Starting phenix.real_space_refine on Sat Jan 20 05:49:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4l_14501/01_2024/7z4l_14501.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4l_14501/01_2024/7z4l_14501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4l_14501/01_2024/7z4l_14501.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4l_14501/01_2024/7z4l_14501.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4l_14501/01_2024/7z4l_14501.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4l_14501/01_2024/7z4l_14501.pdb" } resolution = 2.54 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= 0.001 sd= 0.006 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 133 5.49 5 Mg 1 5.21 5 S 22 5.16 5 C 8289 2.51 5 N 2419 2.21 5 O 2957 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13823 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 2055 Classifications: {'RNA': 96} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 51, 'rna3p_pyr': 33} Link IDs: {'rna2p': 12, 'rna3p': 83} Chain: "B" Number of atoms: 10949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10949 Classifications: {'peptide': 1337} Link IDs: {'PTRANS': 35, 'TRANS': 1301} Chain breaks: 3 Chain: "C" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 565 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "D" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 245 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' K': 2, ' MG': 1} Classifications: {'undetermined': 3, 'water': 5} Link IDs: {None: 7} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.15, per 1000 atoms: 0.59 Number of scatterers: 13823 At special positions: 0 Unit cell: (89.1, 122.85, 120.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 S 22 16.00 P 133 15.00 Mg 1 11.99 O 2957 8.00 N 2419 7.00 C 8289 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 - 3.50 Amino acid : False - 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: 6.59 Conformation dependent library (CDL) restraints added in 2.1 seconds 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2546 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 11 sheets defined 53.5% alpha, 9.7% beta 50 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 6.00 Creating SS restraints... Processing helix chain 'B' and resid 59 through 94 removed outlier: 4.802A pdb=" N ASN B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLU B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS B 92 " --> pdb=" O ASN B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 104 Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 134 through 145 removed outlier: 3.607A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.624A pdb=" N LEU B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 217 through 228 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.696A pdb=" N PHE B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 282 Processing helix chain 'B' and resid 286 through 303 Processing helix chain 'B' and resid 315 through 343 Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 368 through 382 Proline residue: B 378 - end of helix Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.937A pdb=" N GLY B 408 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 removed outlier: 3.922A pdb=" N HIS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'B' and resid 477 through 481 Processing helix chain 'B' and resid 484 through 494 Processing helix chain 'B' and resid 512 through 525 Processing helix chain 'B' and resid 541 through 552 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.547A pdb=" N TYR B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 604 through 609 Processing helix chain 'B' and resid 612 through 626 removed outlier: 3.631A pdb=" N LEU B 616 " --> pdb=" O ASN B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 637 Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 644 through 654 Processing helix chain 'B' and resid 664 through 669 Processing helix chain 'B' and resid 678 through 685 Processing helix chain 'B' and resid 692 through 698 Processing helix chain 'B' and resid 703 through 714 Processing helix chain 'B' and resid 719 through 726 Processing helix chain 'B' and resid 730 through 751 Processing helix chain 'B' and resid 776 through 792 Processing helix chain 'B' and resid 794 through 799 removed outlier: 3.560A pdb=" N HIS B 799 " --> pdb=" O ILE B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 807 Processing helix chain 'B' and resid 808 through 817 Processing helix chain 'B' and resid 851 through 853 No H-bonds generated for 'chain 'B' and resid 851 through 853' Processing helix chain 'B' and resid 860 through 865 Processing helix chain 'B' and resid 872 through 889 removed outlier: 5.945A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TYR B 882 " --> pdb=" O LYS B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 901 Processing helix chain 'B' and resid 909 through 920 Processing helix chain 'B' and resid 925 through 940 Processing helix chain 'B' and resid 959 through 970 removed outlier: 3.974A pdb=" N VAL B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 3.931A pdb=" N ALA B 984 " --> pdb=" O ASN B 980 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 996 " --> pdb=" O VAL B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1009 Processing helix chain 'B' and resid 1032 through 1041 Processing helix chain 'B' and resid 1078 through 1087 Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1170 through 1177 removed outlier: 3.530A pdb=" N ASN B1177 " --> pdb=" O SER B1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1186 Processing helix chain 'B' and resid 1229 through 1240 Processing helix chain 'B' and resid 1248 through 1262 Processing helix chain 'B' and resid 1264 through 1280 Processing helix chain 'B' and resid 1283 through 1297 Processing helix chain 'B' and resid 1301 through 1313 Processing helix chain 'B' and resid 1340 through 1344 Processing helix chain 'B' and resid 1363 through 1365 No H-bonds generated for 'chain 'B' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'B' and resid 954 through 957 Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 46 removed outlier: 9.964A pdb=" N GLU B1357 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS B 33 " --> pdb=" O GLU B1357 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ARG B1359 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 35 " --> pdb=" O ARG B1359 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASP B1361 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B1203 " --> pdb=" O ILE B1348 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER B1202 " --> pdb=" O LEU B1214 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLU B1219 " --> pdb=" O ALA B1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 466 through 467 removed outlier: 4.820A pdb=" N THR B 466 " --> pdb=" O ASP B 483 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 507 through 509 removed outlier: 5.243A pdb=" N LEU B 508 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.919A pdb=" N ALA B 538 " --> pdb=" O TYR B 529 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 529 " --> pdb=" O ALA B 538 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 837 through 840 Processing sheet with id=AA7, first strand: chain 'B' and resid 1049 through 1050 Processing sheet with id=AA8, first strand: chain 'B' and resid 1063 through 1065 removed outlier: 4.081A pdb=" N TRP B1074 " --> pdb=" O GLU B1064 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1156 through 1163 removed outlier: 7.078A pdb=" N ILE B1166 " --> pdb=" O ALA B1140 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1156 through 1163 Processing sheet with id=AB2, first strand: chain 'B' and resid 1324 through 1326 526 hydrogen bonds defined for protein. 1521 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 124 hydrogen bonds 244 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 7.75 Time building geometry restraints manager: 6.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2190 1.32 - 1.44: 4346 1.44 - 1.57: 7508 1.57 - 1.69: 266 1.69 - 1.81: 42 Bond restraints: 14352 Sorted by residual: bond pdb=" C ASP B 10 " pdb=" O ASP B 10 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.14e-02 7.69e+03 9.85e+00 bond pdb=" N THR B 555 " pdb=" CA THR B 555 " ideal model delta sigma weight residual 1.454 1.477 -0.023 1.42e-02 4.96e+03 2.56e+00 bond pdb=" C GLY B 687 " pdb=" O GLY B 687 " ideal model delta sigma weight residual 1.236 1.228 0.008 5.30e-03 3.56e+04 2.47e+00 bond pdb=" CA ASP B 10 " pdb=" C ASP B 10 " ideal model delta sigma weight residual 1.526 1.508 0.017 1.20e-02 6.94e+03 2.09e+00 bond pdb=" C ILE B1110 " pdb=" N LEU B1111 " ideal model delta sigma weight residual 1.340 1.267 0.074 5.87e-02 2.90e+02 1.57e+00 ... (remaining 14347 not shown) Histogram of bond angle deviations from ideal: 96.57 - 104.05: 566 104.05 - 111.54: 6887 111.54 - 119.02: 5099 119.02 - 126.51: 6909 126.51 - 134.00: 494 Bond angle restraints: 19955 Sorted by residual: angle pdb=" N THR B 555 " pdb=" CA THR B 555 " pdb=" CB THR B 555 " ideal model delta sigma weight residual 110.88 114.46 -3.58 1.38e+00 5.25e-01 6.75e+00 angle pdb=" CA TYR B 155 " pdb=" CB TYR B 155 " pdb=" CG TYR B 155 " ideal model delta sigma weight residual 113.90 109.45 4.45 1.80e+00 3.09e-01 6.11e+00 angle pdb=" C VAL B 992 " pdb=" N VAL B 993 " pdb=" CA VAL B 993 " ideal model delta sigma weight residual 120.56 117.71 2.85 1.28e+00 6.10e-01 4.96e+00 angle pdb=" C ASP B 10 " pdb=" CA ASP B 10 " pdb=" CB ASP B 10 " ideal model delta sigma weight residual 111.17 107.94 3.23 1.54e+00 4.22e-01 4.39e+00 angle pdb=" CA GLY B1011 " pdb=" C GLY B1011 " pdb=" N ASP B1012 " ideal model delta sigma weight residual 115.62 117.20 -1.58 7.60e-01 1.73e+00 4.32e+00 ... (remaining 19950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 7660 17.92 - 35.84: 553 35.84 - 53.76: 263 53.76 - 71.68: 134 71.68 - 89.60: 24 Dihedral angle restraints: 8634 sinusoidal: 4700 harmonic: 3934 Sorted by residual: dihedral pdb=" CA ARG B1333 " pdb=" C ARG B1333 " pdb=" N LYS B1334 " pdb=" CA LYS B1334 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ASN B 497 " pdb=" C ASN B 497 " pdb=" N PHE B 498 " pdb=" CA PHE B 498 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA PHE B 86 " pdb=" C PHE B 86 " pdb=" N SER B 87 " pdb=" CA SER B 87 " ideal model delta harmonic sigma weight residual -180.00 -162.44 -17.56 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 8631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1809 0.046 - 0.093: 399 0.093 - 0.139: 71 0.139 - 0.185: 3 0.185 - 0.232: 1 Chirality restraints: 2283 Sorted by residual: chirality pdb=" CA ASP B 10 " pdb=" N ASP B 10 " pdb=" C ASP B 10 " pdb=" CB ASP B 10 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB VAL B 743 " pdb=" CA VAL B 743 " pdb=" CG1 VAL B 743 " pdb=" CG2 VAL B 743 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" C1' A A 51 " pdb=" O4' A A 51 " pdb=" C2' A A 51 " pdb=" N9 A A 51 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 2280 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B1273 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C ILE B1273 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE B1273 " 0.013 2.00e-02 2.50e+03 pdb=" N SER B1274 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 298 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.72e+00 pdb=" C ASP B 298 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP B 298 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA B 299 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 983 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C HIS B 983 " -0.033 2.00e-02 2.50e+03 pdb=" O HIS B 983 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA B 984 " 0.011 2.00e-02 2.50e+03 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.45: 69 2.45 - 3.12: 10515 3.12 - 3.80: 27962 3.80 - 4.47: 43036 4.47 - 5.14: 63090 Nonbonded interactions: 144672 Sorted by model distance: nonbonded pdb="MG MG A 201 " pdb=" O HOH A 301 " model vdw 1.780 2.170 nonbonded pdb="MG MG A 201 " pdb=" O HOH A 302 " model vdw 1.818 2.170 nonbonded pdb="MG MG A 201 " pdb=" O HOH A 304 " model vdw 1.883 2.170 nonbonded pdb="MG MG A 201 " pdb=" O HOH A 305 " model vdw 1.884 2.170 nonbonded pdb="MG MG A 201 " pdb=" O HOH A 303 " model vdw 1.888 2.170 ... (remaining 144667 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 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: 5.700 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: 0.030 Extract box with map and model: 26.820 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 47.610 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14352 Z= 0.345 Angle : 0.527 6.476 19955 Z= 0.291 Chirality : 0.039 0.232 2283 Planarity : 0.004 0.031 2055 Dihedral : 16.996 89.597 6088 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.83 % Allowed : 6.82 % Favored : 90.36 % 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: 0.38 (0.22), residues: 1329 helix: 0.93 (0.20), residues: 661 sheet: -0.89 (0.48), residues: 104 loop : -0.21 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 476 HIS 0.006 0.001 HIS B 328 PHE 0.013 0.002 PHE B 491 TYR 0.018 0.002 TYR B 155 ARG 0.004 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 145 time to evaluate : 1.741 Fit side-chains REVERT: B 4 LYS cc_start: 0.8640 (mttt) cc_final: 0.8415 (mtmt) REVERT: B 312 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7891 (pp) REVERT: B 629 ARG cc_start: 0.7388 (mmt90) cc_final: 0.6965 (ttp80) REVERT: B 655 ARG cc_start: 0.6628 (mtm-85) cc_final: 0.5866 (ttt90) REVERT: B 682 PHE cc_start: 0.8116 (m-80) cc_final: 0.7581 (m-80) REVERT: B 710 LYS cc_start: 0.8614 (mttt) cc_final: 0.8184 (tptp) REVERT: B 809 GLU cc_start: 0.7772 (tt0) cc_final: 0.7116 (mp0) REVERT: B 855 LYS cc_start: 0.4970 (mttt) cc_final: 0.4321 (mtpt) REVERT: B 881 ASN cc_start: 0.8080 (m-40) cc_final: 0.7683 (p0) REVERT: B 925 ARG cc_start: 0.8023 (mtm-85) cc_final: 0.7736 (mtm180) REVERT: B 976 ARG cc_start: 0.8354 (mtp85) cc_final: 0.8145 (mtt-85) REVERT: B 1124 LYS cc_start: 0.8872 (mttp) cc_final: 0.8447 (mptm) REVERT: B 1242 TYR cc_start: 0.5207 (OUTLIER) cc_final: 0.4121 (t80) REVERT: B 1256 GLN cc_start: 0.7606 (tp40) cc_final: 0.7157 (mm-40) REVERT: B 1296 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8061 (mptp) outliers start: 34 outliers final: 8 residues processed: 171 average time/residue: 1.6032 time to fit residues: 296.5491 Evaluate side-chains 88 residues out of total 1203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1296 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN B 116 HIS B 129 HIS B 228 GLN B 695 GLN B 805 GLN B 807 GLN ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 885 GLN B 920 GLN B1041 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14352 Z= 0.179 Angle : 0.496 8.772 19955 Z= 0.266 Chirality : 0.036 0.171 2283 Planarity : 0.003 0.036 2055 Dihedral : 18.134 89.503 3264 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.49 % Allowed : 12.30 % Favored : 85.20 % 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: 0.81 (0.23), residues: 1329 helix: 1.37 (0.20), residues: 675 sheet: -0.70 (0.45), residues: 113 loop : -0.14 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 476 HIS 0.012 0.001 HIS B 641 PHE 0.017 0.001 PHE B1038 TYR 0.026 0.001 TYR B1001 ARG 0.005 0.000 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 82 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: B 4 LYS cc_start: 0.8619 (mttt) cc_final: 0.8417 (mtmt) REVERT: B 228 GLN cc_start: 0.6094 (OUTLIER) cc_final: 0.5845 (mt0) REVERT: B 312 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7889 (pp) REVERT: B 356 LYS cc_start: 0.8840 (tppt) cc_final: 0.8640 (mmtt) REVERT: B 655 ARG cc_start: 0.6542 (mtm-85) cc_final: 0.5963 (tpt170) REVERT: B 682 PHE cc_start: 0.8106 (m-80) cc_final: 0.7635 (m-80) REVERT: B 694 MET cc_start: 0.8562 (mmt) cc_final: 0.8264 (mmm) REVERT: B 706 GLU cc_start: 0.8007 (tp30) cc_final: 0.7792 (pp20) REVERT: B 710 LYS cc_start: 0.8537 (mttt) cc_final: 0.8177 (tptp) REVERT: B 809 GLU cc_start: 0.7834 (tt0) cc_final: 0.7170 (mp0) REVERT: B 855 LYS cc_start: 0.5048 (mttt) cc_final: 0.4334 (mtpp) REVERT: B 881 ASN cc_start: 0.8049 (m-40) cc_final: 0.7687 (p0) REVERT: B 976 ARG cc_start: 0.8327 (mtp85) cc_final: 0.8095 (mtt-85) REVERT: B 1124 LYS cc_start: 0.8841 (mttp) cc_final: 0.8444 (mptm) REVERT: B 1242 TYR cc_start: 0.5132 (OUTLIER) cc_final: 0.4008 (t80) REVERT: B 1256 GLN cc_start: 0.7595 (tp40) cc_final: 0.7038 (mm-40) REVERT: B 1296 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8014 (mptp) outliers start: 30 outliers final: 12 residues processed: 105 average time/residue: 1.5608 time to fit residues: 177.9938 Evaluate side-chains 83 residues out of total 1203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 67 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1274 SER Chi-restraints excluded: chain B residue 1296 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 131 optimal weight: 0.0030 chunk 142 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 44 optimal weight: 0.1980 chunk 105 optimal weight: 4.9990 overall best weight: 3.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS B 459 ASN B 807 GLN ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1066 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 14352 Z= 0.373 Angle : 0.547 7.959 19955 Z= 0.292 Chirality : 0.040 0.170 2283 Planarity : 0.004 0.043 2055 Dihedral : 18.235 91.077 3263 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.83 % Allowed : 13.22 % Favored : 83.96 % 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: 0.69 (0.23), residues: 1329 helix: 1.23 (0.20), residues: 675 sheet: -0.83 (0.45), residues: 118 loop : -0.11 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 476 HIS 0.008 0.001 HIS B 641 PHE 0.024 0.002 PHE B 185 TYR 0.030 0.002 TYR B1001 ARG 0.006 0.000 ARG B 535 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 71 time to evaluate : 1.821 Fit side-chains REVERT: B 4 LYS cc_start: 0.8640 (mttt) cc_final: 0.8428 (mtmt) REVERT: B 312 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7920 (pp) REVERT: B 356 LYS cc_start: 0.8842 (tppt) cc_final: 0.8622 (mmtt) REVERT: B 655 ARG cc_start: 0.6584 (mtm-85) cc_final: 0.6026 (tpt170) REVERT: B 664 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.7014 (ttp-110) REVERT: B 682 PHE cc_start: 0.8160 (m-80) cc_final: 0.7616 (m-80) REVERT: B 694 MET cc_start: 0.8562 (mmt) cc_final: 0.8271 (mmm) REVERT: B 706 GLU cc_start: 0.8013 (tp30) cc_final: 0.7808 (pp20) REVERT: B 710 LYS cc_start: 0.8553 (mttt) cc_final: 0.8196 (tptp) REVERT: B 746 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8505 (tt0) REVERT: B 809 GLU cc_start: 0.7834 (tt0) cc_final: 0.7198 (mp0) REVERT: B 855 LYS cc_start: 0.5001 (mttt) cc_final: 0.4284 (mtpt) REVERT: B 881 ASN cc_start: 0.8064 (m-40) cc_final: 0.7709 (p0) REVERT: B 1049 GLU cc_start: 0.6841 (pp20) cc_final: 0.6609 (OUTLIER) REVERT: B 1124 LYS cc_start: 0.8845 (mttp) cc_final: 0.8424 (mptm) REVERT: B 1242 TYR cc_start: 0.5143 (OUTLIER) cc_final: 0.4035 (t80) REVERT: B 1256 GLN cc_start: 0.7614 (tp40) cc_final: 0.7148 (mm-40) REVERT: B 1296 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8033 (mptp) outliers start: 34 outliers final: 14 residues processed: 99 average time/residue: 1.5642 time to fit residues: 168.7267 Evaluate side-chains 86 residues out of total 1203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 664 ARG Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1129 LYS Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1296 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 0.0060 chunk 88 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 807 GLN ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 HIS B1066 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14352 Z= 0.184 Angle : 0.467 8.012 19955 Z= 0.249 Chirality : 0.035 0.139 2283 Planarity : 0.003 0.043 2055 Dihedral : 18.136 89.728 3263 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.74 % Allowed : 13.80 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.23), residues: 1329 helix: 1.51 (0.20), residues: 675 sheet: -0.68 (0.46), residues: 113 loop : -0.10 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 476 HIS 0.007 0.001 HIS B 641 PHE 0.019 0.001 PHE B 518 TYR 0.025 0.001 TYR B1001 ARG 0.003 0.000 ARG B 951 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 75 time to evaluate : 1.548 Fit side-chains REVERT: B 4 LYS cc_start: 0.8648 (mttt) cc_final: 0.8439 (mtmt) REVERT: B 312 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7888 (pp) REVERT: B 356 LYS cc_start: 0.8856 (tppt) cc_final: 0.8634 (mmtt) REVERT: B 655 ARG cc_start: 0.6546 (mtm-85) cc_final: 0.6043 (tpt170) REVERT: B 661 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7015 (mmm160) REVERT: B 664 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6983 (ttp-110) REVERT: B 682 PHE cc_start: 0.8123 (m-80) cc_final: 0.7701 (m-80) REVERT: B 694 MET cc_start: 0.8528 (mmt) cc_final: 0.8248 (mmm) REVERT: B 710 LYS cc_start: 0.8548 (mttt) cc_final: 0.8202 (tptp) REVERT: B 809 GLU cc_start: 0.7866 (tt0) cc_final: 0.7248 (mp0) REVERT: B 855 LYS cc_start: 0.5035 (mttt) cc_final: 0.4353 (mtpp) REVERT: B 881 ASN cc_start: 0.8091 (m-40) cc_final: 0.7772 (p0) REVERT: B 1049 GLU cc_start: 0.6799 (pp20) cc_final: 0.6553 (OUTLIER) REVERT: B 1124 LYS cc_start: 0.8820 (mttp) cc_final: 0.8410 (mptm) REVERT: B 1242 TYR cc_start: 0.5002 (OUTLIER) cc_final: 0.3893 (t80) REVERT: B 1256 GLN cc_start: 0.7604 (tp40) cc_final: 0.7039 (mm-40) REVERT: B 1296 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8030 (mptp) outliers start: 33 outliers final: 15 residues processed: 103 average time/residue: 1.5439 time to fit residues: 173.7112 Evaluate side-chains 84 residues out of total 1203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 664 ARG Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1274 SER Chi-restraints excluded: chain B residue 1296 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 104 optimal weight: 0.0070 chunk 57 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1066 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 14352 Z= 0.305 Angle : 0.519 8.546 19955 Z= 0.275 Chirality : 0.038 0.152 2283 Planarity : 0.003 0.046 2055 Dihedral : 18.142 90.263 3262 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.74 % Allowed : 14.46 % Favored : 82.79 % 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: 0.85 (0.23), residues: 1329 helix: 1.40 (0.20), residues: 674 sheet: -0.70 (0.46), residues: 113 loop : -0.12 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 476 HIS 0.006 0.001 HIS B 328 PHE 0.021 0.002 PHE B 518 TYR 0.026 0.001 TYR B1001 ARG 0.003 0.000 ARG B1303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 66 time to evaluate : 1.577 Fit side-chains REVERT: B 4 LYS cc_start: 0.8654 (mttt) cc_final: 0.8406 (mtmm) REVERT: B 356 LYS cc_start: 0.8848 (tppt) cc_final: 0.8617 (mmtt) REVERT: B 534 MET cc_start: 0.2011 (ptt) cc_final: 0.0959 (mtm) REVERT: B 655 ARG cc_start: 0.6552 (mtm-85) cc_final: 0.6055 (tpt170) REVERT: B 661 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7080 (mmm160) REVERT: B 664 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.7016 (ttp-110) REVERT: B 694 MET cc_start: 0.8545 (mmt) cc_final: 0.8262 (mmm) REVERT: B 746 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8443 (tt0) REVERT: B 809 GLU cc_start: 0.7894 (tt0) cc_final: 0.7257 (mp0) REVERT: B 855 LYS cc_start: 0.5102 (mttt) cc_final: 0.4406 (mtpp) REVERT: B 881 ASN cc_start: 0.8131 (m-40) cc_final: 0.7838 (p0) REVERT: B 1049 GLU cc_start: 0.6792 (pp20) cc_final: 0.6530 (OUTLIER) REVERT: B 1124 LYS cc_start: 0.8822 (mttp) cc_final: 0.8403 (mptm) REVERT: B 1177 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8215 (t0) REVERT: B 1242 TYR cc_start: 0.5030 (OUTLIER) cc_final: 0.3921 (t80) REVERT: B 1256 GLN cc_start: 0.7605 (tp40) cc_final: 0.7127 (mm-40) REVERT: B 1296 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8036 (mptp) outliers start: 33 outliers final: 14 residues processed: 93 average time/residue: 1.5354 time to fit residues: 155.5307 Evaluate side-chains 80 residues out of total 1203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 664 ARG Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 950 ILE Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1177 ASN Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1296 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 64 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1066 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14352 Z= 0.197 Angle : 0.479 8.844 19955 Z= 0.255 Chirality : 0.035 0.139 2283 Planarity : 0.003 0.045 2055 Dihedral : 18.091 89.729 3260 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.58 % Allowed : 14.88 % Favored : 82.54 % 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: 0.96 (0.23), residues: 1329 helix: 1.53 (0.20), residues: 674 sheet: -0.69 (0.46), residues: 113 loop : -0.10 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 476 HIS 0.005 0.001 HIS B 328 PHE 0.022 0.001 PHE B 518 TYR 0.025 0.001 TYR B1001 ARG 0.006 0.000 ARG B 395 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 64 time to evaluate : 1.475 Fit side-chains REVERT: B 4 LYS cc_start: 0.8654 (mttt) cc_final: 0.8411 (mtmm) REVERT: B 356 LYS cc_start: 0.8854 (tppt) cc_final: 0.8621 (mmtt) REVERT: B 534 MET cc_start: 0.2017 (ptt) cc_final: 0.1377 (mtm) REVERT: B 655 ARG cc_start: 0.6536 (mtm-85) cc_final: 0.6065 (tpt170) REVERT: B 661 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7042 (mmm160) REVERT: B 664 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6987 (ttp-110) REVERT: B 694 MET cc_start: 0.8542 (mmt) cc_final: 0.8262 (mmm) REVERT: B 710 LYS cc_start: 0.8426 (mmtt) cc_final: 0.7902 (tptp) REVERT: B 746 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: B 796 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.5933 (pt) REVERT: B 809 GLU cc_start: 0.7886 (tt0) cc_final: 0.7225 (mp0) REVERT: B 855 LYS cc_start: 0.5119 (mttt) cc_final: 0.4407 (mtpt) REVERT: B 881 ASN cc_start: 0.8149 (m-40) cc_final: 0.7845 (p0) REVERT: B 948 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7678 (mtmt) REVERT: B 1049 GLU cc_start: 0.6760 (pp20) cc_final: 0.6502 (OUTLIER) REVERT: B 1124 LYS cc_start: 0.8813 (mttp) cc_final: 0.8402 (mptm) REVERT: B 1242 TYR cc_start: 0.4967 (OUTLIER) cc_final: 0.3861 (t80) REVERT: B 1256 GLN cc_start: 0.7597 (tp40) cc_final: 0.7106 (mm-40) REVERT: B 1296 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8043 (mptp) outliers start: 31 outliers final: 15 residues processed: 91 average time/residue: 1.4812 time to fit residues: 147.2572 Evaluate side-chains 80 residues out of total 1203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 59 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 664 ARG Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 948 LYS Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1274 SER Chi-restraints excluded: chain B residue 1296 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1066 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 14352 Z= 0.319 Angle : 0.527 9.019 19955 Z= 0.278 Chirality : 0.039 0.319 2283 Planarity : 0.003 0.046 2055 Dihedral : 18.113 90.600 3260 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.66 % Allowed : 15.38 % Favored : 81.96 % 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: 0.85 (0.23), residues: 1329 helix: 1.44 (0.20), residues: 674 sheet: -0.93 (0.45), residues: 118 loop : -0.09 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 476 HIS 0.006 0.001 HIS B 328 PHE 0.022 0.002 PHE B 518 TYR 0.025 0.002 TYR B1001 ARG 0.005 0.000 ARG B 395 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 67 time to evaluate : 1.627 Fit side-chains revert: symmetry clash REVERT: B 4 LYS cc_start: 0.8664 (mttt) cc_final: 0.8414 (mtmm) REVERT: B 356 LYS cc_start: 0.8859 (tppt) cc_final: 0.8620 (mmtt) REVERT: B 655 ARG cc_start: 0.6572 (mtm-85) cc_final: 0.6113 (tpt170) REVERT: B 661 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7093 (mmm160) REVERT: B 664 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.7019 (ttp-110) REVERT: B 694 MET cc_start: 0.8551 (mmt) cc_final: 0.8238 (mmm) REVERT: B 710 LYS cc_start: 0.8437 (mmtt) cc_final: 0.7908 (tptp) REVERT: B 746 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8478 (tt0) REVERT: B 796 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.5942 (pt) REVERT: B 881 ASN cc_start: 0.8229 (m-40) cc_final: 0.7903 (p0) REVERT: B 948 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7686 (mtmt) REVERT: B 1049 GLU cc_start: 0.6758 (pp20) cc_final: 0.6494 (OUTLIER) REVERT: B 1124 LYS cc_start: 0.8810 (mttp) cc_final: 0.8378 (mptm) REVERT: B 1242 TYR cc_start: 0.5020 (OUTLIER) cc_final: 0.3911 (t80) REVERT: B 1256 GLN cc_start: 0.7597 (tp40) cc_final: 0.7124 (mm-40) REVERT: B 1296 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8055 (mptp) outliers start: 32 outliers final: 17 residues processed: 92 average time/residue: 1.4154 time to fit residues: 143.9328 Evaluate side-chains 85 residues out of total 1203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 62 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 664 ARG Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 948 LYS Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1274 SER Chi-restraints excluded: chain B residue 1296 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 109 optimal weight: 0.5980 chunk 127 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1066 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14352 Z= 0.201 Angle : 0.493 10.857 19955 Z= 0.259 Chirality : 0.036 0.348 2283 Planarity : 0.003 0.045 2055 Dihedral : 18.064 89.796 3260 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.66 % Allowed : 15.46 % Favored : 81.88 % 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: 1.00 (0.23), residues: 1329 helix: 1.57 (0.20), residues: 674 sheet: -0.76 (0.45), residues: 113 loop : -0.06 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 476 HIS 0.005 0.001 HIS B 328 PHE 0.025 0.001 PHE B1038 TYR 0.026 0.001 TYR B1001 ARG 0.004 0.000 ARG B 395 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 60 time to evaluate : 1.522 Fit side-chains REVERT: B 4 LYS cc_start: 0.8656 (mttt) cc_final: 0.8412 (mtmm) REVERT: B 356 LYS cc_start: 0.8853 (tppt) cc_final: 0.8614 (mmtt) REVERT: B 631 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6657 (mtm) REVERT: B 655 ARG cc_start: 0.6563 (mtm-85) cc_final: 0.6122 (tpt170) REVERT: B 661 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7100 (mmm160) REVERT: B 664 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6996 (ttp-170) REVERT: B 694 MET cc_start: 0.8551 (mmt) cc_final: 0.8244 (mmm) REVERT: B 710 LYS cc_start: 0.8419 (mmtt) cc_final: 0.7944 (tptp) REVERT: B 746 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8412 (tt0) REVERT: B 796 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.5919 (pt) REVERT: B 809 GLU cc_start: 0.7966 (tt0) cc_final: 0.7311 (mp0) REVERT: B 855 LYS cc_start: 0.4991 (mttt) cc_final: 0.4302 (mtpt) REVERT: B 881 ASN cc_start: 0.8259 (m-40) cc_final: 0.7946 (p0) REVERT: B 948 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7661 (mtmt) REVERT: B 1049 GLU cc_start: 0.6740 (pp20) cc_final: 0.6488 (OUTLIER) REVERT: B 1124 LYS cc_start: 0.8808 (mttp) cc_final: 0.8385 (mptm) REVERT: B 1242 TYR cc_start: 0.4959 (OUTLIER) cc_final: 0.3840 (t80) REVERT: B 1256 GLN cc_start: 0.7586 (tp40) cc_final: 0.7101 (mm-40) REVERT: B 1296 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8064 (mptp) outliers start: 32 outliers final: 20 residues processed: 84 average time/residue: 1.5007 time to fit residues: 137.9972 Evaluate side-chains 85 residues out of total 1203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 58 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 664 ARG Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 948 LYS Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1274 SER Chi-restraints excluded: chain B residue 1296 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 888 ASN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1066 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1221 GLN B1262 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14352 Z= 0.155 Angle : 0.474 11.362 19955 Z= 0.247 Chirality : 0.035 0.346 2283 Planarity : 0.003 0.045 2055 Dihedral : 17.917 87.461 3260 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.33 % Allowed : 15.79 % Favored : 81.88 % 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: 1.12 (0.23), residues: 1329 helix: 1.69 (0.20), residues: 675 sheet: -0.57 (0.45), residues: 109 loop : -0.09 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 476 HIS 0.005 0.001 HIS B 328 PHE 0.025 0.001 PHE B 518 TYR 0.024 0.001 TYR B1001 ARG 0.005 0.000 ARG B1303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 71 time to evaluate : 1.383 Fit side-chains REVERT: B 4 LYS cc_start: 0.8655 (mttt) cc_final: 0.8418 (mtmm) REVERT: B 356 LYS cc_start: 0.8874 (tppt) cc_final: 0.8659 (mmmt) REVERT: B 563 GLN cc_start: 0.8346 (mt0) cc_final: 0.7910 (tt0) REVERT: B 631 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6628 (mtm) REVERT: B 655 ARG cc_start: 0.6573 (mtm-85) cc_final: 0.6139 (tpt170) REVERT: B 661 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7137 (mmm160) REVERT: B 664 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6950 (ttp-170) REVERT: B 694 MET cc_start: 0.8533 (mmt) cc_final: 0.8237 (mmm) REVERT: B 710 LYS cc_start: 0.8394 (mmtt) cc_final: 0.7982 (tptp) REVERT: B 746 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8377 (tt0) REVERT: B 796 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.5884 (pt) REVERT: B 809 GLU cc_start: 0.7964 (tt0) cc_final: 0.7362 (mp0) REVERT: B 855 LYS cc_start: 0.5050 (mttt) cc_final: 0.4348 (mtpp) REVERT: B 879 MET cc_start: 0.0736 (OUTLIER) cc_final: 0.0508 (ptt) REVERT: B 881 ASN cc_start: 0.8303 (m-40) cc_final: 0.7976 (p0) REVERT: B 1049 GLU cc_start: 0.6750 (pp20) cc_final: 0.6529 (OUTLIER) REVERT: B 1124 LYS cc_start: 0.8789 (mttp) cc_final: 0.8388 (mptm) REVERT: B 1242 TYR cc_start: 0.4908 (OUTLIER) cc_final: 0.3740 (t80) REVERT: B 1256 GLN cc_start: 0.7574 (tp40) cc_final: 0.7022 (mm-40) REVERT: B 1296 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8085 (mptp) outliers start: 28 outliers final: 15 residues processed: 92 average time/residue: 1.6102 time to fit residues: 160.8328 Evaluate side-chains 85 residues out of total 1203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 63 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 664 ARG Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 879 MET Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1274 SER Chi-restraints excluded: chain B residue 1296 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 65 optimal weight: 0.3980 chunk 95 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1066 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14352 Z= 0.252 Angle : 0.516 10.738 19955 Z= 0.267 Chirality : 0.037 0.354 2283 Planarity : 0.003 0.046 2055 Dihedral : 17.941 88.837 3259 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.00 % Allowed : 16.54 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.23), residues: 1329 helix: 1.60 (0.20), residues: 675 sheet: -0.66 (0.45), residues: 113 loop : -0.01 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 476 HIS 0.005 0.001 HIS B 328 PHE 0.036 0.002 PHE B1038 TYR 0.033 0.001 TYR B1001 ARG 0.004 0.000 ARG B1303 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 66 time to evaluate : 1.484 Fit side-chains REVERT: B 4 LYS cc_start: 0.8659 (mttt) cc_final: 0.8415 (mtmm) REVERT: B 356 LYS cc_start: 0.8867 (tppt) cc_final: 0.8628 (mmtt) REVERT: B 631 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6667 (mtm) REVERT: B 655 ARG cc_start: 0.6591 (mtm-85) cc_final: 0.6090 (tpt170) REVERT: B 661 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7161 (mmm160) REVERT: B 664 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.7001 (ttp-170) REVERT: B 694 MET cc_start: 0.8543 (mmt) cc_final: 0.8243 (mmm) REVERT: B 710 LYS cc_start: 0.8419 (mmtt) cc_final: 0.7974 (tptp) REVERT: B 746 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8427 (tt0) REVERT: B 796 LEU cc_start: 0.6387 (OUTLIER) cc_final: 0.5891 (pt) REVERT: B 809 GLU cc_start: 0.7981 (tt0) cc_final: 0.7356 (mp0) REVERT: B 855 LYS cc_start: 0.5046 (mttt) cc_final: 0.4354 (mtpp) REVERT: B 881 ASN cc_start: 0.8336 (m-40) cc_final: 0.8006 (p0) REVERT: B 1049 GLU cc_start: 0.6758 (pp20) cc_final: 0.6527 (OUTLIER) REVERT: B 1124 LYS cc_start: 0.8806 (mttp) cc_final: 0.8386 (mptm) REVERT: B 1242 TYR cc_start: 0.4929 (OUTLIER) cc_final: 0.3784 (t80) REVERT: B 1256 GLN cc_start: 0.7559 (tp40) cc_final: 0.7071 (mm-40) REVERT: B 1296 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8081 (mptp) outliers start: 24 outliers final: 14 residues processed: 85 average time/residue: 1.5481 time to fit residues: 144.1270 Evaluate side-chains 82 residues out of total 1203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 62 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 664 ARG Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1274 SER Chi-restraints excluded: chain B residue 1296 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 30.0000 chunk 115 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1066 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 = 0.4023 r_free = 0.4023 target = 0.136114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.086496 restraints weight = 23217.394| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.07 r_work: 0.3113 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14352 Z= 0.155 Angle : 0.484 10.460 19955 Z= 0.249 Chirality : 0.035 0.337 2283 Planarity : 0.003 0.045 2055 Dihedral : 17.864 88.154 3257 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.50 % Allowed : 17.37 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.23), residues: 1329 helix: 1.71 (0.20), residues: 675 sheet: -0.46 (0.47), residues: 106 loop : -0.01 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 476 HIS 0.005 0.001 HIS B 328 PHE 0.025 0.001 PHE B 518 TYR 0.030 0.001 TYR B1001 ARG 0.004 0.000 ARG B1303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4926.16 seconds wall clock time: 105 minutes 0.97 seconds (6300.97 seconds total)