Starting phenix.real_space_refine on Wed Feb 12 19:06:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pzi_20535/02_2025/6pzi_20535_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pzi_20535/02_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_20535/02_2025/6pzi_20535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pzi_20535/02_2025/6pzi_20535.map" model { file = "/net/cci-nas-00/data/ceres_data/6pzi_20535/02_2025/6pzi_20535_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pzi_20535/02_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-5592/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: 4.98, per 1000 atoms: 0.62 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: 2.20 Conformation dependent library (CDL) restraints added in 1.2 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: 1.15 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: 3.01 Time building geometry restraints manager: 2.52 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: 0.420 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.190 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.700 ------------------------------------------------------------------------------- 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 8141 Z= 0.387 Angle : 1.133 21.583 11333 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 *********************** 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 : 0.997 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: 0.1826 time to fit residues: 16.4283 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 : 0.816 ------------------------------------------------------------------------------- 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 = 0.039366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.033360 restraints weight = 97668.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.033962 restraints weight = 68737.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.034415 restraints weight = 51678.696| |-----------------------------------------------------------------------------| 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 8141 Z= 0.220 Angle : 0.579 7.790 11333 Z= 0.330 Chirality : 0.041 0.136 1388 Planarity : 0.005 0.062 1573 Dihedral : 5.761 81.544 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 *********************** 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 : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 363 PHE cc_start: 0.9351 (t80) cc_final: 0.9086 (t80) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1247 time to fit residues: 12.1832 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 : 0.928 ------------------------------------------------------------------------------- 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: 7.9990 chunk 72 optimal weight: 1.9990 chunk 82 optimal weight: 0.0070 chunk 8 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 61 optimal weight: 50.0000 chunk 94 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- 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 = 0.039076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.033041 restraints weight = 96391.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.033631 restraints weight = 66990.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.034046 restraints weight = 50165.235| |-----------------------------------------------------------------------------| r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8141 Z= 0.177 Angle : 0.513 6.255 11333 Z= 0.285 Chirality : 0.041 0.140 1388 Planarity : 0.004 0.041 1573 Dihedral : 5.253 84.235 1478 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: 0.90 (0.23), residues: 1400 helix: 2.02 (0.17), residues: 944 sheet: -2.69 (0.61), residues: 59 loop : -2.53 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G1297 HIS 0.009 0.001 HIS G1098 PHE 0.027 0.001 PHE G1240 TYR 0.012 0.001 TYR G 124 ARG 0.005 0.001 ARG G 168 *********************** 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 54 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1152 time to fit residues: 10.7353 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 : 0.815 ------------------------------------------------------------------------------- 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: 8.9990 chunk 83 optimal weight: 0.6980 chunk 119 optimal weight: 0.1980 chunk 129 optimal weight: 30.0000 chunk 68 optimal weight: 50.0000 chunk 66 optimal weight: 40.0000 chunk 44 optimal weight: 9.9990 chunk 95 optimal weight: 0.4980 chunk 132 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 overall best weight: 3.8784 ------------------------------------------------------------------------------- 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 = 0.038271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.032366 restraints weight = 99045.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.032943 restraints weight = 69752.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.033386 restraints weight = 52356.099| |-----------------------------------------------------------------------------| r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8141 Z= 0.229 Angle : 0.535 6.429 11333 Z= 0.303 Chirality : 0.041 0.135 1388 Planarity : 0.004 0.049 1573 Dihedral : 5.052 82.241 1478 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % 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: 1.47 (0.24), residues: 1400 helix: 2.44 (0.17), residues: 947 sheet: -2.29 (0.61), residues: 59 loop : -2.36 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G1297 HIS 0.008 0.002 HIS G1098 PHE 0.016 0.001 PHE G 363 TYR 0.019 0.002 TYR G 378 ARG 0.007 0.001 ARG G 168 *********************** 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 : 0.905 Fit side-chains revert: symmetry clash REVERT: G 306 ARG cc_start: 0.9128 (tpt-90) cc_final: 0.8926 (tpt-90) REVERT: G 394 LYS cc_start: 0.9781 (tptm) cc_final: 0.9488 (tppt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1399 time to fit residues: 12.0073 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 : 0.935 ------------------------------------------------------------------------------- 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: 0.0060 chunk 105 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.5802 ------------------------------------------------------------------------------- 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 = 0.2844 r_free = 0.2844 target = 0.038670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.032748 restraints weight = 96875.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.033330 restraints weight = 68192.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.033698 restraints weight = 51532.744| |-----------------------------------------------------------------------------| r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8141 Z= 0.166 Angle : 0.495 6.723 11333 Z= 0.271 Chirality : 0.040 0.136 1388 Planarity : 0.004 0.050 1573 Dihedral : 4.843 76.660 1478 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: 2.79 (0.17), residues: 946 sheet: -1.88 (0.62), residues: 62 loop : -2.18 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G1297 HIS 0.007 0.001 HIS G1098 PHE 0.030 0.001 PHE G 518 TYR 0.016 0.001 TYR G 378 ARG 0.004 0.000 ARG G 168 *********************** 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 53 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 27 PHE cc_start: 0.9403 (t80) cc_final: 0.9194 (t80) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1366 time to fit residues: 11.9623 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 : 0.845 ------------------------------------------------------------------------------- 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: 9.9990 chunk 116 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 262 ASN G 491 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 = 0.2781 r_free = 0.2781 target = 0.036874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.031216 restraints weight = 101661.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.031775 restraints weight = 70104.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.032206 restraints weight = 52266.969| |-----------------------------------------------------------------------------| r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8141 Z= 0.339 Angle : 0.607 6.742 11333 Z= 0.357 Chirality : 0.042 0.145 1388 Planarity : 0.004 0.055 1573 Dihedral : 5.287 75.746 1478 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % 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: 1.30 (0.23), residues: 1400 helix: 2.24 (0.17), residues: 948 sheet: -1.76 (0.66), residues: 59 loop : -2.35 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP G1297 HIS 0.008 0.002 HIS G1098 PHE 0.020 0.002 PHE G 363 TYR 0.013 0.002 TYR G 475 ARG 0.006 0.001 ARG G 168 *********************** 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 49 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 306 ARG cc_start: 0.9143 (tpt-90) cc_final: 0.8752 (mmm160) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1179 time to fit residues: 10.1803 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 : 0.811 ------------------------------------------------------------------------------- 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: 10.0000 chunk 33 optimal weight: 10.0000 chunk 121 optimal weight: 50.0000 chunk 56 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 123 optimal weight: 40.0000 chunk 8 optimal weight: 20.0000 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- 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 = 0.037397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.031608 restraints weight = 100560.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.032178 restraints weight = 69724.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.032613 restraints weight = 52098.328| |-----------------------------------------------------------------------------| r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8141 Z= 0.230 Angle : 0.534 6.300 11333 Z= 0.302 Chirality : 0.041 0.137 1388 Planarity : 0.004 0.055 1573 Dihedral : 5.028 69.220 1478 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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: 1.79 (0.24), residues: 1400 helix: 2.61 (0.17), residues: 946 sheet: -1.19 (0.78), residues: 50 loop : -2.19 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G1297 HIS 0.008 0.001 HIS G1098 PHE 0.017 0.001 PHE G 518 TYR 0.016 0.002 TYR G 378 ARG 0.005 0.001 ARG G 168 *********************** 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 49 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1420 time to fit residues: 11.9088 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 : 0.953 ------------------------------------------------------------------------------- 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: 7.9990 chunk 92 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 21 optimal weight: 0.1980 chunk 73 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 chunk 79 optimal weight: 30.0000 chunk 107 optimal weight: 9.9990 chunk 129 optimal weight: 0.0170 chunk 133 optimal weight: 20.0000 overall best weight: 4.6424 ------------------------------------------------------------------------------- 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 = 0.2798 r_free = 0.2798 target = 0.037312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.031549 restraints weight = 100947.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.032123 restraints weight = 69792.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.032496 restraints weight = 52026.400| |-----------------------------------------------------------------------------| r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8141 Z= 0.253 Angle : 0.552 6.348 11333 Z= 0.314 Chirality : 0.041 0.135 1388 Planarity : 0.004 0.055 1573 Dihedral : 5.037 68.780 1478 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: 1.81 (0.24), residues: 1400 helix: 2.61 (0.17), residues: 946 sheet: -1.07 (0.80), residues: 49 loop : -2.15 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP G1297 HIS 0.008 0.002 HIS G1098 PHE 0.017 0.001 PHE G 518 TYR 0.014 0.002 TYR G 475 ARG 0.005 0.001 ARG G 168 *********************** 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 : 0.843 Fit side-chains revert: symmetry clash REVERT: G 394 LYS cc_start: 0.9773 (tptm) cc_final: 0.9409 (tppp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1432 time to fit residues: 11.7607 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 : 0.977 ------------------------------------------------------------------------------- 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: 40.0000 chunk 80 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 66 optimal weight: 30.0000 chunk 113 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 584 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 = 0.2773 r_free = 0.2773 target = 0.036614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.031094 restraints weight = 105336.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.031645 restraints weight = 71240.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.032089 restraints weight = 52561.097| |-----------------------------------------------------------------------------| r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8141 Z= 0.331 Angle : 0.622 6.580 11333 Z= 0.365 Chirality : 0.042 0.153 1388 Planarity : 0.004 0.057 1573 Dihedral : 5.426 66.257 1478 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % 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: 1.20 (0.23), residues: 1400 helix: 2.13 (0.17), residues: 935 sheet: -1.58 (0.80), residues: 46 loop : -2.16 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP G1297 HIS 0.007 0.002 HIS G1098 PHE 0.035 0.002 PHE G1240 TYR 0.017 0.002 TYR G 475 ARG 0.008 0.001 ARG G 370 *********************** 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 51 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1413 time to fit residues: 11.7638 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 : 0.865 ------------------------------------------------------------------------------- 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: 10.0000 chunk 50 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 130 optimal weight: 30.0000 chunk 6 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 61 optimal weight: 30.0000 chunk 34 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.2804 r_free = 0.2804 target = 0.037535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.031869 restraints weight = 100780.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.032455 restraints weight = 69101.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.032824 restraints weight = 51009.162| |-----------------------------------------------------------------------------| r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8141 Z= 0.205 Angle : 0.536 7.572 11333 Z= 0.298 Chirality : 0.041 0.139 1388 Planarity : 0.004 0.055 1573 Dihedral : 5.049 62.892 1478 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % 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: 1.85 (0.24), residues: 1400 helix: 2.68 (0.17), residues: 932 sheet: -1.36 (0.84), residues: 46 loop : -2.01 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP G1297 HIS 0.008 0.001 HIS G1098 PHE 0.015 0.001 PHE G 518 TYR 0.018 0.001 TYR G 378 ARG 0.005 0.001 ARG G 168 ********************** 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 51 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1344 time to fit residues: 11.2071 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 : 0.886 ------------------------------------------------------------------------------- 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: 0.0060 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: 7.9990 chunk 100 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 0.0070 chunk 126 optimal weight: 0.0770 overall best weight: 1.2176 ------------------------------------------------------------------------------- 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 = 0.2849 r_free = 0.2849 target = 0.038849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.033015 restraints weight = 98638.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.033591 restraints weight = 68185.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.034068 restraints weight = 51240.723| |-----------------------------------------------------------------------------| r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8141 Z= 0.134 Angle : 0.490 10.235 11333 Z= 0.259 Chirality : 0.040 0.148 1388 Planarity : 0.003 0.052 1573 Dihedral : 4.641 60.997 1478 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % 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: 2.35 (0.24), residues: 1400 helix: 3.11 (0.17), residues: 948 sheet: -1.21 (0.93), residues: 41 loop : -2.15 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP G1297 HIS 0.007 0.001 HIS G1098 PHE 0.013 0.001 PHE G1240 TYR 0.020 0.001 TYR G 378 ARG 0.005 0.001 ARG G 168 =============================================================================== Job complete usr+sys time: 1819.47 seconds wall clock time: 33 minutes 8.81 seconds (1988.81 seconds total)