Starting phenix.real_space_refine on Mon Apr 8 15:34:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4i_14498/04_2024/7z4i_14498.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4i_14498/04_2024/7z4i_14498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4i_14498/04_2024/7z4i_14498.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4i_14498/04_2024/7z4i_14498.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4i_14498/04_2024/7z4i_14498.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4i_14498/04_2024/7z4i_14498.pdb" } resolution = 3.12 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= 0.008 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 134 5.49 5 S 22 5.16 5 C 8290 2.51 5 N 2417 2.21 5 O 2955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1237": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13820 Number of models: 1 Model: "" Number of chains: 5 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: "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: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 249 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DT%5*END:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 10949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 10949 Classifications: {'peptide': 1338} Link IDs: {'PTRANS': 35, 'TRANS': 1302} Chain breaks: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.25, per 1000 atoms: 0.60 Number of scatterers: 13820 At special positions: 0 Unit cell: (90.35, 123.5, 120.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 22 16.00 P 134 15.00 O 2955 8.00 N 2417 7.00 C 8290 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: 9.47 Conformation dependent library (CDL) restraints added in 2.1 seconds 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2548 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 12 sheets defined 54.5% alpha, 9.7% beta 49 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 5.83 Creating SS restraints... Processing helix chain 'B' and resid 59 through 94 removed outlier: 5.222A pdb=" N ASN B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLU B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 103 Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 134 through 145 removed outlier: 3.621A 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 Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 217 through 229 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.738A 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 285 through 306 removed outlier: 4.219A pdb=" N LEU B 289 " --> pdb=" O GLN B 285 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) 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: 3.527A pdb=" N ASN B 407 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 408 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 removed outlier: 4.159A 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 482 Processing helix chain 'B' and resid 483 through 496 removed outlier: 4.109A pdb=" N MET B 495 " --> pdb=" O PHE B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 526 Processing helix chain 'B' and resid 541 through 552 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.554A 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 removed outlier: 3.571A pdb=" N ILE B 632 " --> pdb=" O ASP B 628 " (cutoff:3.500A) 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 removed outlier: 3.671A pdb=" N ARG B 653 " --> pdb=" O LYS B 649 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) 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 697 Processing helix chain 'B' and resid 702 through 712 removed outlier: 4.486A pdb=" N GLU B 706 " --> pdb=" O LEU B 702 " (cutoff:3.500A) 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: 3.780A 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: 5.681A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) removed outlier: 5.601A 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 919 Processing helix chain 'B' and resid 925 through 940 Processing helix chain 'B' and resid 959 through 970 removed outlier: 3.970A pdb=" N VAL B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.238A pdb=" N ALA B 984 " --> pdb=" O ASN B 980 " (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 1088 Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1168 through 1177 removed outlier: 4.595A pdb=" N SER B1172 " --> pdb=" O ILE B1168 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N SER B1173 " --> pdb=" O MET B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1186 Processing helix chain 'B' and resid 1229 through 1241 removed outlier: 3.571A pdb=" N HIS B1241 " --> pdb=" O TYR B1237 " (cutoff:3.500A) Processing helix chain 'B' and resid 1248 through 1262 Processing helix chain 'B' and resid 1263 through 1280 removed outlier: 4.305A pdb=" N ASP B1267 " --> pdb=" O LYS B1263 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1297 Processing helix chain 'B' and resid 1301 through 1313 removed outlier: 3.526A pdb=" N PHE B1313 " --> pdb=" O ILE B1309 " (cutoff:3.500A) Processing helix chain 'B' and resid 1314 through 1316 No H-bonds generated for 'chain 'B' and resid 1314 through 1316' 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 958 removed outlier: 6.238A pdb=" N ILE B 759 " --> pdb=" O ILE B 956 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU B 958 " --> pdb=" O ILE B 759 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE B 761 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 46 removed outlier: 9.873A pdb=" N GLU B1357 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS B 33 " --> pdb=" O GLU B1357 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ARG B1359 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU B 35 " --> pdb=" O ARG B1359 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ASP B1361 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU B1203 " --> pdb=" O ILE B1348 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER B1202 " --> pdb=" O LEU B1214 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU B1219 " --> pdb=" O ALA B1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 507 through 509 removed outlier: 5.146A pdb=" N LEU B 508 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 528 through 531 Processing sheet with id=AA5, first strand: chain 'B' and resid 837 through 840 Processing sheet with id=AA6, first strand: chain 'B' and resid 943 through 944 removed outlier: 3.708A pdb=" N LYS B 948 " --> pdb=" O ASP B 944 " (cutoff:3.500A) 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: 3.911A pdb=" N TRP B1074 " --> pdb=" O GLU B1064 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1120 through 1121 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 1156 through 1163 Processing sheet with id=AB3, first strand: chain 'B' and resid 1324 through 1326 528 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 120 hydrogen bonds 232 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 8.08 Time building geometry restraints manager: 9.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2499 1.33 - 1.45: 4103 1.45 - 1.57: 7443 1.57 - 1.69: 268 1.69 - 1.81: 42 Bond restraints: 14355 Sorted by residual: bond pdb=" N ASN B 77 " pdb=" CA ASN B 77 " ideal model delta sigma weight residual 1.458 1.407 0.052 1.26e-02 6.30e+03 1.68e+01 bond pdb=" CA SER B1109 " pdb=" C SER B1109 " ideal model delta sigma weight residual 1.524 1.482 0.042 1.30e-02 5.92e+03 1.03e+01 bond pdb=" C LYS B 76 " pdb=" N ASN B 77 " ideal model delta sigma weight residual 1.334 1.289 0.045 1.43e-02 4.89e+03 1.01e+01 bond pdb=" CA LYS B 209 " pdb=" C LYS B 209 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.24e-02 6.50e+03 4.32e+00 bond pdb=" N ASN B 588 " pdb=" CA ASN B 588 " ideal model delta sigma weight residual 1.459 1.435 0.024 1.20e-02 6.94e+03 4.15e+00 ... (remaining 14350 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.43: 993 106.43 - 113.33: 7974 113.33 - 120.22: 5186 120.22 - 127.11: 5421 127.11 - 134.00: 387 Bond angle restraints: 19961 Sorted by residual: angle pdb=" N ASN B 77 " pdb=" CA ASN B 77 " pdb=" C ASN B 77 " ideal model delta sigma weight residual 111.69 106.27 5.42 1.23e+00 6.61e-01 1.94e+01 angle pdb=" N ASN B 588 " pdb=" CA ASN B 588 " pdb=" C ASN B 588 " ideal model delta sigma weight residual 111.14 107.52 3.62 1.08e+00 8.57e-01 1.13e+01 angle pdb=" C LYS B 76 " pdb=" N ASN B 77 " pdb=" CA ASN B 77 " ideal model delta sigma weight residual 120.58 114.96 5.62 1.71e+00 3.42e-01 1.08e+01 angle pdb=" N TYR B 981 " pdb=" CA TYR B 981 " pdb=" C TYR B 981 " ideal model delta sigma weight residual 112.54 109.14 3.40 1.22e+00 6.72e-01 7.75e+00 angle pdb=" C PHE B 587 " pdb=" N ASN B 588 " pdb=" CA ASN B 588 " ideal model delta sigma weight residual 120.44 117.10 3.34 1.36e+00 5.41e-01 6.02e+00 ... (remaining 19956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.05: 8049 27.05 - 54.10: 505 54.10 - 81.15: 176 81.15 - 108.20: 4 108.20 - 135.25: 1 Dihedral angle restraints: 8735 sinusoidal: 4798 harmonic: 3937 Sorted by residual: dihedral pdb=" C4' DG C 16 " pdb=" C3' DG C 16 " pdb=" O3' DG C 16 " pdb=" P DA C 17 " ideal model delta sinusoidal sigma weight residual 220.00 84.75 135.25 1 3.50e+01 8.16e-04 1.34e+01 dihedral pdb=" O4' G A 82 " pdb=" C1' G A 82 " pdb=" N9 G A 82 " pdb=" C4 G A 82 " ideal model delta sinusoidal sigma weight residual 70.00 11.76 58.24 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ILE B 300 " pdb=" C ILE B 300 " pdb=" N LEU B 301 " pdb=" CA LEU B 301 " ideal model delta harmonic sigma weight residual -180.00 -164.15 -15.85 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 8732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1730 0.036 - 0.073: 435 0.073 - 0.109: 90 0.109 - 0.145: 27 0.145 - 0.182: 3 Chirality restraints: 2285 Sorted by residual: chirality pdb=" CA ASN B 77 " pdb=" N ASN B 77 " pdb=" C ASN B 77 " pdb=" CB ASN B 77 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" C1' A A 35 " pdb=" O4' A A 35 " pdb=" C2' A A 35 " pdb=" N9 A A 35 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" C1' A A 42 " pdb=" O4' A A 42 " pdb=" C2' A A 42 " pdb=" N9 A A 42 " both_signs ideal model delta sigma weight residual False 2.46 2.30 0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 2282 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 980 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C ASN B 980 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN B 980 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR B 981 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B1273 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C ILE B1273 " 0.033 2.00e-02 2.50e+03 pdb=" O ILE B1273 " -0.012 2.00e-02 2.50e+03 pdb=" N SER B1274 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 76 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.48e+00 pdb=" C LYS B 76 " 0.032 2.00e-02 2.50e+03 pdb=" O LYS B 76 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN B 77 " -0.011 2.00e-02 2.50e+03 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 3794 2.82 - 3.40: 14916 3.40 - 3.98: 29195 3.98 - 4.56: 39302 4.56 - 5.14: 53744 Nonbonded interactions: 140951 Sorted by model distance: nonbonded pdb=" O2' A A 47 " pdb=" O LEU B 101 " model vdw 2.236 2.440 nonbonded pdb=" OH TYR B1232 " pdb=" OE1 GLU B1268 " model vdw 2.237 2.440 nonbonded pdb=" OD1 ASP B1361 " pdb=" OG SER B1363 " model vdw 2.256 2.440 nonbonded pdb=" OD1 ASN B 14 " pdb=" OG SER B 55 " model vdw 2.262 2.440 nonbonded pdb=" OG1 THR B 474 " pdb=" OD1 ASN B 477 " model vdw 2.263 2.440 ... (remaining 140946 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: 4.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.370 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 51.780 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 : 0.003 0.052 14355 Z= 0.193 Angle : 0.464 5.617 19961 Z= 0.258 Chirality : 0.036 0.182 2285 Planarity : 0.004 0.044 2055 Dihedral : 17.482 135.253 6187 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.58 % Allowed : 5.91 % Favored : 93.51 % 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: 1330 helix: 1.18 (0.20), residues: 668 sheet: -0.27 (0.45), residues: 135 loop : 0.08 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 464 HIS 0.003 0.001 HIS B 328 PHE 0.010 0.001 PHE B1046 TYR 0.010 0.001 TYR B 155 ARG 0.003 0.001 ARG B 653 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 LEU cc_start: 0.8689 (tp) cc_final: 0.8312 (tp) REVERT: B 263 LYS cc_start: 0.9151 (mttt) cc_final: 0.8950 (mmmm) REVERT: B 470 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7443 (tp30) REVERT: B 610 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8078 (tp30) REVERT: B 795 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8105 (tt) REVERT: B 879 MET cc_start: 0.7247 (mmm) cc_final: 0.6935 (tpp) REVERT: B 911 LEU cc_start: 0.9610 (mt) cc_final: 0.9390 (tp) REVERT: B 1037 PHE cc_start: 0.8485 (p90) cc_final: 0.7947 (p90) outliers start: 7 outliers final: 2 residues processed: 135 average time/residue: 0.3727 time to fit residues: 67.4936 Evaluate side-chains 61 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 1145 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 37 optimal weight: 0.0980 chunk 74 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 HIS ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 GLN B 826 GLN ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14355 Z= 0.270 Angle : 0.516 6.589 19961 Z= 0.276 Chirality : 0.037 0.150 2285 Planarity : 0.004 0.052 2055 Dihedral : 18.715 138.284 3345 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.41 % Allowed : 9.15 % Favored : 89.43 % 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: 1.22 (0.23), residues: 1330 helix: 1.54 (0.20), residues: 678 sheet: 0.12 (0.48), residues: 126 loop : 0.14 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 883 HIS 0.007 0.001 HIS B 328 PHE 0.011 0.002 PHE B 196 TYR 0.018 0.002 TYR B1010 ARG 0.005 0.001 ARG B 691 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 263 LYS cc_start: 0.9200 (mttt) cc_final: 0.8948 (mmmm) REVERT: B 470 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7362 (tp30) REVERT: B 610 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8279 (tp30) REVERT: B 724 ILE cc_start: 0.8951 (mt) cc_final: 0.8724 (pt) REVERT: B 810 LYS cc_start: 0.6889 (mmtp) cc_final: 0.6429 (tttt) REVERT: B 882 TYR cc_start: 0.7155 (t80) cc_final: 0.6789 (t80) REVERT: B 911 LEU cc_start: 0.9623 (mt) cc_final: 0.9420 (tp) REVERT: B 933 GLN cc_start: 0.9235 (tt0) cc_final: 0.8755 (tm-30) REVERT: B 1037 PHE cc_start: 0.8600 (p90) cc_final: 0.7942 (p90) REVERT: B 1273 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8743 (mp) outliers start: 17 outliers final: 10 residues processed: 76 average time/residue: 0.3415 time to fit residues: 37.4970 Evaluate side-chains 59 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1273 ILE Chi-restraints excluded: chain B residue 1318 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 117 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 HIS B 826 GLN B 854 ASN B 885 GLN ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14355 Z= 0.293 Angle : 0.511 5.913 19961 Z= 0.274 Chirality : 0.037 0.223 2285 Planarity : 0.003 0.048 2055 Dihedral : 18.757 138.659 3343 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.50 % Allowed : 10.73 % Favored : 87.77 % 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: 1.29 (0.23), residues: 1330 helix: 1.66 (0.20), residues: 677 sheet: 0.30 (0.50), residues: 126 loop : 0.04 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 883 HIS 0.007 0.001 HIS B 167 PHE 0.010 0.001 PHE B 518 TYR 0.013 0.001 TYR B 136 ARG 0.007 0.001 ARG B 919 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 50 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 263 LYS cc_start: 0.9210 (mttt) cc_final: 0.8926 (mmmm) REVERT: B 383 MET cc_start: 0.8548 (mtp) cc_final: 0.8343 (mtp) REVERT: B 610 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8423 (tp30) REVERT: B 795 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8270 (tt) REVERT: B 810 LYS cc_start: 0.7137 (mmtp) cc_final: 0.6629 (tttt) REVERT: B 882 TYR cc_start: 0.7085 (t80) cc_final: 0.6796 (t80) REVERT: B 1037 PHE cc_start: 0.8588 (p90) cc_final: 0.8028 (p90) outliers start: 18 outliers final: 10 residues processed: 67 average time/residue: 0.3007 time to fit residues: 29.9416 Evaluate side-chains 56 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 4.9990 chunk 99 optimal weight: 20.0000 chunk 68 optimal weight: 0.0870 chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14355 Z= 0.218 Angle : 0.461 6.818 19961 Z= 0.248 Chirality : 0.036 0.144 2285 Planarity : 0.003 0.045 2055 Dihedral : 18.657 138.756 3342 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.33 % Allowed : 11.23 % Favored : 87.44 % 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: 1.40 (0.23), residues: 1330 helix: 1.77 (0.20), residues: 685 sheet: 0.32 (0.50), residues: 125 loop : 0.05 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 883 HIS 0.006 0.001 HIS B 167 PHE 0.020 0.001 PHE B 897 TYR 0.011 0.001 TYR B 155 ARG 0.003 0.000 ARG B 919 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 46 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 263 LYS cc_start: 0.9217 (mttt) cc_final: 0.8932 (mmmm) REVERT: B 795 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8225 (tt) REVERT: B 810 LYS cc_start: 0.7158 (mmtp) cc_final: 0.6652 (tttt) REVERT: B 912 ASP cc_start: 0.9266 (m-30) cc_final: 0.8916 (t70) REVERT: B 1037 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8041 (p90) REVERT: B 1273 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8743 (mp) outliers start: 16 outliers final: 10 residues processed: 59 average time/residue: 0.2789 time to fit residues: 25.7961 Evaluate side-chains 56 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1273 ILE Chi-restraints excluded: chain B residue 1342 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 14355 Z= 0.469 Angle : 0.616 7.210 19961 Z= 0.323 Chirality : 0.041 0.178 2285 Planarity : 0.004 0.043 2055 Dihedral : 18.884 141.157 3342 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.91 % Allowed : 11.73 % Favored : 86.36 % 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: 1.07 (0.23), residues: 1330 helix: 1.47 (0.20), residues: 686 sheet: 0.38 (0.50), residues: 121 loop : -0.14 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 18 HIS 0.006 0.002 HIS B 983 PHE 0.015 0.002 PHE B1276 TYR 0.018 0.002 TYR B 882 ARG 0.005 0.001 ARG B 967 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 43 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 263 LYS cc_start: 0.9233 (mttt) cc_final: 0.8925 (mmmm) REVERT: B 353 ASP cc_start: 0.8509 (t70) cc_final: 0.8180 (p0) REVERT: B 795 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8304 (tt) REVERT: B 810 LYS cc_start: 0.7248 (mmtp) cc_final: 0.6761 (tttt) REVERT: B 976 ARG cc_start: 0.8930 (mtm-85) cc_final: 0.8463 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8261 (p90) REVERT: B 1242 TYR cc_start: 0.6897 (OUTLIER) cc_final: 0.6156 (m-10) outliers start: 23 outliers final: 12 residues processed: 62 average time/residue: 0.2829 time to fit residues: 26.9256 Evaluate side-chains 57 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 42 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1342 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 140 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14355 Z= 0.183 Angle : 0.460 6.991 19961 Z= 0.247 Chirality : 0.035 0.148 2285 Planarity : 0.003 0.043 2055 Dihedral : 18.712 140.118 3342 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.66 % Allowed : 12.81 % Favored : 85.52 % 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: 1.34 (0.23), residues: 1330 helix: 1.73 (0.20), residues: 686 sheet: 0.40 (0.50), residues: 123 loop : -0.04 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 476 HIS 0.006 0.001 HIS B 167 PHE 0.022 0.001 PHE B 897 TYR 0.017 0.001 TYR B 882 ARG 0.002 0.000 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 50 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 263 LYS cc_start: 0.9230 (mttt) cc_final: 0.8929 (mmmm) REVERT: B 353 ASP cc_start: 0.8463 (t70) cc_final: 0.8149 (p0) REVERT: B 795 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8272 (tt) REVERT: B 810 LYS cc_start: 0.7288 (mmtp) cc_final: 0.6813 (tttt) REVERT: B 976 ARG cc_start: 0.8904 (mtm-85) cc_final: 0.8439 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.8076 (p90) REVERT: B 1170 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8146 (pt0) REVERT: B 1242 TYR cc_start: 0.6816 (OUTLIER) cc_final: 0.6063 (m-10) outliers start: 20 outliers final: 9 residues processed: 68 average time/residue: 0.2849 time to fit residues: 29.6128 Evaluate side-chains 56 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1170 GLU Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1242 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 79 optimal weight: 0.3980 chunk 102 optimal weight: 6.9990 chunk 118 optimal weight: 0.1980 chunk 78 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.088 14355 Z= 0.135 Angle : 0.420 7.603 19961 Z= 0.227 Chirality : 0.034 0.135 2285 Planarity : 0.003 0.041 2055 Dihedral : 18.558 140.065 3342 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.25 % Allowed : 13.23 % Favored : 85.52 % 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: 1.55 (0.23), residues: 1330 helix: 1.93 (0.20), residues: 687 sheet: 0.47 (0.50), residues: 123 loop : 0.02 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 476 HIS 0.005 0.001 HIS B 167 PHE 0.012 0.001 PHE B 518 TYR 0.017 0.001 TYR B 882 ARG 0.003 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 49 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8269 (mm) REVERT: B 353 ASP cc_start: 0.8407 (t70) cc_final: 0.8096 (p0) REVERT: B 383 MET cc_start: 0.8647 (mtp) cc_final: 0.8420 (mtp) REVERT: B 795 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8092 (tt) REVERT: B 810 LYS cc_start: 0.7317 (mmtp) cc_final: 0.6857 (tttt) REVERT: B 912 ASP cc_start: 0.9293 (m-30) cc_final: 0.8954 (t70) REVERT: B 976 ARG cc_start: 0.8900 (mtm-85) cc_final: 0.8434 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8027 (p90) outliers start: 15 outliers final: 8 residues processed: 63 average time/residue: 0.3127 time to fit residues: 30.1070 Evaluate side-chains 58 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 chunk 133 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14355 Z= 0.158 Angle : 0.427 7.172 19961 Z= 0.231 Chirality : 0.034 0.180 2285 Planarity : 0.003 0.042 2055 Dihedral : 18.585 141.209 3342 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.00 % Allowed : 13.81 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.23), residues: 1330 helix: 1.94 (0.20), residues: 688 sheet: 0.47 (0.50), residues: 123 loop : 0.07 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 476 HIS 0.004 0.001 HIS B 167 PHE 0.023 0.001 PHE B 897 TYR 0.017 0.001 TYR B 882 ARG 0.002 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8288 (mm) REVERT: B 353 ASP cc_start: 0.8428 (t70) cc_final: 0.8119 (p0) REVERT: B 810 LYS cc_start: 0.7319 (mmtp) cc_final: 0.6848 (tttt) REVERT: B 976 ARG cc_start: 0.8905 (mtm-85) cc_final: 0.8442 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8170 (p90) REVERT: B 1170 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8113 (pt0) outliers start: 12 outliers final: 8 residues processed: 56 average time/residue: 0.2932 time to fit residues: 25.3945 Evaluate side-chains 52 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1170 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 123 optimal weight: 0.2980 chunk 129 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14355 Z= 0.125 Angle : 0.420 7.800 19961 Z= 0.227 Chirality : 0.034 0.135 2285 Planarity : 0.003 0.042 2055 Dihedral : 18.541 141.488 3342 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.16 % Allowed : 13.81 % Favored : 85.02 % 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: 1.62 (0.23), residues: 1330 helix: 1.96 (0.20), residues: 688 sheet: 0.52 (0.49), residues: 122 loop : 0.08 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 476 HIS 0.004 0.001 HIS B 167 PHE 0.012 0.001 PHE B 518 TYR 0.016 0.001 TYR B 882 ARG 0.002 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8266 (mm) REVERT: B 353 ASP cc_start: 0.8410 (t70) cc_final: 0.8116 (p0) REVERT: B 810 LYS cc_start: 0.7320 (mmtp) cc_final: 0.6843 (tttt) REVERT: B 976 ARG cc_start: 0.8902 (mtm-85) cc_final: 0.8442 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8169 (p90) outliers start: 14 outliers final: 10 residues processed: 56 average time/residue: 0.2817 time to fit residues: 24.4365 Evaluate side-chains 55 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 43 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 781 MET Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 95 optimal weight: 0.0980 chunk 144 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 GLN B 807 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14355 Z= 0.306 Angle : 0.514 5.448 19961 Z= 0.273 Chirality : 0.037 0.160 2285 Planarity : 0.003 0.043 2055 Dihedral : 18.695 143.240 3342 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.08 % Allowed : 14.06 % Favored : 84.86 % 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: 1.44 (0.23), residues: 1330 helix: 1.83 (0.20), residues: 687 sheet: 0.36 (0.49), residues: 123 loop : 0.01 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 464 HIS 0.004 0.001 HIS B 329 PHE 0.019 0.001 PHE B 518 TYR 0.017 0.001 TYR B 882 ARG 0.003 0.000 ARG B 967 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8304 (mm) REVERT: B 353 ASP cc_start: 0.8484 (t70) cc_final: 0.8186 (p0) REVERT: B 810 LYS cc_start: 0.7364 (mmtp) cc_final: 0.6893 (tttt) REVERT: B 976 ARG cc_start: 0.8919 (mtm-85) cc_final: 0.8454 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8240 (p90) outliers start: 13 outliers final: 9 residues processed: 52 average time/residue: 0.2829 time to fit residues: 22.7462 Evaluate side-chains 52 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 781 MET Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.2980 chunk 35 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 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 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.082309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.057855 restraints weight = 48350.104| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.49 r_work: 0.2990 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14355 Z= 0.130 Angle : 0.435 8.351 19961 Z= 0.234 Chirality : 0.034 0.137 2285 Planarity : 0.003 0.042 2055 Dihedral : 18.578 142.216 3342 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.83 % Allowed : 14.31 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.23), residues: 1330 helix: 1.92 (0.20), residues: 688 sheet: 0.41 (0.50), residues: 122 loop : 0.01 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 476 HIS 0.005 0.001 HIS B 167 PHE 0.016 0.001 PHE B 518 TYR 0.016 0.001 TYR B 155 ARG 0.002 0.000 ARG B 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2779.32 seconds wall clock time: 51 minutes 55.36 seconds (3115.36 seconds total)