Starting phenix.real_space_refine on Tue Sep 24 14:22:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzi_20535/09_2024/6pzi_20535_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzi_20535/09_2024/6pzi_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzi_20535/09_2024/6pzi_20535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzi_20535/09_2024/6pzi_20535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzi_20535/09_2024/6pzi_20535_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzi_20535/09_2024/6pzi_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.40, per 1000 atoms: 0.68 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: 2.31 Conformation dependent library (CDL) restraints added in 1.4 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: 1.22 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: 3.10 Time building geometry restraints manager: 2.65 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: 0.520 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.500 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.200 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.809 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: 0.1733 time to fit residues: 15.3627 Evaluate side-chains 52 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 363 PHE cc_start: 0.9092 (t80) cc_final: 0.8865 (t80) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1133 time to fit residues: 11.0607 Evaluate side-chains 50 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 262 ASN G 817 HIS ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8141 Z= 0.320 Angle : 0.634 6.358 11333 Z= 0.375 Chirality : 0.043 0.144 1388 Planarity : 0.005 0.052 1573 Dihedral : 5.621 84.551 1478 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.44 (0.23), residues: 1400 helix: 1.67 (0.17), residues: 941 sheet: -2.55 (0.59), residues: 61 loop : -2.73 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP G1297 HIS 0.010 0.002 HIS G1098 PHE 0.032 0.002 PHE G1240 TYR 0.020 0.002 TYR G 124 ARG 0.009 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 52 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: G 306 ARG cc_start: 0.9039 (tpt-90) cc_final: 0.8824 (tpt-90) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1178 time to fit residues: 10.9502 Evaluate side-chains 47 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 66 optimal weight: 40.0000 chunk 14 optimal weight: 5.9990 chunk 61 optimal weight: 30.0000 chunk 86 optimal weight: 5.9990 chunk 128 optimal weight: 0.4980 chunk 136 optimal weight: 40.0000 chunk 67 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8141 Z= 0.198 Angle : 0.522 6.308 11333 Z= 0.291 Chirality : 0.041 0.144 1388 Planarity : 0.004 0.052 1573 Dihedral : 5.099 79.279 1478 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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: 1.38 (0.24), residues: 1400 helix: 2.34 (0.17), residues: 950 sheet: -2.11 (0.62), residues: 62 loop : -2.37 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G1297 HIS 0.008 0.001 HIS G1098 PHE 0.018 0.001 PHE G1204 TYR 0.013 0.001 TYR G 475 ARG 0.004 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 50 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: G 306 ARG cc_start: 0.8994 (tpt-90) cc_final: 0.8745 (tpt-90) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1282 time to fit residues: 10.8200 Evaluate side-chains 46 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 94 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 122 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8141 Z= 0.149 Angle : 0.487 7.004 11333 Z= 0.263 Chirality : 0.040 0.140 1388 Planarity : 0.004 0.051 1573 Dihedral : 4.820 77.608 1478 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % 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: 2.86 (0.17), residues: 946 sheet: -1.74 (0.65), residues: 62 loop : -2.15 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G1297 HIS 0.008 0.001 HIS G1098 PHE 0.016 0.001 PHE G 518 TYR 0.009 0.001 TYR G 123 ARG 0.004 0.001 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 51 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.885 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1071 time to fit residues: 9.9541 Evaluate side-chains 47 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 80 optimal weight: 0.0770 chunk 33 optimal weight: 10.0000 chunk 136 optimal weight: 30.0000 chunk 113 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 131 optimal weight: 50.0000 overall best weight: 3.9944 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8141 Z= 0.225 Angle : 0.528 6.271 11333 Z= 0.298 Chirality : 0.041 0.138 1388 Planarity : 0.004 0.056 1573 Dihedral : 4.922 74.027 1478 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.95 (0.24), residues: 1400 helix: 2.75 (0.17), residues: 948 sheet: -1.65 (0.69), residues: 57 loop : -2.11 (0.31), residues: 395 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 0.001 PHE G 518 TYR 0.011 0.001 TYR G 475 ARG 0.005 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 48 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: G 306 ARG cc_start: 0.8990 (tpt-90) cc_final: 0.8660 (mmm160) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1075 time to fit residues: 9.4933 Evaluate side-chains 46 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 82 optimal weight: 50.0000 chunk 62 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8141 Z= 0.286 Angle : 0.576 6.248 11333 Z= 0.333 Chirality : 0.042 0.138 1388 Planarity : 0.004 0.057 1573 Dihedral : 5.195 70.463 1478 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % 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: 1.65 (0.24), residues: 1400 helix: 2.49 (0.17), residues: 944 sheet: -1.30 (0.78), residues: 49 loop : -2.16 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP G1297 HIS 0.007 0.002 HIS G1098 PHE 0.023 0.002 PHE G 518 TYR 0.016 0.002 TYR G 123 ARG 0.007 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 48 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: G 306 ARG cc_start: 0.9044 (tpt-90) cc_final: 0.8839 (tpt-90) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1033 time to fit residues: 9.0901 Evaluate side-chains 47 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 40.0000 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 123 optimal weight: 40.0000 chunk 130 optimal weight: 40.0000 chunk 118 optimal weight: 0.0470 overall best weight: 2.5884 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8141 Z= 0.173 Angle : 0.505 7.962 11333 Z= 0.276 Chirality : 0.040 0.139 1388 Planarity : 0.004 0.054 1573 Dihedral : 4.825 67.783 1478 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % 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: 2.18 (0.24), residues: 1400 helix: 2.92 (0.17), residues: 948 sheet: -1.08 (0.83), residues: 45 loop : -2.07 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G1297 HIS 0.008 0.001 HIS G1098 PHE 0.022 0.001 PHE G1240 TYR 0.012 0.001 TYR G1219 ARG 0.004 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 49 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.882 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1049 time to fit residues: 9.4743 Evaluate side-chains 47 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 76 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 83 optimal weight: 30.0000 chunk 133 optimal weight: 40.0000 chunk 81 optimal weight: 50.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3794 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= 0.216 Angle : 0.527 6.383 11333 Z= 0.295 Chirality : 0.041 0.137 1388 Planarity : 0.004 0.056 1573 Dihedral : 4.865 67.481 1478 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.15 (0.24), residues: 1400 helix: 2.90 (0.17), residues: 944 sheet: -1.37 (0.84), residues: 43 loop : -2.01 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP G1297 HIS 0.007 0.001 HIS G1098 PHE 0.017 0.001 PHE G 518 TYR 0.011 0.001 TYR G 475 ARG 0.004 0.001 ARG G 168 *********************** 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 fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.742 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1130 time to fit residues: 10.3854 Evaluate side-chains 48 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 584 HIS ** G1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8141 Z= 0.333 Angle : 0.615 6.592 11333 Z= 0.359 Chirality : 0.042 0.146 1388 Planarity : 0.004 0.057 1573 Dihedral : 5.270 65.732 1478 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % 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: 1.53 (0.23), residues: 1400 helix: 2.43 (0.16), residues: 930 sheet: -1.40 (0.89), residues: 41 loop : -2.10 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP G1297 HIS 0.007 0.002 HIS G1098 PHE 0.024 0.002 PHE G 518 TYR 0.017 0.002 TYR G 475 ARG 0.006 0.001 ARG G 370 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: G 306 ARG cc_start: 0.9071 (tpt-90) cc_final: 0.8865 (tpt-90) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1287 time to fit residues: 10.8296 Evaluate side-chains 47 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 46 optimal weight: 0.0570 chunk 115 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- 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 = 0.2839 r_free = 0.2839 target = 0.038623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.032818 restraints weight = 97541.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.033403 restraints weight = 67512.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.033846 restraints weight = 50228.301| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8141 Z= 0.137 Angle : 0.496 10.615 11333 Z= 0.263 Chirality : 0.040 0.148 1388 Planarity : 0.003 0.053 1573 Dihedral : 4.690 61.747 1478 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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: 2.30 (0.24), residues: 1400 helix: 3.05 (0.16), residues: 950 sheet: -1.21 (0.90), residues: 43 loop : -2.15 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP G1297 HIS 0.008 0.001 HIS G1098 PHE 0.010 0.001 PHE G 433 TYR 0.015 0.001 TYR G1219 ARG 0.005 0.001 ARG G 168 =============================================================================== Job complete usr+sys time: 1248.55 seconds wall clock time: 22 minutes 56.39 seconds (1376.39 seconds total)