:3.500A) Processing helix chain 'G' and resid 505 through 512 Processing helix chain 'G' and resid 515 through 548 removed outlier: 4.079A pdb=" N THR G 525 " --> pdb=" O ARG G 521 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER G 543 " --> pdb=" O TYR G 539 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE G 544 " --> pdb=" O THR G 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 549 through 564 Processing helix chain 'G' and resid 572 through 615 Proline residue: G 589 - end of helix removed outlier: 4.223A pdb=" N LEU G 592 " --> pdb=" O THR G 588 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER G 594 " --> pdb=" O LEU G 590 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER G 595 " --> pdb=" O PHE G 591 " (cutoff:3.500A) Processing helix chain 'G' and resid 718 through 727 Processing helix chain 'G' and resid 785 through 790 Processing helix chain 'G' and resid 795 through 806 Processing helix chain 'G' and resid 808 through 815 Processing helix chain 'G' and resid 831 through 846 Processing helix chain 'G' and resid 862 through 881 Processing helix chain 'G' and resid 913 through 918 removed outlier: 3.932A pdb=" N PHE G 917 " --> pdb=" O THR G 913 " (cutoff:3.500A) Processing helix chain 'G' and resid 922 through 927 removed outlier: 3.779A pdb=" N GLU G 926 " --> pdb=" O CYS G 922 " (cutoff:3.500A) Processing helix chain 'G' and resid 996 through 1009 removed outlier: 3.642A pdb=" N GLY G1009 " --> pdb=" O LEU G1005 " (cutoff:3.500A) Processing helix chain 'G' and resid 1009 through 1043 removed outlier: 4.262A pdb=" N LEU G1015 " --> pdb=" O LEU G1011 " (cutoff:3.500A) Processing helix chain 'G' and resid 1061 through 1107 removed outlier: 3.699A pdb=" N LEU G1074 " --> pdb=" O LEU G1070 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU G1087 " --> pdb=" O SER G1083 " (cutoff:3.500A) Processing helix chain 'G' and resid 1109 through 1116 removed outlier: 3.565A pdb=" N PHE G1113 " --> pdb=" O PRO G1109 " (cutoff:3.500A) Processing helix chain 'G' and resid 1117 through 1135 removed outlier: 3.602A pdb=" N ILE G1121 " --> pdb=" O PRO G1117 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASP G1128 " --> pdb=" O ARG G1124 " (cutoff:3.500A) Processing helix chain 'G' and resid 1135 through 1161 removed outlier: 4.053A pdb=" N LEU G1148 " --> pdb=" O SER G1144 " (cutoff:3.500A) Processing helix chain 'G' and resid 1163 through 1210 Proline residue: G1170 - end of helix removed outlier: 4.008A pdb=" N ASP G1188 " --> pdb=" O VAL G1184 " (cutoff:3.500A) Proline residue: G1199 - end of helix Processing helix chain 'G' and resid 1210 through 1218 Processing helix chain 'G' and resid 1219 through 1273 removed outlier: 3.890A pdb=" N PHE G1223 " --> pdb=" O TYR G1219 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA G1237 " --> pdb=" O SER G1233 " (cutoff:3.500A) Processing helix chain 'G' and resid 1278 through 1320 removed outlier: 4.501A pdb=" N ASN G1296 " --> pdb=" O SER G1292 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA G1311 " --> pdb=" O ILE G1307 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL G1312 " --> pdb=" O GLN G1308 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG G1314 " --> pdb=" O GLY G1310 " (cutoff:3.500A) Processing helix chain 'G' and resid 1334 through 1339 Processing helix chain 'G' and resid 1385 through 1392 Processing helix chain 'G' and resid 1414 through 1419 Processing helix chain 'G' and resid 1435 through 1441 Processing helix chain 'G' and resid 1447 through 1458 Processing helix chain 'G' and resid 1460 through 1465 Processing helix chain 'G' and resid 1484 through 1498 removed outlier: 3.690A pdb=" N GLN G1488 " --> pdb=" O GLN G1484 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG G1498 " --> pdb=" O ARG G1494 " (cutoff:3.500A) Processing helix chain 'G' and resid 1512 through 1530 Processing helix chain 'G' and resid 1539 through 1543 Processing helix chain 'G' and resid 1563 through 1570 removed outlier: 3.629A pdb=" N LEU G1567 " --> pdb=" O PRO G1563 " (cutoff:3.500A) Processing helix chain 'G' and resid 1570 through 1576 removed outlier: 3.704A pdb=" N PHE G1574 " --> pdb=" O LYS G1570 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 338 through 340 removed outlier: 3.928A pdb=" N THR G 338 " --> pdb=" O PHE G 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 701 through 703 Processing sheet with id=AA3, first strand: chain 'G' and resid 850 through 854 removed outlier: 7.441A pdb=" N ILE G 901 " --> pdb=" O LEU G 708 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N MET G 710 " --> pdb=" O ILE G 901 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N MET G 903 " --> pdb=" O MET G 710 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL G 712 " --> pdb=" O MET G 903 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 1366 through 1368 removed outlier: 3.935A pdb=" N GLN G1346 " --> pdb=" O ILE G1404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 1352 through 1353 Processing sheet with id=AA6, first strand: chain 'G' and resid 1423 through 1424 removed outlier: 7.469A pdb=" N SER G1423 " --> pdb=" O ILE G1504 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N ASP G1506 " --> pdb=" O SER G1423 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE G1503 " --> pdb=" O VAL G1534 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE G1536 " --> pdb=" O PHE G1503 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N MET G1505 " --> pdb=" O ILE G1536 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 1549 through 1551 738 hydrogen bonds defined for protein. 2175 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.65 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2848 1.34 - 1.46: 1845 1.46 - 1.58: 3440 1.58 - 1.70: 5 1.70 - 1.82: 3 Bond restraints: 8141 Sorted by residual: bond pdb=" C4 ATP G1601 " pdb=" C5 ATP G1601 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.80e+01 bond pdb=" C5 ATP G1601 " pdb=" C6 ATP G1601 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.37e+01 bond pdb=" C5 ATP G1601 " pdb=" N7 ATP G1601 " ideal model delta sigma weight residual 1.387 1.343 0.044 1.00e-02 1.00e+04 1.91e+01 bond pdb=" C4 ATP G1601 " pdb=" N9 ATP G1601 " ideal model delta sigma weight residual 1.374 1.331 0.043 1.00e-02 1.00e+04 1.81e+01 bond pdb=" C8 ATP G1601 " pdb=" N7 ATP G1601 " ideal model delta sigma weight residual 1.310 1.348 -0.038 1.00e-02 1.00e+04 1.47e+01 ... (remaining 8136 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.32: 11222 4.32 - 8.63: 94 8.63 - 12.95: 14 12.95 - 17.27: 0 17.27 - 21.58: 3 Bond angle restraints: 11333 Sorted by residual: angle pdb=" PA ATP G1601 " pdb=" O3A ATP G1601 " pdb=" PB ATP G1601 " ideal model delta sigma weight residual 136.83 115.25 21.58 1.00e+00 1.00e+00 4.66e+02 angle pdb=" PB ATP G1601 " pdb=" O3B ATP G1601 " pdb=" PG ATP G1601 " ideal model delta sigma weight residual 139.87 121.63 18.24 1.00e+00 1.00e+00 3.33e+02 angle pdb=" C5' ATP G1601 " pdb=" O5' ATP G1601 " pdb=" PA ATP G1601 " ideal model delta sigma weight residual 121.27 109.37 11.90 1.00e+00 1.00e+00 1.42e+02 angle pdb=" C5 ATP G1601 " pdb=" C4 ATP G1601 " pdb=" N3 ATP G1601 " ideal model delta sigma weight residual 126.80 118.39 8.41 1.00e+00 1.00e+00 7.07e+01 angle pdb=" O3A ATP G1601 " pdb=" PA ATP G1601 " pdb=" O5' ATP G1601 " ideal model delta sigma weight residual 102.67 120.99 -18.32 2.38e+00 1.77e-01 5.92e+01 ... (remaining 11328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4554 17.76 - 35.51: 78 35.51 - 53.27: 17 53.27 - 71.02: 2 71.02 - 88.78: 1 Dihedral angle restraints: 4652 sinusoidal: 543 harmonic: 4109 Sorted by residual: dihedral pdb=" CA ILE G 996 " pdb=" C ILE G 996 " pdb=" N PRO G 997 " pdb=" CA PRO G 997 " ideal model delta harmonic sigma weight residual -180.00 -142.55 -37.45 0 5.00e+00 4.00e-02 5.61e+01 dihedral pdb=" CB CYS G 6 " pdb=" SG CYS G 6 " pdb=" SG CYS G 26 " pdb=" CB CYS G 26 " ideal model delta sinusoidal sigma weight residual 93.00 143.69 -50.69 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" CA LYS G1562 " pdb=" C LYS G1562 " pdb=" N PRO G1563 " pdb=" CA PRO G1563 " ideal model delta harmonic sigma weight residual 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 4649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 926 0.046 - 0.092: 356 0.092 - 0.138: 86 0.138 - 0.184: 13 0.184 - 0.231: 7 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CB VAL G1352 " pdb=" CA VAL G1352 " pdb=" CG1 VAL G1352 " pdb=" CG2 VAL G1352 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA TRP G1297 " pdb=" N TRP G1297 " pdb=" C TRP G1297 " pdb=" CB TRP G1297 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA TRP G1339 " pdb=" N TRP G1339 " pdb=" C TRP G1339 " pdb=" CB TRP G1339 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1385 not shown) Planarity restraints: 1573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G1311 " 0.035 2.00e-02 2.50e+03 6.95e-02 4.84e+01 pdb=" C ALA G1311 " -0.120 2.00e-02 2.50e+03 pdb=" O ALA G1311 " 0.045 2.00e-02 2.50e+03 pdb=" N VAL G1312 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G1286 " -0.030 2.00e-02 2.50e+03 5.92e-02 3.51e+01 pdb=" C THR G1286 " 0.102 2.00e-02 2.50e+03 pdb=" O THR G1286 " -0.038 2.00e-02 2.50e+03 pdb=" N TYR G1287 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 94 " 0.024 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" C LEU G 94 " -0.082 2.00e-02 2.50e+03 pdb=" O LEU G 94 " 0.030 2.00e-02 2.50e+03 pdb=" N SER G 95 " 0.028 2.00e-02 2.50e+03 ... (remaining 1570 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2102 2.78 - 3.31: 7702 3.31 - 3.84: 13032 3.84 - 4.37: 12630 4.37 - 4.90: 22231 Nonbonded interactions: 57697 Sorted by model distance: nonbonded pdb=" O ALA G1288 " pdb=" OG SER G1292 " model vdw 2.253 3.040 nonbonded pdb=" O THR G 789 " pdb=" OG SER G 792 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR G 123 " pdb=" O LEU G 135 " model vdw 2.279 3.040 nonbonded pdb=" O LEU G 39 " pdb=" OG1 THR G 43 " model vdw 2.293 3.040 nonbonded pdb=" O ALA G 235 " pdb=" OG1 THR G 239 " model vdw 2.303 3.040 ... (remaining 57692 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: 0.360 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.520 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 8142 Z= 0.332 Angle : 1.133 21.583 11335 Z= 0.721 Chirality : 0.052 0.231 1388 Planarity : 0.010 0.070 1573 Dihedral : 9.013 88.779 1975 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.83 (0.18), residues: 1400 helix: -1.92 (0.13), residues: 907 sheet: -3.79 (0.50), residues: 61 loop : -3.40 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG G 370 TYR 0.042 0.003 TYR G1294 PHE 0.038 0.002 PHE G 433 TRP 0.062 0.004 TRP G1297 HIS 0.022 0.004 HIS G1098 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 8141) covalent geometry : angle 1.13334 (11333) SS BOND : bond 0.00332 ( 1) SS BOND : angle 1.11326 ( 2) hydrogen bonds : bond 0.12929 ( 738) hydrogen bonds : angle 6.44285 ( 2175) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 306 ARG cc_start: 0.8910 (tpt-90) cc_final: 0.8609 (tpt-90) REVERT: G 363 PHE cc_start: 0.8968 (t80) cc_final: 0.8725 (t80) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0828 time to fit residues: 7.0578 Evaluate side-chains 52 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 40.0000 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 0.0570 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 overall best weight: 5.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 125 HIS ** G1098 HIS ** 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 = 0.2856 r_free = 0.2856 target = 0.038425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.032558 restraints weight = 100140.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.033144 restraints weight = 70078.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.033581 restraints weight = 52558.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.033890 restraints weight = 41587.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.034155 restraints weight = 34675.457| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8142 Z= 0.255 Angle : 0.642 7.800 11335 Z= 0.375 Chirality : 0.042 0.130 1388 Planarity : 0.006 0.060 1573 Dihedral : 5.789 82.850 1478 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.22), residues: 1400 helix: 0.77 (0.16), residues: 925 sheet: -3.08 (0.59), residues: 58 loop : -2.93 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 168 TYR 0.023 0.002 TYR G 124 PHE 0.023 0.002 PHE G 433 TRP 0.035 0.003 TRP G1297 HIS 0.012 0.002 HIS G1098 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 8141) covalent geometry : angle 0.64234 (11333) SS BOND : bond 0.00212 ( 1) SS BOND : angle 0.40964 ( 2) hydrogen bonds : bond 0.04925 ( 738) hydrogen bonds : angle 4.59951 ( 2175) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 306 ARG cc_start: 0.9125 (tpt-90) cc_final: 0.8696 (mmm160) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0502 time to fit residues: 4.7066 Evaluate side-chains 48 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 43 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 139 optimal weight: 30.0000 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 262 ASN G 817 HIS ** G1098 HIS ** 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 = 0.2807 r_free = 0.2807 target = 0.037569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.031746 restraints weight = 99809.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.032311 restraints weight = 70317.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.032737 restraints weight = 52925.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.033063 restraints weight = 42075.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.033240 restraints weight = 34833.002| |-----------------------------------------------------------------------------| r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8142 Z= 0.241 Angle : 0.596 6.385 11335 Z= 0.349 Chirality : 0.042 0.142 1388 Planarity : 0.005 0.051 1573 Dihedral : 5.389 81.710 1478 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.23), residues: 1400 helix: 1.84 (0.17), residues: 942 sheet: -2.49 (0.63), residues: 59 loop : -2.63 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 168 TYR 0.019 0.002 TYR G 378 PHE 0.029 0.002 PHE G1240 TRP 0.042 0.003 TRP G1297 HIS 0.010 0.002 HIS G1098 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 8141) covalent geometry : angle 0.59577 (11333) SS BOND : bond 0.00104 ( 1) SS BOND : angle 0.29949 ( 2) hydrogen bonds : bond 0.04690 ( 738) hydrogen bonds : angle 4.34697 ( 2175) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0530 time to fit residues: 4.6041 Evaluate side-chains 48 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 19 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 55 optimal weight: 0.4980 chunk 65 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 133 optimal weight: 40.0000 chunk 23 optimal weight: 5.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.037565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.031769 restraints weight = 102193.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.032347 restraints weight = 70874.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.032796 restraints weight = 52833.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.033130 restraints weight = 41535.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.033315 restraints weight = 34247.328| |-----------------------------------------------------------------------------| r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8142 Z= 0.191 Angle : 0.542 6.435 11335 Z= 0.308 Chirality : 0.041 0.142 1388 Planarity : 0.004 0.053 1573 Dihedral : 5.181 80.041 1478 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.24), residues: 1400 helix: 2.33 (0.17), residues: 946 sheet: -2.02 (0.63), residues: 61 loop : -2.38 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 168 TYR 0.017 0.002 TYR G 378 PHE 0.023 0.001 PHE G1204 TRP 0.024 0.002 TRP G 288 HIS 0.008 0.001 HIS G1098 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8141) covalent geometry : angle 0.54202 (11333) SS BOND : bond 0.00135 ( 1) SS BOND : angle 0.35345 ( 2) hydrogen bonds : bond 0.04330 ( 738) hydrogen bonds : angle 4.12198 ( 2175) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 306 ARG cc_start: 0.9111 (tpt-90) cc_final: 0.8705 (mmm160) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0655 time to fit residues: 5.1126 Evaluate side-chains 47 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 120 optimal weight: 8.9990 chunk 124 optimal weight: 40.0000 chunk 49 optimal weight: 20.0000 chunk 81 optimal weight: 50.0000 chunk 24 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 491 HIS G 584 HIS ** G1098 HIS ** 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 = 0.2762 r_free = 0.2762 target = 0.036309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.030691 restraints weight = 104575.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.031270 restraints weight = 71480.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.031696 restraints weight = 52746.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.032012 restraints weight = 41229.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.032254 restraints weight = 33836.199| |-----------------------------------------------------------------------------| r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 8142 Z= 0.320 Angle : 0.662 7.701 11335 Z= 0.394 Chirality : 0.043 0.150 1388 Planarity : 0.005 0.060 1573 Dihedral : 5.665 75.205 1478 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.23), residues: 1400 helix: 1.69 (0.17), residues: 951 sheet: -1.87 (0.82), residues: 41 loop : -2.49 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 168 TYR 0.023 0.002 TYR G 475 PHE 0.025 0.002 PHE G 518 TRP 0.042 0.003 TRP G1297 HIS 0.009 0.002 HIS G1098 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 8141) covalent geometry : angle 0.66215 (11333) SS BOND : bond 0.00175 ( 1) SS BOND : angle 0.32838 ( 2) hydrogen bonds : bond 0.05196 ( 738) hydrogen bonds : angle 4.82596 ( 2175) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: G 306 ARG cc_start: 0.9084 (tpt-90) cc_final: 0.8736 (mmm160) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0527 time to fit residues: 4.3137 Evaluate side-chains 47 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 127 optimal weight: 7.9990 chunk 23 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.037818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.031988 restraints weight = 99092.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.032565 restraints weight = 69001.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.032994 restraints weight = 51593.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.033333 restraints weight = 40714.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.033570 restraints weight = 33615.506| |-----------------------------------------------------------------------------| r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 8142 Z= 0.138 Angle : 0.513 6.535 11335 Z= 0.281 Chirality : 0.040 0.144 1388 Planarity : 0.004 0.055 1573 Dihedral : 5.041 70.687 1478 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.24), residues: 1400 helix: 2.59 (0.17), residues: 944 sheet: -1.28 (0.78), residues: 50 loop : -2.11 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 168 TYR 0.019 0.001 TYR G 378 PHE 0.012 0.001 PHE G 518 TRP 0.027 0.001 TRP G1297 HIS 0.008 0.001 HIS G1098 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8141) covalent geometry : angle 0.51312 (11333) SS BOND : bond 0.00244 ( 1) SS BOND : angle 0.58933 ( 2) hydrogen bonds : bond 0.04203 ( 738) hydrogen bonds : angle 3.99949 ( 2175) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0542 time to fit residues: 4.6084 Evaluate side-chains 49 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 37 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 15 optimal weight: 20.0000 chunk 23 optimal weight: 0.4980 chunk 74 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.038674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.032682 restraints weight = 98190.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.033276 restraints weight = 69178.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.033724 restraints weight = 51973.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.034065 restraints weight = 41196.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.034319 restraints weight = 34088.515| |-----------------------------------------------------------------------------| r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8142 Z= 0.115 Angle : 0.485 7.711 11335 Z= 0.260 Chirality : 0.040 0.149 1388 Planarity : 0.004 0.053 1573 Dihedral : 4.673 68.784 1478 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.24), residues: 1400 helix: 2.96 (0.17), residues: 952 sheet: -1.15 (0.83), residues: 45 loop : -2.17 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 168 TYR 0.017 0.001 TYR G 378 PHE 0.032 0.001 PHE G1240 TRP 0.020 0.001 TRP G1297 HIS 0.007 0.001 HIS G1098 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 8141) covalent geometry : angle 0.48463 (11333) SS BOND : bond 0.00053 ( 1) SS BOND : angle 0.50582 ( 2) hydrogen bonds : bond 0.03797 ( 738) hydrogen bonds : angle 3.60165 ( 2175) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0506 time to fit residues: 4.1852 Evaluate side-chains 48 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 120 optimal weight: 30.0000 chunk 35 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.037115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.031401 restraints weight = 103070.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.031984 restraints weight = 70513.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.032362 restraints weight = 51919.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.032712 restraints weight = 41487.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.032922 restraints weight = 33877.079| |-----------------------------------------------------------------------------| r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8142 Z= 0.274 Angle : 0.591 6.203 11335 Z= 0.345 Chirality : 0.042 0.140 1388 Planarity : 0.004 0.057 1573 Dihedral : 5.051 68.484 1478 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.24), residues: 1400 helix: 2.66 (0.17), residues: 930 sheet: -1.12 (0.91), residues: 38 loop : -2.14 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 168 TYR 0.016 0.002 TYR G 475 PHE 0.017 0.002 PHE G 363 TRP 0.032 0.002 TRP G1297 HIS 0.006 0.002 HIS G1098 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 8141) covalent geometry : angle 0.59063 (11333) SS BOND : bond 0.00077 ( 1) SS BOND : angle 0.11071 ( 2) hydrogen bonds : bond 0.04557 ( 738) hydrogen bonds : angle 4.24453 ( 2175) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0552 time to fit residues: 4.6491 Evaluate side-chains 48 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 64 optimal weight: 50.0000 chunk 106 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 133 optimal weight: 40.0000 chunk 47 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.037338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.031750 restraints weight = 102737.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.032343 restraints weight = 69548.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.032769 restraints weight = 50950.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.033085 restraints weight = 39628.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.033316 restraints weight = 32487.848| |-----------------------------------------------------------------------------| r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8142 Z= 0.225 Angle : 0.568 6.251 11335 Z= 0.325 Chirality : 0.041 0.140 1388 Planarity : 0.004 0.056 1573 Dihedral : 5.091 63.270 1478 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.23), residues: 1400 helix: 2.60 (0.17), residues: 932 sheet: -1.41 (0.84), residues: 46 loop : -2.06 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 168 TYR 0.015 0.002 TYR G 475 PHE 0.018 0.002 PHE G 518 TRP 0.030 0.002 TRP G 288 HIS 0.007 0.002 HIS G 71 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8141) covalent geometry : angle 0.56761 (11333) SS BOND : bond 0.00113 ( 1) SS BOND : angle 0.20885 ( 2) hydrogen bonds : bond 0.04520 ( 738) hydrogen bonds : angle 4.21941 ( 2175) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: G 394 LYS cc_start: 0.9802 (tptm) cc_final: 0.9470 (tppt) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0657 time to fit residues: 5.1248 Evaluate side-chains 48 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 4 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 133 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.038202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.032449 restraints weight = 100321.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.033048 restraints weight = 68358.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.033492 restraints weight = 50362.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.033818 restraints weight = 39444.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.034069 restraints weight = 32324.744| |-----------------------------------------------------------------------------| r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8142 Z= 0.129 Angle : 0.504 8.442 11335 Z= 0.273 Chirality : 0.040 0.145 1388 Planarity : 0.004 0.053 1573 Dihedral : 4.790 61.800 1478 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.24), residues: 1400 helix: 2.99 (0.17), residues: 940 sheet: -1.28 (0.93), residues: 41 loop : -2.13 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 168 TYR 0.018 0.001 TYR G 378 PHE 0.011 0.001 PHE G 518 TRP 0.026 0.001 TRP G1297 HIS 0.006 0.001 HIS G1098 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8141) covalent geometry : angle 0.50357 (11333) SS BOND : bond 0.00036 ( 1) SS BOND : angle 0.43482 ( 2) hydrogen bonds : bond 0.04047 ( 738) hydrogen bonds : angle 3.77050 ( 2175) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: G 306 ARG cc_start: 0.9107 (tpt-90) cc_final: 0.8578 (mmm160) REVERT: G 394 LYS cc_start: 0.9748 (tptm) cc_final: 0.9418 (tppt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0659 time to fit residues: 5.1470 Evaluate side-chains 48 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 92 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 125 optimal weight: 40.0000 chunk 58 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.037344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.031736 restraints weight = 103382.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.032289 restraints weight = 70195.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.032740 restraints weight = 52060.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.033042 restraints weight = 40313.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.033302 restraints weight = 33268.078| |-----------------------------------------------------------------------------| r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8142 Z= 0.224 Angle : 0.566 6.132 11335 Z= 0.324 Chirality : 0.042 0.140 1388 Planarity : 0.004 0.057 1573 Dihedral : 5.033 59.695 1478 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.23), residues: 1400 helix: 2.74 (0.16), residues: 930 sheet: -1.29 (0.97), residues: 40 loop : -2.08 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 168 TYR 0.015 0.002 TYR G 475 PHE 0.019 0.002 PHE G 518 TRP 0.029 0.002 TRP G 288 HIS 0.006 0.002 HIS G 71 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8141) covalent geometry : angle 0.56607 (11333) SS BOND : bond 0.00086 ( 1) SS BOND : angle 0.13017 ( 2) hydrogen bonds : bond 0.04464 ( 738) hydrogen bonds : angle 4.13122 ( 2175) =============================================================================== Job complete usr+sys time: 950.13 seconds wall clock time: 16 minutes 59.09 seconds (1019.09 seconds total)