Starting phenix.real_space_refine on Sat Dec 9 20:16:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4v_24835/12_2023/7s4v_24835.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4v_24835/12_2023/7s4v_24835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4v_24835/12_2023/7s4v_24835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4v_24835/12_2023/7s4v_24835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4v_24835/12_2023/7s4v_24835.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4v_24835/12_2023/7s4v_24835.pdb" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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: 5 Type Number sf(0) Gaussians P 141 5.49 5 S 18 5.16 5 C 7249 2.51 5 N 2149 2.21 5 O 2658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A GLU 441": "OE1" <-> "OE2" Residue "A ASP 550": "OD1" <-> "OD2" Residue "A PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 746": "OE1" <-> "OE2" Residue "A ASP 947": "OD1" <-> "OD2" Residue "A TYR 1131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1225": "OE1" <-> "OE2" Residue "A GLU 1304": "OE1" <-> "OE2" Residue "A ASP 1332": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12215 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 9167 Classifications: {'peptide': 1122} Link IDs: {'PTRANS': 30, 'TRANS': 1091} Chain breaks: 5 Chain: "B" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2100 Classifications: {'RNA': 98} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 52, 'rna3p_pyr': 33} Link IDs: {'rna2p': 13, 'rna3p': 84} Chain: "C" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 665 Classifications: {'DNA': 33} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 32} Chain: "D" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 283 Inner-chain residues flagged as termini: ['pdbres=" DC D 30 "'] Classifications: {'DNA': 14} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 13} Time building chain proxies: 6.98, per 1000 atoms: 0.57 Number of scatterers: 12215 At special positions: 0 Unit cell: (88, 143, 129.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 141 15.00 O 2658 8.00 N 2149 7.00 C 7249 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: 5.48 Conformation dependent library (CDL) restraints added in 1.8 seconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 7 sheets defined 54.2% alpha, 8.2% beta 22 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 3.673A pdb=" N ARG A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 76 " --> pdb=" O TYR A 72 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 4.059A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 184 through 196 Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.928A pdb=" N GLU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.571A pdb=" N PHE A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 246 Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 275 through 280 removed outlier: 4.185A pdb=" N ALA A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 304 removed outlier: 3.949A pdb=" N LYS A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.548A pdb=" N ALA A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.627A pdb=" N PHE A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 368 through 382 Proline residue: A 378 - end of helix removed outlier: 3.919A pdb=" N LYS A 382 " --> pdb=" O PRO A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 removed outlier: 3.500A pdb=" N ASN A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.645A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.164A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.960A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 445 removed outlier: 3.649A pdb=" N ILE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.552A pdb=" N GLU A 480 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 494 removed outlier: 3.862A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 553 removed outlier: 3.906A pdb=" N ASP A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 567 removed outlier: 3.554A pdb=" N LEU A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 removed outlier: 4.053A pdb=" N LYS A 571 " --> pdb=" O TYR A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 576 removed outlier: 4.299A pdb=" N ASP A 576 " --> pdb=" O GLU A 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 573 through 576' Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.989A pdb=" N LEU A 621 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 623 " --> pdb=" O ILE A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 643 removed outlier: 4.928A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.814A pdb=" N ILE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 686 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 705 through 712 removed outlier: 3.547A pdb=" N GLN A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.579A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 940 Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.603A pdb=" N SER A 964 " --> pdb=" O SER A 960 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 998 Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.028A pdb=" N VAL A1083 " --> pdb=" O ASP A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1184 Processing helix chain 'A' and resid 1229 through 1240 removed outlier: 3.627A pdb=" N SER A1240 " --> pdb=" O LEU A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1251 Processing helix chain 'A' and resid 1252 through 1262 removed outlier: 3.533A pdb=" N GLN A1256 " --> pdb=" O ASN A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1280 removed outlier: 4.380A pdb=" N GLU A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1296 Processing helix chain 'A' and resid 1301 through 1310 Processing helix chain 'A' and resid 1311 through 1316 removed outlier: 3.766A pdb=" N THR A1314 " --> pdb=" O HIS A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1343 removed outlier: 3.940A pdb=" N VAL A1342 " --> pdb=" O THR A1339 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1339 through 1343' Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 956 through 957 removed outlier: 6.144A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A1095 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.114A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A1210 " --> pdb=" O LEU A1206 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 530 through 531 Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1162 removed outlier: 3.648A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE A1166 " --> pdb=" O ALA A1140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1162 removed outlier: 3.648A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1325 removed outlier: 3.592A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 5.82 Time building geometry restraints manager: 5.81 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: 3053 1.33 - 1.45: 3123 1.45 - 1.58: 6250 1.58 - 1.70: 282 1.70 - 1.82: 34 Bond restraints: 12742 Sorted by residual: bond pdb=" CB PRO A 503 " pdb=" CG PRO A 503 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 1.99e+00 bond pdb=" CA MET A 751 " pdb=" C MET A 751 " ideal model delta sigma weight residual 1.525 1.541 -0.016 1.38e-02 5.25e+03 1.31e+00 bond pdb=" C3' DG C 11 " pdb=" O3' DG C 11 " ideal model delta sigma weight residual 1.422 1.452 -0.030 3.00e-02 1.11e+03 1.00e+00 bond pdb=" CD GLU A1260 " pdb=" OE1 GLU A1260 " ideal model delta sigma weight residual 1.249 1.230 0.019 1.90e-02 2.77e+03 9.75e-01 bond pdb=" C3' DC D 2 " pdb=" O3' DC D 2 " ideal model delta sigma weight residual 1.422 1.451 -0.029 3.00e-02 1.11e+03 9.53e-01 ... (remaining 12737 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.79: 1034 106.79 - 113.60: 7156 113.60 - 120.41: 4878 120.41 - 127.22: 4395 127.22 - 134.03: 365 Bond angle restraints: 17828 Sorted by residual: angle pdb=" N GLU A1260 " pdb=" CA GLU A1260 " pdb=" CB GLU A1260 " ideal model delta sigma weight residual 110.16 115.21 -5.05 1.48e+00 4.57e-01 1.17e+01 angle pdb=" N VAL A 481 " pdb=" CA VAL A 481 " pdb=" C VAL A 481 " ideal model delta sigma weight residual 111.62 109.03 2.59 7.90e-01 1.60e+00 1.08e+01 angle pdb=" CA MET A 751 " pdb=" CB MET A 751 " pdb=" CG MET A 751 " ideal model delta sigma weight residual 114.10 119.97 -5.87 2.00e+00 2.50e-01 8.61e+00 angle pdb=" C MET A 534 " pdb=" CA MET A 534 " pdb=" CB MET A 534 " ideal model delta sigma weight residual 110.79 115.49 -4.70 1.63e+00 3.76e-01 8.32e+00 angle pdb=" CB MET A 694 " pdb=" CG MET A 694 " pdb=" SD MET A 694 " ideal model delta sigma weight residual 112.70 121.33 -8.63 3.00e+00 1.11e-01 8.27e+00 ... (remaining 17823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.01: 7180 35.01 - 70.03: 401 70.03 - 105.04: 29 105.04 - 140.06: 1 140.06 - 175.07: 7 Dihedral angle restraints: 7618 sinusoidal: 4319 harmonic: 3299 Sorted by residual: dihedral pdb=" O4' C B 70 " pdb=" C1' C B 70 " pdb=" N1 C B 70 " pdb=" C2 C B 70 " ideal model delta sinusoidal sigma weight residual 200.00 54.05 145.95 1 1.50e+01 4.44e-03 7.80e+01 dihedral pdb=" CA LEU A 258 " pdb=" C LEU A 258 " pdb=" N ALA A 259 " pdb=" CA ALA A 259 " ideal model delta harmonic sigma weight residual 180.00 152.00 28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" C4' DC D 2 " pdb=" C3' DC D 2 " pdb=" O3' DC D 2 " pdb=" P DT D 3 " ideal model delta sinusoidal sigma weight residual -140.00 35.07 -175.07 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1649 0.043 - 0.086: 343 0.086 - 0.129: 57 0.129 - 0.173: 10 0.173 - 0.216: 2 Chirality restraints: 2061 Sorted by residual: chirality pdb=" CB VAL A1259 " pdb=" CA VAL A1259 " pdb=" CG1 VAL A1259 " pdb=" CG2 VAL A1259 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA GLU A1260 " pdb=" N GLU A1260 " pdb=" C GLU A1260 " pdb=" CB GLU A1260 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" C3' A B 38 " pdb=" C4' A B 38 " pdb=" O3' A B 38 " pdb=" C2' A B 38 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 2058 not shown) Planarity restraints: 1745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 343 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO A 344 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A B 69 " 0.031 2.00e-02 2.50e+03 1.43e-02 5.65e+00 pdb=" N9 A B 69 " -0.035 2.00e-02 2.50e+03 pdb=" C8 A B 69 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A B 69 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A B 69 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A B 69 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 69 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A B 69 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A B 69 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A B 69 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A B 69 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 502 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO A 503 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 503 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 503 " -0.025 5.00e-02 4.00e+02 ... (remaining 1742 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1082 2.74 - 3.28: 11247 3.28 - 3.82: 19240 3.82 - 4.36: 23326 4.36 - 4.90: 37704 Nonbonded interactions: 92599 Sorted by model distance: nonbonded pdb=" OH TYR A 515 " pdb=" OP1 C B 5 " model vdw 2.202 2.440 nonbonded pdb=" OH TYR A 5 " pdb=" O HIS A 754 " model vdw 2.253 2.440 nonbonded pdb=" N2 G B 73 " pdb=" OP2 A B 76 " model vdw 2.271 2.520 nonbonded pdb=" OG SER A 541 " pdb=" OE2 GLU A 543 " model vdw 2.291 2.440 nonbonded pdb=" O GLY A 533 " pdb=" NH1 ARG A 535 " model vdw 2.309 2.520 ... (remaining 92594 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=0.00 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: 3.210 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: 11.980 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 39.150 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 0.071 12742 Z= 0.163 Angle : 0.537 8.627 17828 Z= 0.290 Chirality : 0.037 0.216 2061 Planarity : 0.004 0.067 1745 Dihedral : 19.296 175.071 5478 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -1.46 (0.24), residues: 1110 helix: -0.28 (0.23), residues: 518 sheet: -0.79 (0.55), residues: 101 loop : -1.71 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 476 HIS 0.004 0.001 HIS A1262 PHE 0.010 0.001 PHE A 97 TYR 0.013 0.001 TYR A 325 ARG 0.007 0.000 ARG A 951 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.3282 time to fit residues: 36.6447 Evaluate side-chains 42 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.267 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 50 optimal weight: 0.0870 chunk 97 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 342 GLN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS A1256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12742 Z= 0.411 Angle : 0.661 9.957 17828 Z= 0.350 Chirality : 0.042 0.187 2061 Planarity : 0.004 0.042 1745 Dihedral : 20.253 175.406 3100 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.50 % Allowed : 9.05 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.30 (0.24), residues: 1110 helix: -0.05 (0.22), residues: 536 sheet: -1.04 (0.52), residues: 108 loop : -1.73 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 476 HIS 0.010 0.002 HIS A 167 PHE 0.019 0.002 PHE A 97 TYR 0.020 0.002 TYR A 325 ARG 0.006 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 1.307 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 47 average time/residue: 0.3082 time to fit residues: 21.3826 Evaluate side-chains 38 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 1.208 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2279 time to fit residues: 3.2248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12742 Z= 0.185 Angle : 0.507 7.275 17828 Z= 0.272 Chirality : 0.036 0.179 2061 Planarity : 0.003 0.042 1745 Dihedral : 20.135 175.141 3100 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.50 % Allowed : 11.63 % Favored : 87.87 % 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: -0.91 (0.25), residues: 1110 helix: 0.41 (0.23), residues: 541 sheet: -1.01 (0.52), residues: 109 loop : -1.70 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 476 HIS 0.005 0.001 HIS A 167 PHE 0.021 0.001 PHE A 643 TYR 0.014 0.001 TYR A 325 ARG 0.003 0.000 ARG A 951 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 1.214 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 43 average time/residue: 0.2492 time to fit residues: 17.0240 Evaluate side-chains 34 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1050 time to fit residues: 1.6987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 76 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12742 Z= 0.291 Angle : 0.557 7.891 17828 Z= 0.298 Chirality : 0.038 0.190 2061 Planarity : 0.003 0.044 1745 Dihedral : 20.268 175.707 3100 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.80 % Allowed : 14.02 % 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: -0.94 (0.24), residues: 1110 helix: 0.42 (0.23), residues: 543 sheet: -1.19 (0.51), residues: 109 loop : -1.72 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 476 HIS 0.007 0.001 HIS A 167 PHE 0.016 0.001 PHE A 432 TYR 0.018 0.001 TYR A 325 ARG 0.003 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 1.170 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 39 average time/residue: 0.2335 time to fit residues: 14.7724 Evaluate side-chains 33 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1151 time to fit residues: 1.9252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 0.0870 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 980 ASN A1177 ASN ** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12742 Z= 0.230 Angle : 0.518 6.819 17828 Z= 0.277 Chirality : 0.037 0.183 2061 Planarity : 0.003 0.043 1745 Dihedral : 20.266 176.051 3100 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.70 % Allowed : 14.91 % Favored : 84.39 % 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: -0.87 (0.25), residues: 1110 helix: 0.51 (0.23), residues: 547 sheet: -1.18 (0.52), residues: 109 loop : -1.75 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 476 HIS 0.010 0.001 HIS A1262 PHE 0.011 0.001 PHE A 491 TYR 0.015 0.001 TYR A 325 ARG 0.002 0.000 ARG A 951 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 1.071 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 41 average time/residue: 0.2879 time to fit residues: 17.9096 Evaluate side-chains 35 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1166 time to fit residues: 2.3087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.4980 chunk 23 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 chunk 63 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12742 Z= 0.343 Angle : 0.584 6.766 17828 Z= 0.312 Chirality : 0.039 0.195 2061 Planarity : 0.004 0.045 1745 Dihedral : 20.379 176.679 3100 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.99 % Allowed : 15.51 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.24), residues: 1110 helix: 0.42 (0.23), residues: 536 sheet: -1.20 (0.53), residues: 106 loop : -1.80 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 476 HIS 0.007 0.002 HIS A 167 PHE 0.015 0.001 PHE A 491 TYR 0.017 0.002 TYR A 325 ARG 0.003 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 1.127 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 43 average time/residue: 0.2339 time to fit residues: 16.2780 Evaluate side-chains 33 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1105 time to fit residues: 2.1210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.9990 chunk 68 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12742 Z= 0.167 Angle : 0.487 5.800 17828 Z= 0.261 Chirality : 0.036 0.178 2061 Planarity : 0.003 0.042 1745 Dihedral : 20.268 176.702 3100 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.50 % Allowed : 16.00 % Favored : 83.50 % 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: -0.67 (0.25), residues: 1110 helix: 0.75 (0.23), residues: 540 sheet: -1.09 (0.53), residues: 106 loop : -1.72 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.006 0.001 HIS A1262 PHE 0.008 0.001 PHE A1235 TYR 0.012 0.001 TYR A 325 ARG 0.002 0.000 ARG A 951 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 1.320 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 41 average time/residue: 0.2684 time to fit residues: 17.7282 Evaluate side-chains 36 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 1.464 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1201 time to fit residues: 2.6681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 76 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 109 optimal weight: 0.0570 chunk 115 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12742 Z= 0.178 Angle : 0.493 7.657 17828 Z= 0.263 Chirality : 0.036 0.182 2061 Planarity : 0.003 0.042 1745 Dihedral : 20.241 176.740 3100 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.50 % Allowed : 16.30 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.25), residues: 1110 helix: 0.85 (0.23), residues: 534 sheet: -0.97 (0.50), residues: 118 loop : -1.67 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.005 0.001 HIS A1262 PHE 0.009 0.001 PHE A1235 TYR 0.012 0.001 TYR A 325 ARG 0.002 0.000 ARG A 951 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 1.183 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 39 average time/residue: 0.2416 time to fit residues: 15.2245 Evaluate side-chains 36 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1085 time to fit residues: 1.9407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12742 Z= 0.254 Angle : 0.532 7.539 17828 Z= 0.283 Chirality : 0.037 0.189 2061 Planarity : 0.003 0.044 1745 Dihedral : 20.292 177.012 3100 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.20 % Allowed : 16.70 % Favored : 83.10 % 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: -0.68 (0.25), residues: 1110 helix: 0.70 (0.23), residues: 537 sheet: -1.03 (0.50), residues: 118 loop : -1.67 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.006 0.001 HIS A 167 PHE 0.024 0.001 PHE A 432 TYR 0.016 0.001 TYR A 325 ARG 0.003 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 1.233 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 35 average time/residue: 0.2577 time to fit residues: 14.5818 Evaluate side-chains 34 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 1.210 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1437 time to fit residues: 2.1159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 105 optimal weight: 0.0270 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12742 Z= 0.175 Angle : 0.498 7.997 17828 Z= 0.265 Chirality : 0.036 0.180 2061 Planarity : 0.003 0.043 1745 Dihedral : 20.255 177.144 3100 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 17.00 % Favored : 83.00 % 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: -0.54 (0.25), residues: 1110 helix: 0.86 (0.23), residues: 531 sheet: -0.97 (0.50), residues: 118 loop : -1.64 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.004 0.001 HIS A1262 PHE 0.009 0.001 PHE A 432 TYR 0.012 0.001 TYR A 325 ARG 0.002 0.000 ARG A 951 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.231 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2734 time to fit residues: 14.3263 Evaluate side-chains 33 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.0970 chunk 91 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 5 optimal weight: 0.0980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.099206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.071037 restraints weight = 31397.531| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.25 r_work: 0.2983 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12742 Z= 0.145 Angle : 0.476 7.821 17828 Z= 0.252 Chirality : 0.035 0.176 2061 Planarity : 0.003 0.041 1745 Dihedral : 20.190 176.988 3100 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 17.20 % Favored : 82.80 % 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: -0.36 (0.25), residues: 1110 helix: 1.00 (0.24), residues: 530 sheet: -0.84 (0.49), residues: 118 loop : -1.55 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 476 HIS 0.003 0.001 HIS A 167 PHE 0.012 0.001 PHE A1258 TYR 0.011 0.001 TYR A 325 ARG 0.002 0.000 ARG A 629 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2048.56 seconds wall clock time: 38 minutes 25.39 seconds (2305.39 seconds total)