Starting phenix.real_space_refine on Sat Jul 26 01:35:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pzi_20535/07_2025/6pzi_20535_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pzi_20535/07_2025/6pzi_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_20535/07_2025/6pzi_20535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pzi_20535/07_2025/6pzi_20535.map" model { file = "/net/cci-nas-00/data/ceres_data/6pzi_20535/07_2025/6pzi_20535_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pzi_20535/07_2025/6pzi_20535_neut.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 57, 'ARG:plan': 63, 'TYR:plan': 8, 'ASN:plan1': 37, 'TRP:plan': 6, 'HIS:plan': 13, 'PHE:plan': 51, 'GLU:plan': 56, 'ASP:plan': 51} 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: 6.51, per 1000 atoms: 0.82 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: 3.10 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.56 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: 5.47 Time building geometry restraints manager: 3.11 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: 51.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.110 Process input model: 29.860 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.440 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.062 0.004 TRP G1297 HIS 0.022 0.004 HIS G1098 PHE 0.038 0.002 PHE G 433 TYR 0.042 0.003 TYR G1294 ARG 0.019 0.002 ARG G 370 Details of bonding type rmsd hydrogen bonds : bond 0.12929 ( 738) hydrogen bonds : angle 6.44285 ( 2175) SS BOND : bond 0.00332 ( 1) SS BOND : angle 1.11326 ( 2) covalent geometry : bond 0.00544 ( 8141) covalent geometry : angle 1.13334 (11333) *********************** 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 : 0.830 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: 0.2676 time to fit residues: 23.8675 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 : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 72 optimal weight: 0.0070 chunk 57 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 overall best weight: 3.3804 ------------------------------------------------------------------------------- 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 = 0.2887 r_free = 0.2887 target = 0.039367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.033362 restraints weight = 97661.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.033964 restraints weight = 68639.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.034413 restraints weight = 51612.103| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8142 Z= 0.182 Angle : 0.579 7.790 11335 Z= 0.330 Chirality : 0.041 0.136 1388 Planarity : 0.005 0.062 1573 Dihedral : 5.761 81.545 1478 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.22), residues: 1400 helix: 0.69 (0.16), residues: 932 sheet: -3.15 (0.52), residues: 70 loop : -2.97 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G1297 HIS 0.010 0.001 HIS G1098 PHE 0.022 0.001 PHE G 433 TYR 0.017 0.002 TYR G 124 ARG 0.003 0.001 ARG G 168 Details of bonding type rmsd hydrogen bonds : bond 0.04655 ( 738) hydrogen bonds : angle 4.44385 ( 2175) SS BOND : bond 0.00221 ( 1) SS BOND : angle 0.59736 ( 2) covalent geometry : bond 0.00307 ( 8141) covalent geometry : angle 0.57942 (11333) *********************** 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 56 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 363 PHE cc_start: 0.9352 (t80) cc_final: 0.9087 (t80) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1575 time to fit residues: 15.7777 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 : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 56 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 72 optimal weight: 0.0060 chunk 82 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 21 optimal weight: 0.0170 chunk 27 optimal weight: 6.9990 chunk 61 optimal weight: 30.0000 chunk 94 optimal weight: 0.0980 chunk 127 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.4036 ------------------------------------------------------------------------------- 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 = 0.2897 r_free = 0.2897 target = 0.039996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.034033 restraints weight = 97250.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.034624 restraints weight = 68324.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.035082 restraints weight = 51594.454| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8142 Z= 0.117 Angle : 0.495 6.865 11335 Z= 0.269 Chirality : 0.040 0.143 1388 Planarity : 0.004 0.040 1573 Dihedral : 5.214 82.982 1478 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.23), residues: 1400 helix: 1.99 (0.17), residues: 934 sheet: -2.64 (0.57), residues: 70 loop : -2.63 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G1297 HIS 0.009 0.001 HIS G1098 PHE 0.025 0.001 PHE G1240 TYR 0.012 0.001 TYR G 230 ARG 0.003 0.001 ARG G 168 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 738) hydrogen bonds : angle 3.81468 ( 2175) SS BOND : bond 0.00023 ( 1) SS BOND : angle 0.68423 ( 2) covalent geometry : bond 0.00203 ( 8141) covalent geometry : angle 0.49509 (11333) *********************** 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 56 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 225 LEU cc_start: 0.9402 (tp) cc_final: 0.9113 (tt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1442 time to fit residues: 13.1188 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 : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 138 optimal weight: 9.9990 chunk 83 optimal weight: 0.0060 chunk 119 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 44 optimal weight: 9.9990 chunk 95 optimal weight: 0.0170 chunk 132 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 15 optimal weight: 0.0060 overall best weight: 4.0054 ------------------------------------------------------------------------------- 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 = 0.2830 r_free = 0.2830 target = 0.038289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.032355 restraints weight = 98697.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.032941 restraints weight = 69256.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.033383 restraints weight = 52049.598| |-----------------------------------------------------------------------------| r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8142 Z= 0.194 Angle : 0.546 6.326 11335 Z= 0.312 Chirality : 0.041 0.140 1388 Planarity : 0.004 0.051 1573 Dihedral : 5.102 80.731 1478 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.23), residues: 1400 helix: 2.37 (0.17), residues: 950 sheet: -2.36 (0.60), residues: 59 loop : -2.39 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G1297 HIS 0.007 0.002 HIS G1098 PHE 0.017 0.002 PHE G 363 TYR 0.017 0.002 TYR G 378 ARG 0.007 0.001 ARG G 168 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 738) hydrogen bonds : angle 3.94219 ( 2175) SS BOND : bond 0.00046 ( 1) SS BOND : angle 0.43922 ( 2) covalent geometry : bond 0.00337 ( 8141) covalent geometry : angle 0.54566 (11333) *********************** 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 53 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: G 306 ARG cc_start: 0.9150 (tpt-90) cc_final: 0.8706 (mmm160) REVERT: G 394 LYS cc_start: 0.9766 (tptm) cc_final: 0.9455 (tppt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1451 time to fit residues: 12.8285 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 : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 10.0000 chunk 105 optimal weight: 0.0000 chunk 83 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 39 optimal weight: 0.0050 overall best weight: 1.8002 ------------------------------------------------------------------------------- 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 = 0.2865 r_free = 0.2865 target = 0.039176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.033229 restraints weight = 95520.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.033811 restraints weight = 67658.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.034217 restraints weight = 51023.652| |-----------------------------------------------------------------------------| r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8142 Z= 0.114 Angle : 0.481 7.971 11335 Z= 0.258 Chirality : 0.040 0.141 1388 Planarity : 0.003 0.046 1573 Dihedral : 4.732 76.138 1478 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.24), residues: 1400 helix: 2.83 (0.17), residues: 949 sheet: -1.87 (0.62), residues: 62 loop : -2.12 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G1297 HIS 0.007 0.001 HIS G1098 PHE 0.028 0.001 PHE G 518 TYR 0.013 0.001 TYR G 378 ARG 0.004 0.001 ARG G 168 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 738) hydrogen bonds : angle 3.59907 ( 2175) SS BOND : bond 0.00073 ( 1) SS BOND : angle 0.46467 ( 2) covalent geometry : bond 0.00200 ( 8141) covalent geometry : angle 0.48078 (11333) *********************** 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 55 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1605 time to fit residues: 13.5774 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 : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 85 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 491 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 = 0.2817 r_free = 0.2817 target = 0.037931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.032111 restraints weight = 98972.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.032691 restraints weight = 69992.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.033122 restraints weight = 52575.645| |-----------------------------------------------------------------------------| r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8142 Z= 0.195 Angle : 0.536 6.238 11335 Z= 0.304 Chirality : 0.041 0.149 1388 Planarity : 0.004 0.053 1573 Dihedral : 4.919 75.321 1478 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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 (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: 1.94 (0.24), residues: 1400 helix: 2.74 (0.17), residues: 947 sheet: -1.54 (0.67), residues: 56 loop : -2.13 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G1297 HIS 0.008 0.002 HIS G1098 PHE 0.013 0.002 PHE G 363 TYR 0.013 0.002 TYR G 123 ARG 0.005 0.001 ARG G 168 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 738) hydrogen bonds : angle 3.86553 ( 2175) SS BOND : bond 0.00005 ( 1) SS BOND : angle 0.14212 ( 2) covalent geometry : bond 0.00340 ( 8141) covalent geometry : angle 0.53591 (11333) *********************** 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 52 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: G 306 ARG cc_start: 0.9126 (tpt-90) cc_final: 0.8791 (mmm160) REVERT: G 394 LYS cc_start: 0.9763 (tptm) cc_final: 0.9401 (tppp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1214 time to fit residues: 10.9911 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 : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 21 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 121 optimal weight: 50.0000 chunk 56 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 119 optimal weight: 0.0870 chunk 123 optimal weight: 50.0000 chunk 8 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- 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 = 0.2822 r_free = 0.2822 target = 0.038100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.032241 restraints weight = 99320.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.032783 restraints weight = 69668.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.033243 restraints weight = 53002.462| |-----------------------------------------------------------------------------| r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8142 Z= 0.164 Angle : 0.511 7.054 11335 Z= 0.284 Chirality : 0.040 0.135 1388 Planarity : 0.004 0.053 1573 Dihedral : 4.808 69.943 1478 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.24), residues: 1400 helix: 2.88 (0.17), residues: 950 sheet: -1.39 (0.71), residues: 57 loop : -2.10 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G1297 HIS 0.007 0.001 HIS G1098 PHE 0.016 0.001 PHE G 518 TYR 0.010 0.001 TYR G 123 ARG 0.007 0.001 ARG G 168 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 738) hydrogen bonds : angle 3.75249 ( 2175) SS BOND : bond 0.00065 ( 1) SS BOND : angle 0.13510 ( 2) covalent geometry : bond 0.00287 ( 8141) covalent geometry : angle 0.51072 (11333) *********************** 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 53 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1377 time to fit residues: 12.0000 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 : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 59 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 73 optimal weight: 30.0000 chunk 5 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 129 optimal weight: 20.0000 chunk 133 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 262 ASN ** 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 = 0.2770 r_free = 0.2770 target = 0.036614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.030907 restraints weight = 103207.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.031474 restraints weight = 71031.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.031840 restraints weight = 52796.637| |-----------------------------------------------------------------------------| r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8142 Z= 0.284 Angle : 0.627 7.119 11335 Z= 0.369 Chirality : 0.042 0.141 1388 Planarity : 0.005 0.056 1573 Dihedral : 5.376 70.095 1478 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.23), residues: 1400 helix: 2.24 (0.17), residues: 946 sheet: -0.99 (0.81), residues: 46 loop : -2.27 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP G 288 HIS 0.008 0.002 HIS G 71 PHE 0.025 0.002 PHE G 518 TYR 0.015 0.002 TYR G 453 ARG 0.008 0.001 ARG G 168 Details of bonding type rmsd hydrogen bonds : bond 0.04888 ( 738) hydrogen bonds : angle 4.48345 ( 2175) SS BOND : bond 0.00290 ( 1) SS BOND : angle 0.51478 ( 2) covalent geometry : bond 0.00497 ( 8141) covalent geometry : angle 0.62709 (11333) *********************** 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 50 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1333 time to fit residues: 10.9344 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 : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 61 optimal weight: 30.0000 chunk 80 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 66 optimal weight: 30.0000 chunk 113 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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 = 0.2793 r_free = 0.2793 target = 0.037183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.031395 restraints weight = 102617.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.031979 restraints weight = 70859.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.032327 restraints weight = 52659.558| |-----------------------------------------------------------------------------| r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8142 Z= 0.204 Angle : 0.554 7.009 11335 Z= 0.315 Chirality : 0.041 0.138 1388 Planarity : 0.004 0.055 1573 Dihedral : 5.115 65.009 1478 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % 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 (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: 1.73 (0.24), residues: 1400 helix: 2.54 (0.17), residues: 945 sheet: -0.97 (0.85), residues: 45 loop : -2.13 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 288 HIS 0.008 0.001 HIS G1098 PHE 0.018 0.001 PHE G 518 TYR 0.014 0.002 TYR G 123 ARG 0.005 0.001 ARG G 168 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 738) hydrogen bonds : angle 4.13666 ( 2175) SS BOND : bond 0.00247 ( 1) SS BOND : angle 0.27327 ( 2) covalent geometry : bond 0.00353 ( 8141) covalent geometry : angle 0.55431 (11333) *********************** 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 : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1246 time to fit residues: 10.8068 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 : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 48 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 130 optimal weight: 30.0000 chunk 6 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 61 optimal weight: 40.0000 chunk 34 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 = 0.2799 r_free = 0.2799 target = 0.037328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.031678 restraints weight = 101680.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.032259 restraints weight = 69768.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.032690 restraints weight = 51410.826| |-----------------------------------------------------------------------------| r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3994 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= 0.209 Angle : 0.556 6.181 11335 Z= 0.317 Chirality : 0.041 0.138 1388 Planarity : 0.004 0.056 1573 Dihedral : 5.079 63.933 1478 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % 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 (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: 1.78 (0.24), residues: 1400 helix: 2.63 (0.17), residues: 939 sheet: -0.97 (0.98), residues: 36 loop : -2.18 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 288 HIS 0.008 0.002 HIS G1098 PHE 0.017 0.001 PHE G 518 TYR 0.013 0.002 TYR G 475 ARG 0.005 0.001 ARG G 168 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 738) hydrogen bonds : angle 4.09453 ( 2175) SS BOND : bond 0.00096 ( 1) SS BOND : angle 0.52397 ( 2) covalent geometry : bond 0.00364 ( 8141) covalent geometry : angle 0.55561 (11333) ********************** 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 48 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1140 time to fit residues: 9.8018 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 : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 49 optimal weight: 20.0000 chunk 21 optimal weight: 0.1980 chunk 35 optimal weight: 9.9990 chunk 120 optimal weight: 30.0000 chunk 55 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.2832 r_free = 0.2832 target = 0.038355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.032515 restraints weight = 98381.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.033114 restraints weight = 67900.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.033579 restraints weight = 50407.018| |-----------------------------------------------------------------------------| r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8142 Z= 0.121 Angle : 0.498 9.470 11335 Z= 0.268 Chirality : 0.040 0.148 1388 Planarity : 0.004 0.052 1573 Dihedral : 4.725 61.167 1478 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % 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 (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: 2.23 (0.24), residues: 1400 helix: 3.02 (0.17), residues: 948 sheet: -1.09 (0.93), residues: 41 loop : -2.22 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 288 HIS 0.008 0.001 HIS G1098 PHE 0.026 0.001 PHE G1240 TYR 0.016 0.001 TYR G1219 ARG 0.005 0.001 ARG G 370 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 738) hydrogen bonds : angle 3.64990 ( 2175) SS BOND : bond 0.00109 ( 1) SS BOND : angle 0.29187 ( 2) covalent geometry : bond 0.00215 ( 8141) covalent geometry : angle 0.49775 (11333) =============================================================================== Job complete usr+sys time: 2332.85 seconds wall clock time: 42 minutes 0.61 seconds (2520.61 seconds total)