Starting phenix.real_space_refine (version: dev) on Wed Mar 15 06:02:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4i_14498/03_2023/7z4i_14498.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4i_14498/03_2023/7z4i_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_14498/03_2023/7z4i_14498.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4i_14498/03_2023/7z4i_14498.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4i_14498/03_2023/7z4i_14498.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4i_14498/03_2023/7z4i_14498.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 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-4893/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: 8.65, per 1000 atoms: 0.63 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: 6.54 Conformation dependent library (CDL) restraints added in 1.8 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: 5.27 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: 7.59 Time building geometry restraints manager: 6.89 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: 7913 27.05 - 54.10: 409 54.10 - 81.15: 74 81.15 - 108.20: 4 108.20 - 135.25: 1 Dihedral angle restraints: 8401 sinusoidal: 4464 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 8398 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 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. 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: 2.710 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: 12.500 Check model and map are aligned: 0.190 Process input model: 46.720 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.130 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 : 15.030 135.253 5853 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 % 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 *********************** 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 : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 135 average time/residue: 0.3949 time to fit residues: 71.9835 Evaluate side-chains 56 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 1.436 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1260 time to fit residues: 2.3911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 74 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 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: 3.5990 ------------------------------------------------------------------------------- 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 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 HIS B 712 GLN B 826 GLN ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 885 GLN B 926 GLN B1041 ASN ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 14355 Z= 0.338 Angle : 0.566 7.118 19961 Z= 0.301 Chirality : 0.039 0.159 2285 Planarity : 0.004 0.054 2055 Dihedral : 14.516 139.617 3007 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 1.50 % 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: 1.06 (0.23), residues: 1330 helix: 1.38 (0.20), residues: 683 sheet: 0.12 (0.49), residues: 126 loop : 0.07 (0.26), residues: 521 *********************** 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 76 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 58 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 74 average time/residue: 0.3314 time to fit residues: 35.6724 Evaluate side-chains 55 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 1.362 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1235 time to fit residues: 4.1943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 109 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 295 ASN B 854 ASN ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 14355 Z= 0.161 Angle : 0.455 6.295 19961 Z= 0.247 Chirality : 0.035 0.153 2285 Planarity : 0.003 0.048 2055 Dihedral : 14.387 138.361 3007 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 0.92 % 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: 1.31 (0.23), residues: 1330 helix: 1.65 (0.20), residues: 682 sheet: 0.26 (0.49), residues: 126 loop : 0.10 (0.26), residues: 522 *********************** 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 61 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 50 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 59 average time/residue: 0.3191 time to fit residues: 27.9472 Evaluate side-chains 48 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 1.620 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1291 time to fit residues: 2.7108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 8.9990 chunk 99 optimal weight: 30.0000 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** B 690 ASN ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 14355 Z= 0.374 Angle : 0.569 6.532 19961 Z= 0.300 Chirality : 0.039 0.173 2285 Planarity : 0.004 0.045 2055 Dihedral : 14.678 140.621 3007 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 1.33 % 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: 1330 helix: 1.55 (0.20), residues: 691 sheet: 0.44 (0.50), residues: 123 loop : -0.05 (0.26), residues: 516 *********************** 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 61 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 45 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 57 average time/residue: 0.3191 time to fit residues: 27.0482 Evaluate side-chains 48 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 1.486 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1464 time to fit residues: 3.9820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 9.9990 chunk 79 optimal weight: 0.0980 chunk 2 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- 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: 0.8342 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 14355 Z= 0.291 Angle : 0.498 6.090 19961 Z= 0.268 Chirality : 0.037 0.157 2285 Planarity : 0.003 0.043 2055 Dihedral : 14.545 140.044 3007 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 0.67 % 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: 1.25 (0.23), residues: 1330 helix: 1.64 (0.20), residues: 690 sheet: 0.42 (0.50), residues: 123 loop : -0.10 (0.26), residues: 517 *********************** 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 54 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 53 average time/residue: 0.3011 time to fit residues: 24.2766 Evaluate side-chains 39 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.414 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 7.9990 chunk 126 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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: 0.8331 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 14355 Z= 0.212 Angle : 0.466 11.382 19961 Z= 0.250 Chirality : 0.036 0.148 2285 Planarity : 0.003 0.042 2055 Dihedral : 14.443 140.010 3007 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.67 % 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: 685 sheet: 0.53 (0.50), residues: 123 loop : -0.05 (0.26), residues: 522 *********************** 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 50 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 49 average time/residue: 0.2158 time to fit residues: 16.7640 Evaluate side-chains 42 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1284 time to fit residues: 2.4078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 79 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.8311 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 14355 Z= 0.164 Angle : 0.443 8.658 19961 Z= 0.238 Chirality : 0.035 0.150 2285 Planarity : 0.003 0.042 2055 Dihedral : 14.356 140.325 3007 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 0.33 % 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: 1.54 (0.23), residues: 1330 helix: 1.90 (0.20), residues: 686 sheet: 0.59 (0.50), residues: 123 loop : 0.03 (0.27), residues: 521 *********************** 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 50 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 48 average time/residue: 0.3052 time to fit residues: 22.7456 Evaluate side-chains 41 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.571 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 42 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.8302 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 14355 Z= 0.139 Angle : 0.433 8.721 19961 Z= 0.234 Chirality : 0.034 0.137 2285 Planarity : 0.003 0.042 2055 Dihedral : 14.301 140.969 3007 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 0.67 % 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: 686 sheet: 0.62 (0.50), residues: 123 loop : 0.04 (0.27), residues: 521 *********************** 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 54 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 53 average time/residue: 0.2670 time to fit residues: 22.1846 Evaluate side-chains 47 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 1.402 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1238 time to fit residues: 2.6570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 133 optimal weight: 6.9990 chunk 78 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 123 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: