Starting phenix.real_space_refine on Wed Mar 12 12:40:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pzb_20533/03_2025/6pzb_20533_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pzb_20533/03_2025/6pzb_20533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pzb_20533/03_2025/6pzb_20533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pzb_20533/03_2025/6pzb_20533.map" model { file = "/net/cci-nas-00/data/ceres_data/6pzb_20533/03_2025/6pzb_20533_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pzb_20533/03_2025/6pzb_20533_neut.cif" } resolution = 4.55 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= 0.002 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 4834 2.51 5 N 1468 2.21 5 O 1440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7747 Number of models: 1 Model: "" Number of chains: 1 Chain: "G" Number of atoms: 7747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1357, 7747 Classifications: {'peptide': 1357} Incomplete info: {'truncation_to_alanine': 915} Link IDs: {'CIS': 1, 'PTRANS': 42, 'TRANS': 1313} Chain breaks: 11 Unresolved non-hydrogen bonds: 3073 Unresolved non-hydrogen angles: 3921 Unresolved non-hydrogen dihedrals: 2428 Unresolved non-hydrogen chiralities: 416 Planarities with less than four sites: {'GLN:plan1': 52, 'ARG:plan': 58, 'TYR:plan': 12, 'ASN:plan1': 36, 'TRP:plan': 7, 'HIS:plan': 13, 'PHE:plan': 46, 'GLU:plan': 51, 'ASP:plan': 46} Unresolved non-hydrogen planarities: 1436 Time building chain proxies: 5.01, per 1000 atoms: 0.65 Number of scatterers: 7747 At special positions: 0 Unit cell: (113.212, 96.778, 142.428, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 1440 8.00 N 1468 7.00 C 4834 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: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2568 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 68.9% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'G' and resid 26 through 52 removed outlier: 3.662A pdb=" N ALA G 30 " --> pdb=" O CYS G 26 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) Proline residue: G 35 - end of helix Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 71 through 98 removed outlier: 4.272A pdb=" N VAL G 98 " --> pdb=" O LEU G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 130 removed outlier: 3.755A pdb=" N MET G 112 " --> pdb=" O MET G 108 " (cutoff:3.500A) removed outlier: 3.637A 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 Processing helix chain 'G' and resid 166 through 194 removed outlier: 4.071A pdb=" N CYS G 170 " --> pdb=" O GLN G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 213 Processing helix chain 'G' and resid 223 through 230 Processing helix chain 'G' and resid 231 through 241 removed outlier: 4.321A pdb=" N ALA G 235 " --> pdb=" O TRP G 231 " (cutoff:3.500A) removed outlier: 3.787A 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 276 Processing helix chain 'G' and resid 284 through 329 removed outlier: 5.731A pdb=" N ARG G 297 " --> pdb=" O HIS G 293 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ARG G 298 " --> pdb=" O ALA G 294 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY G 316 " --> pdb=" O LEU G 312 " (cutoff:3.500A) Proline residue: G 317 - end of helix Processing helix chain 'G' and resid 347 through 352 Processing helix chain 'G' and resid 355 through 400 removed outlier: 4.588A pdb=" N THR G 371 " --> pdb=" O LEU G 367 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLN G 374 " --> pdb=" O ARG G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 435 Processing helix chain 'G' and resid 436 through 457 Proline residue: G 442 - end of helix Processing helix chain 'G' and resid 466 through 469 Processing helix chain 'G' and resid 470 through 505 removed outlier: 3.507A pdb=" N GLN G 474 " --> pdb=" O LEU G 470 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU G 494 " --> pdb=" O GLU G 490 " (cutoff:3.500A) removed outlier: 4.187A 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: 4.080A pdb=" N SER G 543 " --> pdb=" O TYR G 539 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE G 544 " --> pdb=" O THR G 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 549 through 564 removed outlier: 3.515A pdb=" N ALA G 553 " --> pdb=" O ALA G 549 " (cutoff:3.500A) Processing helix chain 'G' and resid 577 through 615 Proline residue: G 589 - end of helix removed outlier: 4.295A pdb=" N LEU G 592 " --> pdb=" O THR G 588 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER G 615 " --> pdb=" O SER G 611 " (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 removed outlier: 3.530A pdb=" N TYR G 799 " --> pdb=" O ASN G 795 " (cutoff:3.500A) Processing helix chain 'G' and resid 808 through 815 Processing helix chain 'G' and resid 831 through 846 removed outlier: 4.056A pdb=" N GLN G 846 " --> pdb=" O ARG G 842 " (cutoff:3.500A) Processing helix chain 'G' and resid 862 through 881 removed outlier: 3.755A pdb=" N LYS G 881 " --> pdb=" O LEU G 877 " (cutoff:3.500A) Processing helix chain 'G' and resid 913 through 918 removed outlier: 3.885A pdb=" N PHE G 917 " --> pdb=" O THR G 913 " (cutoff:3.500A) Processing helix chain 'G' and resid 922 through 927 removed outlier: 3.842A pdb=" N GLU G 926 " --> pdb=" O CYS G 922 " (cutoff:3.500A) Processing helix chain 'G' and resid 996 through 1009 removed outlier: 3.513A pdb=" N GLY G1009 " --> pdb=" O LEU G1005 " (cutoff:3.500A) Processing helix chain 'G' and resid 1009 through 1041 removed outlier: 4.376A pdb=" N LEU G1015 " --> pdb=" O LEU G1011 " (cutoff:3.500A) Processing helix chain 'G' and resid 1070 through 1107 Processing helix chain 'G' and resid 1109 through 1116 removed outlier: 3.974A pdb=" N PHE G1113 " --> pdb=" O PRO G1109 " (cutoff:3.500A) Processing helix chain 'G' and resid 1117 through 1135 removed outlier: 3.796A pdb=" N ILE G1121 " --> pdb=" O PRO G1117 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASP G1128 " --> pdb=" O ARG G1124 " (cutoff:3.500A) Processing helix chain 'G' and resid 1135 through 1161 removed outlier: 3.707A pdb=" N THR G1139 " --> pdb=" O HIS G1135 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU G1148 " --> pdb=" O SER G1144 " (cutoff:3.500A) Processing helix chain 'G' and resid 1164 through 1210 Proline residue: G1170 - end of helix removed outlier: 4.003A pdb=" N ASP G1188 " --> pdb=" O VAL G1184 " (cutoff:3.500A) Proline residue: G1199 - end of helix removed outlier: 3.614A pdb=" N GLY G1210 " --> pdb=" O GLU G1206 " (cutoff:3.500A) Processing helix chain 'G' and resid 1210 through 1218 removed outlier: 3.678A pdb=" N ILE G1214 " --> pdb=" O GLY G1210 " (cutoff:3.500A) Processing helix chain 'G' and resid 1219 through 1273 removed outlier: 4.025A pdb=" N PHE G1223 " --> pdb=" O TYR G1219 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA G1237 " --> pdb=" O SER G1233 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS G1273 " --> pdb=" O SER G1269 " (cutoff:3.500A) Processing helix chain 'G' and resid 1278 through 1321 removed outlier: 3.625A pdb=" N SER G1292 " --> pdb=" O ALA G1288 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN G1293 " --> pdb=" O LEU G1289 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN G1296 " --> pdb=" O SER G1292 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA G1311 " --> pdb=" O ILE G1307 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL G1312 " --> pdb=" O GLN G1308 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG G1314 " --> pdb=" O GLY G1310 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR G1321 " --> pdb=" O ALA G1317 " (cutoff:3.500A) Processing helix chain 'G' and resid 1385 through 1392 Processing helix chain 'G' and resid 1414 through 1421 removed outlier: 3.855A pdb=" N ARG G1421 " --> pdb=" O THR G1417 " (cutoff:3.500A) Processing helix chain 'G' and resid 1435 through 1441 Processing helix chain 'G' and resid 1447 through 1458 removed outlier: 3.668A pdb=" N LEU G1451 " --> pdb=" O SER G1447 " (cutoff:3.500A) Processing helix chain 'G' and resid 1460 through 1465 Processing helix chain 'G' and resid 1484 through 1498 removed outlier: 4.240A pdb=" N GLN G1488 " --> pdb=" O GLN G1484 " (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 1564 through 1570 removed outlier: 3.832A pdb=" N SER G1568 " --> pdb=" O GLU G1564 " (cutoff:3.500A) Processing helix chain 'G' and resid 1571 through 1576 Processing sheet with id=AA1, first strand: chain 'G' and resid 701 through 703 Processing sheet with id=AA2, first strand: chain 'G' and resid 696 through 697 Processing sheet with id=AA3, first strand: chain 'G' and resid 850 through 854 removed outlier: 6.514A pdb=" N VAL G 851 " --> pdb=" O VAL G 885 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL G 887 " --> pdb=" O VAL G 851 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU G 853 " --> pdb=" O VAL G 887 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE G 901 " --> pdb=" O LEU G 708 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET G 710 " --> pdb=" O ILE G 901 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N MET G 903 " --> pdb=" O MET G 710 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL G 712 " --> pdb=" O MET G 903 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA G 902 " --> pdb=" O GLN G 909 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 1347 through 1348 Processing sheet with id=AA5, first strand: chain 'G' and resid 1352 through 1353 removed outlier: 3.805A pdb=" N ASP G1397 " --> pdb=" O ARG G1353 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 1549 through 1551 693 hydrogen bonds defined for protein. 2037 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: 2.97 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2166 1.33 - 1.45: 1399 1.45 - 1.56: 4312 1.56 - 1.68: 0 1.68 - 1.80: 6 Bond restraints: 7883 Sorted by residual: bond pdb=" CB TRP G 75 " pdb=" CG TRP G 75 " ideal model delta sigma weight residual 1.498 1.404 0.094 3.10e-02 1.04e+03 9.26e+00 bond pdb=" CB TRP G 778 " pdb=" CG TRP G 778 " ideal model delta sigma weight residual 1.498 1.414 0.084 3.10e-02 1.04e+03 7.33e+00 bond pdb=" CB TRP G 231 " pdb=" CG TRP G 231 " ideal model delta sigma weight residual 1.498 1.421 0.077 3.10e-02 1.04e+03 6.14e+00 bond pdb=" CA TYR G1287 " pdb=" C TYR G1287 " ideal model delta sigma weight residual 1.522 1.488 0.033 1.37e-02 5.33e+03 5.97e+00 bond pdb=" CB VAL G 596 " pdb=" CG2 VAL G 596 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.82e+00 ... (remaining 7878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 10350 2.53 - 5.05: 506 5.05 - 7.58: 51 7.58 - 10.11: 17 10.11 - 12.64: 9 Bond angle restraints: 10933 Sorted by residual: angle pdb=" N LEU G 104 " pdb=" CA LEU G 104 " pdb=" C LEU G 104 " ideal model delta sigma weight residual 111.54 120.73 -9.19 1.36e+00 5.41e-01 4.57e+01 angle pdb=" N GLY G 97 " pdb=" CA GLY G 97 " pdb=" C GLY G 97 " ideal model delta sigma weight residual 113.86 123.25 -9.39 1.50e+00 4.44e-01 3.92e+01 angle pdb=" N GLY G 316 " pdb=" CA GLY G 316 " pdb=" C GLY G 316 " ideal model delta sigma weight residual 112.34 124.86 -12.52 2.04e+00 2.40e-01 3.77e+01 angle pdb=" C ARG G 102 " pdb=" N HIS G 103 " pdb=" CA HIS G 103 " ideal model delta sigma weight residual 121.70 132.56 -10.86 1.80e+00 3.09e-01 3.64e+01 angle pdb=" CA ARG G 370 " pdb=" CB ARG G 370 " pdb=" CG ARG G 370 " ideal model delta sigma weight residual 114.10 102.33 11.77 2.00e+00 2.50e-01 3.46e+01 ... (remaining 10928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.87: 4349 13.87 - 27.74: 130 27.74 - 41.61: 19 41.61 - 55.48: 4 55.48 - 69.35: 2 Dihedral angle restraints: 4504 sinusoidal: 568 harmonic: 3936 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 -137.28 -42.72 0 5.00e+00 4.00e-02 7.30e+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 93.00 143.56 -50.56 1 1.00e+01 1.00e-02 3.50e+01 dihedral pdb=" CA ARG G 102 " pdb=" C ARG G 102 " pdb=" N HIS G 103 " pdb=" CA HIS G 103 " ideal model delta harmonic sigma weight residual 0.00 -28.18 28.18 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 4501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1114 0.074 - 0.149: 203 0.149 - 0.223: 24 0.223 - 0.297: 8 0.297 - 0.372: 2 Chirality restraints: 1351 Sorted by residual: chirality pdb=" CA PHE G 79 " pdb=" N PHE G 79 " pdb=" C PHE G 79 " pdb=" CB PHE G 79 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA ARG G 370 " pdb=" N ARG G 370 " pdb=" C ARG G 370 " pdb=" CB ARG G 370 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA PHE G 295 " pdb=" N PHE G 295 " pdb=" C PHE G 295 " pdb=" CB PHE G 295 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1348 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR G1286 " 0.046 2.00e-02 2.50e+03 9.17e-02 8.41e+01 pdb=" C THR G1286 " -0.159 2.00e-02 2.50e+03 pdb=" O THR G1286 " 0.058 2.00e-02 2.50e+03 pdb=" N TYR G1287 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG G 297 " -0.041 2.00e-02 2.50e+03 8.10e-02 6.56e+01 pdb=" C ARG G 297 " 0.140 2.00e-02 2.50e+03 pdb=" O ARG G 297 " -0.052 2.00e-02 2.50e+03 pdb=" N ARG G 298 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G1283 " -0.028 2.00e-02 2.50e+03 5.65e-02 3.19e+01 pdb=" C LEU G1283 " 0.098 2.00e-02 2.50e+03 pdb=" O LEU G1283 " -0.037 2.00e-02 2.50e+03 pdb=" N GLY G1284 " -0.033 2.00e-02 2.50e+03 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1763 2.76 - 3.30: 7690 3.30 - 3.83: 12664 3.83 - 4.37: 12260 4.37 - 4.90: 20825 Nonbonded interactions: 55202 Sorted by model distance: nonbonded pdb=" OG1 THR G 371 " pdb=" OH TYR G1254 " model vdw 2.231 3.040 nonbonded pdb=" O ALA G 484 " pdb=" OG1 THR G 488 " model vdw 2.258 3.040 nonbonded pdb=" O GLU G 791 " pdb=" OH TYR G1219 " model vdw 2.285 3.040 nonbonded pdb=" O TRP G 778 " pdb=" NH2 ARG G 842 " model vdw 2.330 3.120 nonbonded pdb=" O THR G 789 " pdb=" OG SER G 792 " model vdw 2.354 3.040 ... (remaining 55197 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: 0.080 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.650 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: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 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 : 0.009 0.098 7883 Z= 0.613 Angle : 1.243 12.636 10933 Z= 0.756 Chirality : 0.061 0.372 1351 Planarity : 0.012 0.092 1508 Dihedral : 8.371 69.349 1933 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.44 % 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: -3.87 (0.18), residues: 1333 helix: -1.89 (0.13), residues: 886 sheet: -3.83 (0.50), residues: 61 loop : -3.62 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.007 TRP G1297 HIS 0.018 0.004 HIS G 125 PHE 0.046 0.004 PHE G 221 TYR 0.039 0.005 TYR G1219 ARG 0.008 0.002 ARG G 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.866 Fit side-chains REVERT: G 28 VAL cc_start: 0.9010 (m) cc_final: 0.8749 (p) REVERT: G 217 PHE cc_start: 0.8479 (t80) cc_final: 0.7943 (t80) REVERT: G 264 GLN cc_start: 0.9479 (mm110) cc_final: 0.9163 (mm110) REVERT: G 394 LYS cc_start: 0.9805 (tptm) cc_final: 0.9569 (tppp) REVERT: G 433 PHE cc_start: 0.9060 (m-10) cc_final: 0.8513 (m-80) REVERT: G 485 GLN cc_start: 0.9564 (tt0) cc_final: 0.9328 (tm-30) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1356 time to fit residues: 17.4998 Evaluate side-chains 62 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 40.0000 chunk 102 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 30.0000 chunk 122 optimal weight: 50.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 32 ASN G 262 ASN G 293 HIS G 386 ASN G 584 HIS ** G1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.070747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.057663 restraints weight = 52283.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.058768 restraints weight = 37015.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.059548 restraints weight = 28263.841| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7883 Z= 0.226 Angle : 0.616 8.071 10933 Z= 0.350 Chirality : 0.042 0.162 1351 Planarity : 0.005 0.050 1508 Dihedral : 4.921 39.688 1381 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.38 % Allowed : 3.80 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.44 % 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: -0.99 (0.22), residues: 1333 helix: 0.54 (0.17), residues: 896 sheet: -3.50 (0.56), residues: 61 loop : -3.06 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 288 HIS 0.005 0.002 HIS G 71 PHE 0.015 0.002 PHE G1182 TYR 0.019 0.002 TYR G 799 ARG 0.006 0.001 ARG G 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: G 217 PHE cc_start: 0.8192 (t80) cc_final: 0.7768 (t80) REVERT: G 262 ASN cc_start: 0.8596 (m-40) cc_final: 0.8265 (m-40) REVERT: G 263 TYR cc_start: 0.8696 (t80) cc_final: 0.8286 (t80) REVERT: G 264 GLN cc_start: 0.9262 (mm110) cc_final: 0.9031 (mm110) REVERT: G 394 LYS cc_start: 0.9810 (tptm) cc_final: 0.9005 (tppp) REVERT: G 433 PHE cc_start: 0.9231 (m-10) cc_final: 0.8729 (m-80) outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.1194 time to fit residues: 13.6082 Evaluate side-chains 59 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 39 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 43 optimal weight: 30.0000 chunk 81 optimal weight: 0.0870 chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 125 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.071511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.058425 restraints weight = 52411.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.059562 restraints weight = 37049.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.060394 restraints weight = 28140.526| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 7883 Z= 0.164 Angle : 0.532 7.099 10933 Z= 0.292 Chirality : 0.041 0.141 1351 Planarity : 0.004 0.044 1508 Dihedral : 4.297 33.282 1381 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.44 % 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: 0.41 (0.24), residues: 1333 helix: 1.65 (0.17), residues: 904 sheet: -3.31 (0.58), residues: 61 loop : -2.70 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 288 HIS 0.003 0.001 HIS G 71 PHE 0.019 0.001 PHE G1204 TYR 0.016 0.001 TYR G 124 ARG 0.005 0.001 ARG G 798 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: G 217 PHE cc_start: 0.8283 (t80) cc_final: 0.7823 (t80) REVERT: G 263 TYR cc_start: 0.8693 (t80) cc_final: 0.8154 (t80) REVERT: G 264 GLN cc_start: 0.9213 (mm110) cc_final: 0.9010 (mm110) REVERT: G 394 LYS cc_start: 0.9804 (tptm) cc_final: 0.9269 (tppp) REVERT: G 433 PHE cc_start: 0.9116 (m-10) cc_final: 0.8899 (m-80) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1145 time to fit residues: 12.6754 Evaluate side-chains 58 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 81 optimal weight: 50.0000 chunk 26 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 chunk 61 optimal weight: 30.0000 chunk 1 optimal weight: 0.3980 chunk 92 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.071217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.058382 restraints weight = 54093.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.059417 restraints weight = 38659.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.060124 restraints weight = 29633.636| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7883 Z= 0.187 Angle : 0.538 7.386 10933 Z= 0.300 Chirality : 0.041 0.133 1351 Planarity : 0.004 0.045 1508 Dihedral : 4.182 33.707 1381 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.44 % 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: 0.87 (0.24), residues: 1333 helix: 2.02 (0.17), residues: 905 sheet: -3.63 (0.59), residues: 54 loop : -2.53 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 288 HIS 0.007 0.001 HIS G 71 PHE 0.018 0.002 PHE G 44 TYR 0.020 0.002 TYR G 124 ARG 0.005 0.001 ARG G 798 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 1.228 Fit side-chains REVERT: G 262 ASN cc_start: 0.8433 (m110) cc_final: 0.8116 (m-40) REVERT: G 263 TYR cc_start: 0.8639 (t80) cc_final: 0.8137 (t80) REVERT: G 394 LYS cc_start: 0.9795 (tptm) cc_final: 0.9173 (tppp) REVERT: G 485 GLN cc_start: 0.9303 (tm-30) cc_final: 0.9055 (tm-30) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1227 time to fit residues: 13.7102 Evaluate side-chains 57 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 115 optimal weight: 40.0000 chunk 15 optimal weight: 30.0000 chunk 79 optimal weight: 0.9990 chunk 38 optimal weight: 40.0000 chunk 31 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 40 optimal weight: 0.0020 chunk 42 optimal weight: 9.9990 chunk 120 optimal weight: 50.0000 overall best weight: 3.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.072148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.059951 restraints weight = 56309.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.060851 restraints weight = 41304.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.061516 restraints weight = 32142.335| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7883 Z= 0.154 Angle : 0.507 7.093 10933 Z= 0.278 Chirality : 0.041 0.129 1351 Planarity : 0.004 0.043 1508 Dihedral : 3.975 32.517 1381 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.44 % 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: 1.23 (0.24), residues: 1333 helix: 2.27 (0.17), residues: 908 sheet: -3.00 (0.61), residues: 61 loop : -2.44 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 288 HIS 0.003 0.001 HIS G 71 PHE 0.032 0.001 PHE G 433 TYR 0.025 0.002 TYR G 142 ARG 0.004 0.001 ARG G 798 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: G 112 MET cc_start: 0.6333 (mtm) cc_final: 0.6011 (ttm) REVERT: G 262 ASN cc_start: 0.8010 (m110) cc_final: 0.7557 (m-40) REVERT: G 263 TYR cc_start: 0.8085 (t80) cc_final: 0.7700 (t80) REVERT: G 394 LYS cc_start: 0.9734 (tptm) cc_final: 0.9259 (tppp) REVERT: G 433 PHE cc_start: 0.8719 (m-80) cc_final: 0.8330 (m-80) REVERT: G 485 GLN cc_start: 0.9367 (tm-30) cc_final: 0.9132 (tm-30) REVERT: G 1204 PHE cc_start: 0.8248 (m-80) cc_final: 0.7384 (m-80) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1859 time to fit residues: 21.0939 Evaluate side-chains 56 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 40.0000 chunk 22 optimal weight: 0.0870 chunk 17 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 116 optimal weight: 30.0000 chunk 14 optimal weight: 5.9990 chunk 49 optimal weight: 30.0000 chunk 87 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 81 optimal weight: 50.0000 overall best weight: 6.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.070213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.058053 restraints weight = 57004.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.058956 restraints weight = 41821.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.059586 restraints weight = 32559.213| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7883 Z= 0.210 Angle : 0.551 6.967 10933 Z= 0.307 Chirality : 0.042 0.140 1351 Planarity : 0.004 0.045 1508 Dihedral : 4.173 31.946 1381 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.44 % 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: 1.12 (0.24), residues: 1333 helix: 2.20 (0.17), residues: 903 sheet: -3.56 (0.55), residues: 59 loop : -2.37 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 439 HIS 0.008 0.001 HIS G 71 PHE 0.024 0.002 PHE G1182 TYR 0.021 0.002 TYR G 142 ARG 0.005 0.001 ARG G 798 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 112 MET cc_start: 0.6455 (mtm) cc_final: 0.5903 (ttm) REVERT: G 263 TYR cc_start: 0.8599 (t80) cc_final: 0.7921 (t80) REVERT: G 394 LYS cc_start: 0.9784 (tptm) cc_final: 0.9205 (tppp) REVERT: G 433 PHE cc_start: 0.8987 (m-80) cc_final: 0.8484 (m-80) REVERT: G 485 GLN cc_start: 0.9376 (tm-30) cc_final: 0.9090 (tm-30) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1095 time to fit residues: 11.3447 Evaluate side-chains 54 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 83 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 30.0000 chunk 2 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 133 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 115 optimal weight: 40.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 262 ASN ** 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 = 0.3364 r_free = 0.3364 target = 0.071436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.059284 restraints weight = 56809.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.060163 restraints weight = 41781.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.060815 restraints weight = 32677.671| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7883 Z= 0.153 Angle : 0.498 7.091 10933 Z= 0.272 Chirality : 0.041 0.129 1351 Planarity : 0.004 0.043 1508 Dihedral : 3.951 31.370 1381 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.44 % 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: 1.46 (0.24), residues: 1333 helix: 2.46 (0.17), residues: 913 sheet: -3.56 (0.53), residues: 59 loop : -2.34 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 288 HIS 0.004 0.001 HIS G 71 PHE 0.025 0.001 PHE G1182 TYR 0.019 0.001 TYR G 142 ARG 0.004 0.001 ARG G 798 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 112 MET cc_start: 0.6307 (mtm) cc_final: 0.5930 (ttm) REVERT: G 263 TYR cc_start: 0.8090 (t80) cc_final: 0.7660 (t80) REVERT: G 394 LYS cc_start: 0.9743 (tptm) cc_final: 0.9271 (tppp) REVERT: G 433 PHE cc_start: 0.8590 (m-80) cc_final: 0.8362 (m-80) REVERT: G 485 GLN cc_start: 0.9273 (tm-30) cc_final: 0.8973 (tm-30) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1107 time to fit residues: 11.4610 Evaluate side-chains 57 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 40.0000 chunk 26 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 22 optimal weight: 0.0170 chunk 3 optimal weight: 0.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 262 ASN ** 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 = 0.3375 r_free = 0.3375 target = 0.072015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.059808 restraints weight = 56950.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.060665 restraints weight = 42098.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.061349 restraints weight = 32929.018| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7883 Z= 0.141 Angle : 0.490 6.974 10933 Z= 0.266 Chirality : 0.041 0.127 1351 Planarity : 0.004 0.042 1508 Dihedral : 3.795 29.626 1381 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 1.69 (0.24), residues: 1333 helix: 2.68 (0.17), residues: 914 sheet: -3.72 (0.47), residues: 69 loop : -2.28 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 288 HIS 0.004 0.001 HIS G 71 PHE 0.025 0.002 PHE G1182 TYR 0.027 0.002 TYR G1219 ARG 0.003 0.001 ARG G 798 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 112 MET cc_start: 0.6243 (mtm) cc_final: 0.5923 (ttm) REVERT: G 263 TYR cc_start: 0.8074 (t80) cc_final: 0.7662 (t80) REVERT: G 327 LEU cc_start: 0.7789 (tp) cc_final: 0.7318 (pp) REVERT: G 394 LYS cc_start: 0.9703 (tptm) cc_final: 0.9200 (tppp) REVERT: G 485 GLN cc_start: 0.9188 (tm-30) cc_final: 0.8844 (tm-30) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1097 time to fit residues: 11.5925 Evaluate side-chains 57 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 94 optimal weight: 20.0000 chunk 80 optimal weight: 30.0000 chunk 30 optimal weight: 5.9990 chunk 73 optimal weight: 40.0000 chunk 107 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 30.0000 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 50 optimal weight: 30.0000 chunk 9 optimal weight: 50.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 262 ASN ** 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 = 0.3303 r_free = 0.3303 target = 0.068735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.056462 restraints weight = 58399.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.057330 restraints weight = 42492.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.057972 restraints weight = 33297.499| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7883 Z= 0.298 Angle : 0.614 7.018 10933 Z= 0.356 Chirality : 0.043 0.149 1351 Planarity : 0.004 0.045 1508 Dihedral : 4.493 31.685 1381 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.44 % 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: 0.73 (0.24), residues: 1333 helix: 1.85 (0.17), residues: 905 sheet: -3.55 (0.54), residues: 58 loop : -2.38 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 688 HIS 0.009 0.002 HIS G 71 PHE 0.024 0.002 PHE G 431 TYR 0.021 0.003 TYR G 142 ARG 0.005 0.001 ARG G 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 263 TYR cc_start: 0.8287 (t80) cc_final: 0.7745 (t80) REVERT: G 394 LYS cc_start: 0.9777 (tptm) cc_final: 0.9181 (tppp) REVERT: G 433 PHE cc_start: 0.8804 (m-80) cc_final: 0.8573 (m-80) REVERT: G 485 GLN cc_start: 0.9366 (tm-30) cc_final: 0.9050 (tm-30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1098 time to fit residues: 10.9195 Evaluate side-chains 55 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 45 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 125 optimal weight: 50.0000 chunk 8 optimal weight: 0.0980 chunk 19 optimal weight: 40.0000 chunk 71 optimal weight: 50.0000 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 262 ASN ** 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 = 0.3335 r_free = 0.3335 target = 0.070574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.057685 restraints weight = 53467.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.058706 restraints weight = 38004.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.059491 restraints weight = 29056.286| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7883 Z= 0.161 Angle : 0.507 7.112 10933 Z= 0.281 Chirality : 0.041 0.142 1351 Planarity : 0.004 0.043 1508 Dihedral : 4.026 30.358 1381 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.44 % 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: 1.39 (0.24), residues: 1333 helix: 2.43 (0.17), residues: 914 sheet: -3.96 (0.49), residues: 59 loop : -2.36 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 288 HIS 0.003 0.001 HIS G 71 PHE 0.018 0.001 PHE G1204 TYR 0.020 0.002 TYR G 142 ARG 0.005 0.001 ARG G 798 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 112 MET cc_start: 0.6326 (mtm) cc_final: 0.5621 (ttm) REVERT: G 263 TYR cc_start: 0.8461 (t80) cc_final: 0.8056 (t80) REVERT: G 266 LEU cc_start: 0.9685 (tp) cc_final: 0.9402 (pp) REVERT: G 327 LEU cc_start: 0.7737 (tp) cc_final: 0.7181 (pp) REVERT: G 394 LYS cc_start: 0.9767 (tptm) cc_final: 0.9340 (tppp) REVERT: G 433 PHE cc_start: 0.8865 (m-80) cc_final: 0.8607 (m-80) REVERT: G 485 GLN cc_start: 0.9441 (tm-30) cc_final: 0.9128 (tm-30) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1356 time to fit residues: 13.8083 Evaluate side-chains 55 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 81 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 115 optimal weight: 50.0000 chunk 87 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 262 ASN ** 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 = 0.3343 r_free = 0.3343 target = 0.071062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.058827 restraints weight = 56854.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.059715 restraints weight = 41528.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.060351 restraints weight = 32493.324| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7883 Z= 0.170 Angle : 0.511 7.005 10933 Z= 0.283 Chirality : 0.041 0.145 1351 Planarity : 0.004 0.042 1508 Dihedral : 3.940 29.328 1381 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 1.60 (0.24), residues: 1333 helix: 2.56 (0.17), residues: 919 sheet: -3.63 (0.58), residues: 48 loop : -2.42 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 288 HIS 0.004 0.001 HIS G 71 PHE 0.018 0.001 PHE G 433 TYR 0.020 0.002 TYR G 142 ARG 0.003 0.001 ARG G 798 =============================================================================== Job complete usr+sys time: 2012.96 seconds wall clock time: 36 minutes 27.38 seconds (2187.38 seconds total)