Starting phenix.real_space_refine on Tue Sep 24 17:36:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f43_50182/09_2024/9f43_50182.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f43_50182/09_2024/9f43_50182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f43_50182/09_2024/9f43_50182.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f43_50182/09_2024/9f43_50182.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f43_50182/09_2024/9f43_50182.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f43_50182/09_2024/9f43_50182.cif" } resolution = 3.49 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.000 sd= 0.027 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 57 5.16 5 C 5413 2.51 5 N 1462 2.21 5 O 1533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8465 Number of models: 1 Model: "" Number of chains: 2 Chain: "E" Number of atoms: 8385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8385 Classifications: {'peptide': 1052} Link IDs: {'PTRANS': 56, 'TRANS': 995} Chain breaks: 5 Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 80 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Time building chain proxies: 7.75, per 1000 atoms: 0.92 Number of scatterers: 8465 At special positions: 0 Unit cell: (102.18, 144.1, 82.53, 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 57 16.00 O 1533 8.00 N 1462 7.00 C 5413 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.24 Conformation dependent library (CDL) restraints added in 1.0 seconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 9 sheets defined 47.8% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'E' and resid 19 through 25 removed outlier: 3.793A pdb=" N ASP E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 37 Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 94 through 112 Processing helix chain 'E' and resid 126 through 141 Processing helix chain 'E' and resid 179 through 186 Processing helix chain 'E' and resid 198 through 219 removed outlier: 3.533A pdb=" N ILE E 202 " --> pdb=" O ASN E 198 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL E 219 " --> pdb=" O GLN E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 269 Processing helix chain 'E' and resid 269 through 280 Processing helix chain 'E' and resid 281 through 287 Processing helix chain 'E' and resid 291 through 297 Processing helix chain 'E' and resid 307 through 328 Processing helix chain 'E' and resid 329 through 338 removed outlier: 3.540A pdb=" N ARG E 338 " --> pdb=" O GLN E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 359 removed outlier: 3.784A pdb=" N LEU E 352 " --> pdb=" O ARG E 348 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER E 359 " --> pdb=" O ARG E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 391 removed outlier: 3.644A pdb=" N ALA E 381 " --> pdb=" O ALA E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 398 Processing helix chain 'E' and resid 407 through 422 removed outlier: 3.797A pdb=" N MET E 422 " --> pdb=" O VAL E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 442 removed outlier: 3.788A pdb=" N LEU E 441 " --> pdb=" O LEU E 437 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER E 442 " --> pdb=" O GLN E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 458 Processing helix chain 'E' and resid 460 through 471 Processing helix chain 'E' and resid 472 through 480 removed outlier: 3.695A pdb=" N LEU E 480 " --> pdb=" O VAL E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 486 No H-bonds generated for 'chain 'E' and resid 484 through 486' Processing helix chain 'E' and resid 487 through 502 Processing helix chain 'E' and resid 504 through 512 removed outlier: 4.558A pdb=" N ASP E 508 " --> pdb=" O SER E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 523 removed outlier: 4.007A pdb=" N TYR E 517 " --> pdb=" O ASN E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 543 Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 557 through 565 Processing helix chain 'E' and resid 570 through 585 removed outlier: 3.606A pdb=" N TRP E 585 " --> pdb=" O LEU E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 598 Processing helix chain 'E' and resid 599 through 605 Processing helix chain 'E' and resid 606 through 610 Processing helix chain 'E' and resid 612 through 628 Processing helix chain 'E' and resid 634 through 650 removed outlier: 3.564A pdb=" N GLN E 650 " --> pdb=" O MET E 646 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 674 Processing helix chain 'E' and resid 674 through 685 removed outlier: 3.691A pdb=" N PHE E 685 " --> pdb=" O VAL E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 820 Processing helix chain 'E' and resid 823 through 839 removed outlier: 3.516A pdb=" N TYR E 839 " --> pdb=" O ASN E 835 " (cutoff:3.500A) Processing helix chain 'E' and resid 950 through 954 Processing helix chain 'E' and resid 958 through 969 removed outlier: 3.836A pdb=" N TYR E 966 " --> pdb=" O TRP E 962 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE E 967 " --> pdb=" O SER E 963 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA E 968 " --> pdb=" O ALA E 964 " (cutoff:3.500A) Processing helix chain 'E' and resid 982 through 1008 Processing sheet with id=AA1, first strand: chain 'E' and resid 118 through 123 removed outlier: 7.403A pdb=" N VAL E 58 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N LYS E 120 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL E 60 " --> pdb=" O LYS E 120 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N SER E 122 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU E 62 " --> pdb=" O SER E 122 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG E 145 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER E 59 " --> pdb=" O ARG E 145 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL E 146 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL E 193 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE E 148 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP E 195 " --> pdb=" O PHE E 148 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR E 150 " --> pdb=" O ASP E 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 163 through 167 Processing sheet with id=AA3, first strand: chain 'E' and resid 1015 through 1016 removed outlier: 3.953A pdb=" N ASP E1015 " --> pdb=" O SER E1329 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER E1329 " --> pdb=" O ASP E1015 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS E1306 " --> pdb=" O GLY E1319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 1028 through 1031 removed outlier: 3.728A pdb=" N VAL E1028 " --> pdb=" O ALA E1041 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE E1046 " --> pdb=" O TYR E1059 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR E1059 " --> pdb=" O ILE E1046 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE E1048 " --> pdb=" O LEU E1057 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 1070 through 1076 removed outlier: 4.318A pdb=" N ALA E1092 " --> pdb=" O THR E1088 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE E1093 " --> pdb=" O ALA E1111 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA E1111 " --> pdb=" O ILE E1093 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL E1095 " --> pdb=" O VAL E1109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 1127 through 1131 removed outlier: 4.694A pdb=" N GLY E1142 " --> pdb=" O ILE E1146 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE E1146 " --> pdb=" O GLY E1142 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL E1147 " --> pdb=" O ASP E1160 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASP E1160 " --> pdb=" O VAL E1147 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE E1149 " --> pdb=" O VAL E1158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 1169 through 1173 removed outlier: 6.959A pdb=" N ILE E1190 " --> pdb=" O THR E1206 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N THR E1206 " --> pdb=" O ILE E1190 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL E1192 " --> pdb=" O VAL E1204 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 1214 through 1218 removed outlier: 7.068A pdb=" N VAL E1230 " --> pdb=" O VAL E1215 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA E1217 " --> pdb=" O VAL E1228 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL E1228 " --> pdb=" O ALA E1217 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER E1229 " --> pdb=" O ARG E1237 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER E1231 " --> pdb=" O ASP E1235 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASP E1235 " --> pdb=" O SER E1231 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN E1248 " --> pdb=" O ILE E1238 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASP E1240 " --> pdb=" O SER E1246 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N SER E1246 " --> pdb=" O ASP E1240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 1259 through 1261 removed outlier: 3.513A pdb=" N ALA E1278 " --> pdb=" O CYS E1270 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN E1288 " --> pdb=" O ILE E1279 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1161 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: 3.09 Time building geometry restraints manager: 2.62 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: 2764 1.34 - 1.46: 1613 1.46 - 1.58: 4204 1.58 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 8666 Sorted by residual: bond pdb=" N VAL G 406 " pdb=" CA VAL G 406 " ideal model delta sigma weight residual 1.474 1.458 0.016 1.57e-02 4.06e+03 1.08e+00 bond pdb=" CA TYR E 839 " pdb=" CB TYR E 839 " ideal model delta sigma weight residual 1.524 1.534 -0.011 1.31e-02 5.83e+03 6.56e-01 bond pdb=" CB ASN E 557 " pdb=" CG ASN E 557 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.51e-01 bond pdb=" CA VAL G 406 " pdb=" CB VAL G 406 " ideal model delta sigma weight residual 1.532 1.543 -0.011 1.42e-02 4.96e+03 6.07e-01 bond pdb=" C ALA E1125 " pdb=" N GLY E1126 " ideal model delta sigma weight residual 1.331 1.319 0.011 1.46e-02 4.69e+03 5.76e-01 ... (remaining 8661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 11505 1.31 - 2.61: 212 2.61 - 3.92: 60 3.92 - 5.23: 8 5.23 - 6.53: 2 Bond angle restraints: 11787 Sorted by residual: angle pdb=" CA TYR E 839 " pdb=" CB TYR E 839 " pdb=" CG TYR E 839 " ideal model delta sigma weight residual 113.90 120.43 -6.53 1.80e+00 3.09e-01 1.32e+01 angle pdb=" N VAL G 406 " pdb=" CA VAL G 406 " pdb=" C VAL G 406 " ideal model delta sigma weight residual 106.21 108.54 -2.33 1.07e+00 8.73e-01 4.74e+00 angle pdb=" N PRO E 407 " pdb=" CA PRO E 407 " pdb=" C PRO E 407 " ideal model delta sigma weight residual 114.92 112.40 2.52 1.19e+00 7.06e-01 4.47e+00 angle pdb=" C TYR E 839 " pdb=" CA TYR E 839 " pdb=" CB TYR E 839 " ideal model delta sigma weight residual 111.50 114.21 -2.71 1.29e+00 6.01e-01 4.42e+00 angle pdb=" CB LYS E1056 " pdb=" CG LYS E1056 " pdb=" CD LYS E1056 " ideal model delta sigma weight residual 111.30 115.45 -4.15 2.30e+00 1.89e-01 3.25e+00 ... (remaining 11782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4670 17.56 - 35.13: 415 35.13 - 52.69: 97 52.69 - 70.25: 15 70.25 - 87.82: 8 Dihedral angle restraints: 5205 sinusoidal: 2092 harmonic: 3113 Sorted by residual: dihedral pdb=" CA ASP E1042 " pdb=" CB ASP E1042 " pdb=" CG ASP E1042 " pdb=" OD1 ASP E1042 " ideal model delta sinusoidal sigma weight residual -30.00 -88.48 58.48 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA PHE E1060 " pdb=" C PHE E1060 " pdb=" N HIS E1061 " pdb=" CA HIS E1061 " ideal model delta harmonic sigma weight residual 180.00 164.01 15.99 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA GLN E 242 " pdb=" CB GLN E 242 " pdb=" CG GLN E 242 " pdb=" CD GLN E 242 " ideal model delta sinusoidal sigma weight residual 180.00 122.65 57.35 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 5202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 838 0.028 - 0.056: 305 0.056 - 0.084: 104 0.084 - 0.112: 61 0.112 - 0.140: 24 Chirality restraints: 1332 Sorted by residual: chirality pdb=" CG LEU E 667 " pdb=" CB LEU E 667 " pdb=" CD1 LEU E 667 " pdb=" CD2 LEU E 667 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA ILE E1146 " pdb=" N ILE E1146 " pdb=" C ILE E1146 " pdb=" CB ILE E1146 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA VAL E1192 " pdb=" N VAL E1192 " pdb=" C VAL E1192 " pdb=" CB VAL E1192 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 1329 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 213 " 0.186 9.50e-02 1.11e+02 8.38e-02 5.01e+00 pdb=" NE ARG E 213 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG E 213 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG E 213 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG E 213 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET E1243 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO E1244 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO E1244 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E1244 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 527 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO E 528 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO E 528 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 528 " -0.018 5.00e-02 4.00e+02 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 112 2.64 - 3.20: 7897 3.20 - 3.77: 13218 3.77 - 4.33: 17952 4.33 - 4.90: 29896 Nonbonded interactions: 69075 Sorted by model distance: nonbonded pdb=" OD2 ASP E 89 " pdb=" OG SER E 92 " model vdw 2.074 3.040 nonbonded pdb=" OG1 THR E1071 " pdb=" O MET E1127 " model vdw 2.094 3.040 nonbonded pdb=" NH2 ARG E 660 " pdb=" O ALA E1111 " model vdw 2.141 3.120 nonbonded pdb=" OD1 ASN E 170 " pdb=" OG1 THR E 172 " model vdw 2.167 3.040 nonbonded pdb=" O THR E 264 " pdb=" OG1 THR E 268 " model vdw 2.177 3.040 ... (remaining 69070 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic 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: 26.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.520 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 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 : 0.002 0.030 8666 Z= 0.145 Angle : 0.490 6.534 11787 Z= 0.257 Chirality : 0.040 0.140 1332 Planarity : 0.004 0.084 1503 Dihedral : 14.266 87.817 3175 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.21 % Allowed : 15.90 % Favored : 83.88 % 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: 1.09 (0.27), residues: 1047 helix: 2.48 (0.25), residues: 465 sheet: -1.11 (0.40), residues: 153 loop : -0.52 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E1051 HIS 0.003 0.001 HIS E1061 PHE 0.010 0.001 PHE E 626 TYR 0.009 0.001 TYR E 808 ARG 0.015 0.000 ARG E 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 31 MET cc_start: 0.9029 (tpp) cc_final: 0.8701 (tpp) REVERT: E 242 GLN cc_start: 0.8394 (mt0) cc_final: 0.7933 (mp10) REVERT: E 339 GLN cc_start: 0.8495 (tp40) cc_final: 0.8142 (tp-100) REVERT: E 593 TRP cc_start: 0.7434 (m-10) cc_final: 0.6594 (m-90) REVERT: E 1323 TYR cc_start: 0.6919 (m-10) cc_final: 0.6660 (m-10) REVERT: G 403 MET cc_start: 0.6463 (ttm) cc_final: 0.6262 (ttp) outliers start: 2 outliers final: 1 residues processed: 128 average time/residue: 0.2201 time to fit residues: 38.8157 Evaluate side-chains 114 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.0270 chunk 53 optimal weight: 0.0020 chunk 42 optimal weight: 0.9980 chunk 82 optimal weight: 0.0980 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 95 optimal weight: 0.0970 overall best weight: 0.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 153 HIS E 326 ASN E1113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8666 Z= 0.179 Angle : 0.508 7.493 11787 Z= 0.263 Chirality : 0.042 0.204 1332 Planarity : 0.004 0.046 1503 Dihedral : 3.739 24.888 1147 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.45 % Allowed : 13.02 % Favored : 84.53 % 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: 0.92 (0.27), residues: 1047 helix: 2.31 (0.24), residues: 472 sheet: -1.35 (0.39), residues: 158 loop : -0.54 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E1051 HIS 0.005 0.001 HIS E 531 PHE 0.011 0.001 PHE E 588 TYR 0.012 0.001 TYR E 517 ARG 0.007 0.000 ARG E1178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 475 TYR cc_start: 0.6876 (m-80) cc_final: 0.6651 (m-80) REVERT: G 403 MET cc_start: 0.6452 (ttm) cc_final: 0.6123 (ttp) outliers start: 23 outliers final: 8 residues processed: 138 average time/residue: 0.1868 time to fit residues: 36.9704 Evaluate side-chains 115 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 658 MET Chi-restraints excluded: chain E residue 670 LEU Chi-restraints excluded: chain E residue 1109 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1330 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 79 optimal weight: 0.3980 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 76 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 GLN E 326 ASN ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8666 Z= 0.303 Angle : 0.579 12.283 11787 Z= 0.297 Chirality : 0.045 0.163 1332 Planarity : 0.004 0.041 1503 Dihedral : 4.116 35.290 1147 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.63 % Favored : 96.28 % Rotamer: Outliers : 3.95 % Allowed : 13.23 % Favored : 82.82 % 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: 0.58 (0.27), residues: 1047 helix: 2.04 (0.24), residues: 471 sheet: -1.62 (0.38), residues: 169 loop : -0.64 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E1049 HIS 0.009 0.001 HIS E1262 PHE 0.016 0.002 PHE E 626 TYR 0.020 0.002 TYR E 475 ARG 0.003 0.000 ARG E 330 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 130 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 31 MET cc_start: 0.9076 (tpp) cc_final: 0.8518 (mpp) REVERT: E 52 LYS cc_start: 0.6420 (mmtm) cc_final: 0.6206 (mmtm) REVERT: E 55 MET cc_start: 0.8415 (mmm) cc_final: 0.8026 (mmp) REVERT: E 89 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7962 (p0) REVERT: E 123 LEU cc_start: 0.8701 (mt) cc_final: 0.8425 (mp) REVERT: E 254 MET cc_start: 0.7794 (mmt) cc_final: 0.7567 (mmt) REVERT: E 479 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8870 (mm) REVERT: E 512 ASP cc_start: 0.7834 (t70) cc_final: 0.7215 (t0) REVERT: E 1146 ILE cc_start: 0.8165 (mt) cc_final: 0.7722 (pt) REVERT: E 1172 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8302 (tp) REVERT: E 1323 TYR cc_start: 0.7196 (m-10) cc_final: 0.6743 (m-10) outliers start: 37 outliers final: 18 residues processed: 153 average time/residue: 0.1813 time to fit residues: 39.6698 Evaluate side-chains 126 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 479 LEU Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 670 LEU Chi-restraints excluded: chain E residue 836 SER Chi-restraints excluded: chain E residue 1025 VAL Chi-restraints excluded: chain E residue 1038 ILE Chi-restraints excluded: chain E residue 1109 VAL Chi-restraints excluded: chain E residue 1161 ILE Chi-restraints excluded: chain E residue 1172 LEU Chi-restraints excluded: chain E residue 1197 MET Chi-restraints excluded: chain E residue 1207 TYR Chi-restraints excluded: chain E residue 1257 THR Chi-restraints excluded: chain E residue 1330 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.0980 chunk 71 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 101 optimal weight: 0.0270 chunk 50 optimal weight: 0.1980 chunk 90 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 overall best weight: 0.2838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 326 ASN ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1315 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8666 Z= 0.191 Angle : 0.511 8.611 11787 Z= 0.261 Chirality : 0.043 0.161 1332 Planarity : 0.004 0.038 1503 Dihedral : 3.880 20.801 1146 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.63 % Allowed : 14.73 % Favored : 81.64 % 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: 0.67 (0.27), residues: 1047 helix: 2.12 (0.24), residues: 472 sheet: -1.59 (0.39), residues: 157 loop : -0.65 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E1213 HIS 0.004 0.001 HIS E1315 PHE 0.009 0.001 PHE E 626 TYR 0.010 0.001 TYR E 517 ARG 0.006 0.000 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 118 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 31 MET cc_start: 0.9119 (tpp) cc_final: 0.8605 (mpp) REVERT: E 55 MET cc_start: 0.8380 (mmm) cc_final: 0.8055 (mmp) REVERT: E 254 MET cc_start: 0.7826 (mmt) cc_final: 0.7550 (mmt) REVERT: E 479 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8719 (mm) REVERT: E 512 ASP cc_start: 0.7734 (t70) cc_final: 0.7417 (t70) REVERT: E 638 THR cc_start: 0.8078 (p) cc_final: 0.7870 (t) REVERT: E 646 MET cc_start: 0.7858 (mmm) cc_final: 0.7319 (mpp) REVERT: E 1146 ILE cc_start: 0.8181 (mt) cc_final: 0.7654 (pt) REVERT: E 1315 HIS cc_start: 0.6927 (OUTLIER) cc_final: 0.6597 (m90) REVERT: E 1323 TYR cc_start: 0.7074 (m-10) cc_final: 0.6579 (m-10) outliers start: 34 outliers final: 22 residues processed: 139 average time/residue: 0.1850 time to fit residues: 36.8473 Evaluate side-chains 135 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 239 ASN Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 479 LEU Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 658 MET Chi-restraints excluded: chain E residue 670 LEU Chi-restraints excluded: chain E residue 836 SER Chi-restraints excluded: chain E residue 969 GLN Chi-restraints excluded: chain E residue 1051 TRP Chi-restraints excluded: chain E residue 1088 THR Chi-restraints excluded: chain E residue 1109 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1156 MET Chi-restraints excluded: chain E residue 1197 MET Chi-restraints excluded: chain E residue 1207 TYR Chi-restraints excluded: chain E residue 1257 THR Chi-restraints excluded: chain E residue 1259 LEU Chi-restraints excluded: chain E residue 1315 HIS Chi-restraints excluded: chain E residue 1330 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 75 optimal weight: 0.0370 chunk 41 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 70 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 HIS E1315 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8666 Z= 0.280 Angle : 0.537 8.998 11787 Z= 0.275 Chirality : 0.044 0.159 1332 Planarity : 0.004 0.045 1503 Dihedral : 3.973 21.146 1146 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.84 % Allowed : 15.47 % Favored : 80.68 % 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: 0.58 (0.26), residues: 1047 helix: 1.96 (0.24), residues: 477 sheet: -1.55 (0.39), residues: 162 loop : -0.63 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 24 HIS 0.010 0.001 HIS E1315 PHE 0.015 0.001 PHE E 626 TYR 0.011 0.001 TYR E1059 ARG 0.005 0.000 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 122 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 31 MET cc_start: 0.9130 (tpp) cc_final: 0.8616 (mpp) REVERT: E 55 MET cc_start: 0.8375 (mmm) cc_final: 0.8026 (mmp) REVERT: E 89 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7968 (p0) REVERT: E 261 ASP cc_start: 0.7924 (t70) cc_final: 0.7570 (p0) REVERT: E 479 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8748 (mm) REVERT: E 485 ARG cc_start: 0.7926 (tpp-160) cc_final: 0.7615 (tpp-160) REVERT: E 512 ASP cc_start: 0.7742 (t70) cc_final: 0.7419 (t70) REVERT: E 638 THR cc_start: 0.8078 (p) cc_final: 0.7865 (t) REVERT: E 1256 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6975 (tt) REVERT: E 1315 HIS cc_start: 0.6975 (OUTLIER) cc_final: 0.6648 (m90) REVERT: E 1323 TYR cc_start: 0.7198 (m-10) cc_final: 0.6769 (m-10) outliers start: 36 outliers final: 25 residues processed: 145 average time/residue: 0.1973 time to fit residues: 40.3521 Evaluate side-chains 139 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 239 ASN Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 479 LEU Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 658 MET Chi-restraints excluded: chain E residue 670 LEU Chi-restraints excluded: chain E residue 836 SER Chi-restraints excluded: chain E residue 969 GLN Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1051 TRP Chi-restraints excluded: chain E residue 1064 ASN Chi-restraints excluded: chain E residue 1088 THR Chi-restraints excluded: chain E residue 1109 VAL Chi-restraints excluded: chain E residue 1156 MET Chi-restraints excluded: chain E residue 1197 MET Chi-restraints excluded: chain E residue 1207 TYR Chi-restraints excluded: chain E residue 1210 HIS Chi-restraints excluded: chain E residue 1256 LEU Chi-restraints excluded: chain E residue 1257 THR Chi-restraints excluded: chain E residue 1259 LEU Chi-restraints excluded: chain E residue 1315 HIS Chi-restraints excluded: chain E residue 1330 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 101 optimal weight: 0.0050 chunk 84 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.0030 chunk 53 optimal weight: 0.9980 overall best weight: 0.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1315 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8666 Z= 0.222 Angle : 0.521 8.194 11787 Z= 0.266 Chirality : 0.043 0.184 1332 Planarity : 0.004 0.043 1503 Dihedral : 3.961 21.398 1146 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.51 % Rotamer: Outliers : 3.84 % Allowed : 16.01 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1047 helix: 1.99 (0.24), residues: 477 sheet: -1.56 (0.40), residues: 157 loop : -0.64 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E1051 HIS 0.005 0.001 HIS E1315 PHE 0.013 0.001 PHE E 626 TYR 0.009 0.001 TYR E 517 ARG 0.006 0.000 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 116 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 31 MET cc_start: 0.9123 (tpp) cc_final: 0.8595 (mpp) REVERT: E 55 MET cc_start: 0.8324 (mmm) cc_final: 0.8068 (mmp) REVERT: E 89 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7964 (p0) REVERT: E 261 ASP cc_start: 0.8014 (t70) cc_final: 0.7754 (p0) REVERT: E 479 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8752 (mm) REVERT: E 485 ARG cc_start: 0.7938 (tpp-160) cc_final: 0.7590 (tpp-160) REVERT: E 512 ASP cc_start: 0.7719 (t70) cc_final: 0.7323 (t70) REVERT: E 646 MET cc_start: 0.7986 (mmm) cc_final: 0.7386 (mpp) REVERT: E 1146 ILE cc_start: 0.8028 (mt) cc_final: 0.7591 (pt) REVERT: E 1256 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7035 (tt) REVERT: E 1315 HIS cc_start: 0.7119 (OUTLIER) cc_final: 0.6637 (m90) REVERT: E 1323 TYR cc_start: 0.7205 (m-10) cc_final: 0.6746 (m-10) outliers start: 36 outliers final: 24 residues processed: 141 average time/residue: 0.2148 time to fit residues: 44.1680 Evaluate side-chains 136 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 479 LEU Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 658 MET Chi-restraints excluded: chain E residue 670 LEU Chi-restraints excluded: chain E residue 836 SER Chi-restraints excluded: chain E residue 969 GLN Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1051 TRP Chi-restraints excluded: chain E residue 1088 THR Chi-restraints excluded: chain E residue 1109 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1156 MET Chi-restraints excluded: chain E residue 1197 MET Chi-restraints excluded: chain E residue 1207 TYR Chi-restraints excluded: chain E residue 1210 HIS Chi-restraints excluded: chain E residue 1256 LEU Chi-restraints excluded: chain E residue 1257 THR Chi-restraints excluded: chain E residue 1259 LEU Chi-restraints excluded: chain E residue 1315 HIS Chi-restraints excluded: chain E residue 1330 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.0072 > 50: distance: 37 - 53: 6.056 distance: 41 - 61: 4.013 distance: 45 - 68: 4.635 distance: 49 - 53: 3.111 distance: 50 - 75: 9.081 distance: 54 - 55: 4.530 distance: 54 - 57: 4.370 distance: 55 - 56: 6.416 distance: 55 - 61: 3.920 distance: 56 - 80: 15.519 distance: 57 - 58: 12.597 distance: 58 - 59: 15.454 distance: 58 - 60: 7.718 distance: 62 - 63: 4.131 distance: 62 - 65: 3.539 distance: 63 - 64: 3.315 distance: 63 - 68: 8.757 distance: 64 - 88: 15.861 distance: 65 - 66: 7.890 distance: 65 - 67: 8.924 distance: 69 - 70: 6.190 distance: 69 - 72: 4.264 distance: 70 - 71: 3.288 distance: 70 - 75: 7.683 distance: 71 - 94: 12.510 distance: 72 - 74: 10.061 distance: 75 - 76: 7.664 distance: 76 - 77: 3.590 distance: 76 - 79: 4.422 distance: 77 - 78: 5.181 distance: 77 - 80: 10.724 distance: 78 - 104: 9.681 distance: 80 - 81: 6.726 distance: 81 - 84: 13.843 distance: 82 - 83: 5.243 distance: 82 - 88: 5.687 distance: 83 - 112: 17.929 distance: 84 - 85: 14.180 distance: 85 - 86: 7.272 distance: 85 - 87: 23.251 distance: 88 - 89: 8.723 distance: 89 - 90: 5.162 distance: 89 - 92: 8.570 distance: 90 - 94: 5.554 distance: 91 - 119: 7.951 distance: 92 - 93: 10.130 distance: 95 - 98: 5.641 distance: 96 - 97: 8.278 distance: 96 - 104: 9.155 distance: 97 - 126: 6.878 distance: 99 - 100: 3.219 distance: 99 - 101: 14.859 distance: 100 - 102: 9.597 distance: 101 - 103: 3.858 distance: 102 - 103: 10.206 distance: 104 - 105: 4.849 distance: 105 - 106: 4.628 distance: 105 - 108: 6.619 distance: 106 - 107: 8.414 distance: 106 - 112: 9.060 distance: 107 - 134: 16.361 distance: 108 - 109: 5.898 distance: 109 - 110: 8.694 distance: 109 - 111: 7.588 distance: 112 - 113: 17.589 distance: 113 - 114: 28.304 distance: 113 - 116: 19.101 distance: 114 - 115: 14.125 distance: 114 - 119: 20.064 distance: 116 - 117: 17.773 distance: 116 - 118: 26.478 distance: 119 - 120: 9.682 distance: 120 - 121: 9.259 distance: 120 - 123: 4.338 distance: 121 - 122: 4.913 distance: 121 - 126: 4.266 distance: 123 - 124: 5.730 distance: 123 - 125: 10.360