Starting phenix.real_space_refine on Sun Jul 21 14:56:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4x_24838/07_2024/7s4x_24838_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4x_24838/07_2024/7s4x_24838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4x_24838/07_2024/7s4x_24838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4x_24838/07_2024/7s4x_24838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4x_24838/07_2024/7s4x_24838_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4x_24838/07_2024/7s4x_24838_neut.cif" } resolution = 2.76 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: 6 Type Number sf(0) Gaussians P 161 5.49 5 Mg 5 5.21 5 S 23 5.16 5 C 8614 2.51 5 N 2546 2.21 5 O 3142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A ASP 567": "OD1" <-> "OD2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 585": "OD1" <-> "OD2" Residue "A GLU 766": "OE1" <-> "OE2" Residue "A TYR 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 827": "OE1" <-> "OE2" Residue "A GLU 874": "OE1" <-> "OE2" Residue "A GLU 952": "OE1" <-> "OE2" Residue "A TYR 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1028": "OE1" <-> "OE2" Residue "A GLU 1068": "OE1" <-> "OE2" Residue "A GLU 1271": "OE1" <-> "OE2" Residue "A TYR 1326": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14491 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 11090 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1354, 11079 Classifications: {'peptide': 1354} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 1318} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 1354, 11079 Classifications: {'peptide': 1354} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 1318} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 11262 Chain: "B" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2103 Classifications: {'RNA': 98} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 52, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 86} Chain: "C" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 325 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "c" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 405 Classifications: {'DNA': 20} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 556 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "c" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 783 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 783 " occ=0.50 Time building chain proxies: 15.17, per 1000 atoms: 1.05 Number of scatterers: 14491 At special positions: 0 Unit cell: (89.1, 134.46, 131.22, 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) S 23 16.00 P 161 15.00 Mg 5 11.99 O 3142 8.00 N 2546 7.00 C 8614 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: 6.90 Conformation dependent library (CDL) restraints added in 4.0 seconds 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 9 sheets defined 55.4% alpha, 8.2% beta 56 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 5.64 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.799A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.707A 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 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 208 through 214 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 238 through 244 removed outlier: 3.726A pdb=" N ALA A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.586A pdb=" N ALA A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 291 Processing helix chain 'A' and resid 292 through 306 removed outlier: 5.047A pdb=" N ASP A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 343 through 352 removed outlier: 4.576A pdb=" N LYS A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLU A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix removed outlier: 3.529A pdb=" N MET A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.013A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.035A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.745A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.698A 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 Processing helix chain 'A' and resid 560 through 567 Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.966A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 654 removed outlier: 3.613A pdb=" N ARG A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 703 through 711 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 731 through 751 removed outlier: 4.067A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 779 through 792 Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 804 through 807 Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 832 through 834 No H-bonds generated for 'chain 'A' and resid 832 through 834' Processing helix chain 'A' and resid 860 through 866 Processing helix chain 'A' and resid 872 through 889 removed outlier: 5.319A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 902 through 906 removed outlier: 3.741A pdb=" N GLY A 906 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.525A pdb=" N LYS A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 940 removed outlier: 4.175A pdb=" N LEU A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 922 " --> pdb=" O LYS A 918 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.390A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 Processing helix chain 'A' and resid 1017 through 1021 Processing helix chain 'A' and resid 1030 through 1042 Processing helix chain 'A' and resid 1043 through 1047 removed outlier: 3.522A pdb=" N PHE A1046 " --> pdb=" O MET A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1087 removed outlier: 3.898A pdb=" N ALA A1081 " --> pdb=" O GLY A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.672A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1240 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1281 removed outlier: 3.505A pdb=" N GLU A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1317 removed outlier: 3.908A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A1312 " --> pdb=" O ASN A1308 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR A1314 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU A1315 " --> pdb=" O HIS A1311 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR A1316 " --> pdb=" O LEU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 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 954 through 959 removed outlier: 7.185A pdb=" N TYR A 5 " --> pdb=" O ASN A 758 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N VAL A 760 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N GLU A 762 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU A 9 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 9.943A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA4, first strand: chain 'A' and resid 836 through 840 Processing sheet with id=AA5, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA6, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 6.596A pdb=" N GLU A1064 " --> pdb=" O VAL A1073 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.503A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1324 through 1326 503 hydrogen bonds defined for protein. 1447 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 139 hydrogen bonds 270 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 7.95 Time building geometry restraints manager: 7.38 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: 2929 1.33 - 1.45: 4075 1.45 - 1.57: 7714 1.57 - 1.69: 317 1.69 - 1.81: 44 Bond restraints: 15079 Sorted by residual: bond pdb=" CA ARG A 976 " pdb=" C ARG A 976 " ideal model delta sigma weight residual 1.522 1.484 0.039 1.38e-02 5.25e+03 7.79e+00 bond pdb=" C3' DG C 8 " pdb=" O3' DG C 8 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 1.95e+00 bond pdb=" CB THR A 740 " pdb=" CG2 THR A 740 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.94e+00 bond pdb=" CG LEU A1312 " pdb=" CD1 LEU A1312 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.92e+00 bond pdb=" CA SER A1136 " pdb=" C SER A1136 " ideal model delta sigma weight residual 1.531 1.522 0.009 7.40e-03 1.83e+04 1.62e+00 ... (remaining 15074 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.82: 952 105.82 - 112.87: 8304 112.87 - 119.91: 5131 119.91 - 126.96: 6179 126.96 - 134.00: 478 Bond angle restraints: 21044 Sorted by residual: angle pdb=" N VAL A1018 " pdb=" CA VAL A1018 " pdb=" C VAL A1018 " ideal model delta sigma weight residual 112.50 106.96 5.54 1.39e+00 5.18e-01 1.59e+01 angle pdb=" C TYR A1326 " pdb=" N PHE A1327 " pdb=" CA PHE A1327 " ideal model delta sigma weight residual 121.54 128.60 -7.06 1.91e+00 2.74e-01 1.37e+01 angle pdb=" N CYS A 574 " pdb=" CA CYS A 574 " pdb=" C CYS A 574 " ideal model delta sigma weight residual 109.96 115.20 -5.24 1.49e+00 4.50e-01 1.24e+01 angle pdb=" N ILE A 312 " pdb=" CA ILE A 312 " pdb=" C ILE A 312 " ideal model delta sigma weight residual 112.80 109.26 3.54 1.15e+00 7.56e-01 9.46e+00 angle pdb=" N LEU A 258 " pdb=" CA LEU A 258 " pdb=" C LEU A 258 " ideal model delta sigma weight residual 113.43 109.56 3.87 1.26e+00 6.30e-01 9.44e+00 ... (remaining 21039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.91: 8512 33.91 - 67.81: 542 67.81 - 101.72: 45 101.72 - 135.62: 0 135.62 - 169.53: 5 Dihedral angle restraints: 9104 sinusoidal: 5117 harmonic: 3987 Sorted by residual: dihedral pdb=" O4' U B 59 " pdb=" C1' U B 59 " pdb=" N1 U B 59 " pdb=" C2 U B 59 " ideal model delta sinusoidal sigma weight residual -160.00 9.53 -169.53 1 1.50e+01 4.44e-03 8.46e+01 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 32.57 167.43 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" CA ARG A1122 " pdb=" C ARG A1122 " pdb=" N LYS A1123 " pdb=" CA LYS A1123 " ideal model delta harmonic sigma weight residual 180.00 158.17 21.83 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 9101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1765 0.040 - 0.081: 506 0.081 - 0.121: 121 0.121 - 0.161: 15 0.161 - 0.202: 3 Chirality restraints: 2410 Sorted by residual: chirality pdb=" C3' A B 8 " pdb=" C4' A B 8 " pdb=" O3' A B 8 " pdb=" C2' A B 8 " both_signs ideal model delta sigma weight residual False -2.48 -2.28 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE A 122 " pdb=" CA ILE A 122 " pdb=" CG1 ILE A 122 " pdb=" CG2 ILE A 122 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.49e-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 6.93e-01 ... (remaining 2407 not shown) Planarity restraints: 2107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 75 " -0.023 2.00e-02 2.50e+03 1.10e-02 3.33e+00 pdb=" N9 A B 75 " 0.027 2.00e-02 2.50e+03 pdb=" C8 A B 75 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B 75 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A B 75 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 75 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B 75 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A B 75 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A B 75 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A B 75 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A B 75 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 42 " -0.023 2.00e-02 2.50e+03 1.04e-02 2.98e+00 pdb=" N9 A B 42 " 0.024 2.00e-02 2.50e+03 pdb=" C8 A B 42 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B 42 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A B 42 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 42 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B 42 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A B 42 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A B 42 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B 42 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A B 42 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 54 " 0.022 2.00e-02 2.50e+03 9.52e-03 2.72e+00 pdb=" N9 G B 54 " -0.023 2.00e-02 2.50e+03 pdb=" C8 G B 54 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G B 54 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 54 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 54 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G B 54 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G B 54 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G B 54 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G B 54 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G B 54 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G B 54 " -0.004 2.00e-02 2.50e+03 ... (remaining 2104 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 76 2.48 - 3.09: 9975 3.09 - 3.69: 23748 3.69 - 4.30: 36736 4.30 - 4.90: 56487 Nonbonded interactions: 127022 Sorted by model distance: nonbonded pdb=" OP1 DC D 34 " pdb="MG MG A1402 " model vdw 1.878 2.170 nonbonded pdb=" OE1 GLU A 762 " pdb="MG MG A1401 " model vdw 1.915 2.170 nonbonded pdb=" OD2 ASP A 10 " pdb="MG MG A1402 " model vdw 1.956 2.170 nonbonded pdb=" OD1 ASP A 10 " pdb="MG MG A1401 " model vdw 2.010 2.170 nonbonded pdb=" ND1 HIS A 983 " pdb="MG MG A1402 " model vdw 2.091 2.250 ... (remaining 127017 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: 11.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 57.430 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 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 : 0.006 0.055 15079 Z= 0.362 Angle : 0.598 7.670 21044 Z= 0.341 Chirality : 0.041 0.202 2410 Planarity : 0.003 0.038 2107 Dihedral : 19.275 169.530 6524 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 0.02 (0.22), residues: 1351 helix: 0.57 (0.20), residues: 646 sheet: -0.55 (0.46), residues: 117 loop : -0.37 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.004 0.001 HIS A1241 PHE 0.021 0.002 PHE A1327 TYR 0.016 0.002 TYR A1265 ARG 0.007 0.001 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.408 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 1.6742 time to fit residues: 132.8351 Evaluate side-chains 52 residues out of total 1217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 2.9990 chunk 112 optimal weight: 0.0670 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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: 0.8572 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15079 Z= 0.174 Angle : 0.512 7.130 21044 Z= 0.276 Chirality : 0.037 0.164 2410 Planarity : 0.003 0.041 2107 Dihedral : 20.701 172.937 3634 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.66 % Allowed : 4.02 % Favored : 95.32 % 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 (0.23), residues: 1351 helix: 1.10 (0.21), residues: 645 sheet: -0.74 (0.43), residues: 120 loop : -0.11 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.003 0.001 HIS A 328 PHE 0.019 0.001 PHE A1327 TYR 0.010 0.001 TYR A 271 ARG 0.007 0.000 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 1.958 Fit side-chains REVERT: A 1275 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6415 (mm-30) outliers start: 7 outliers final: 2 residues processed: 69 average time/residue: 1.8799 time to fit residues: 141.3269 Evaluate side-chains 55 residues out of total 1217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 1018 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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: 0.8629 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 15079 Z= 0.333 Angle : 0.557 7.134 21044 Z= 0.298 Chirality : 0.040 0.183 2410 Planarity : 0.003 0.045 2107 Dihedral : 20.710 169.897 3634 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.74 % Allowed : 5.58 % Favored : 93.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.23), residues: 1351 helix: 1.10 (0.21), residues: 648 sheet: -0.62 (0.44), residues: 123 loop : -0.16 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.004 0.001 HIS A1241 PHE 0.020 0.001 PHE A1327 TYR 0.016 0.001 TYR A 136 ARG 0.007 0.001 ARG A1058 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 1.423 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 1.8289 time to fit residues: 122.8927 Evaluate side-chains 59 residues out of total 1217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1062 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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: 0.8645 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 15079 Z= 0.381 Angle : 0.572 7.328 21044 Z= 0.305 Chirality : 0.041 0.196 2410 Planarity : 0.004 0.046 2107 Dihedral : 20.740 169.750 3634 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.82 % Allowed : 6.57 % Favored : 92.61 % 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: 0.45 (0.23), residues: 1351 helix: 1.04 (0.20), residues: 648 sheet: -0.64 (0.44), residues: 123 loop : -0.22 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.005 0.001 HIS A1241 PHE 0.020 0.002 PHE A1327 TYR 0.016 0.002 TYR A 155 ARG 0.008 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: A 674 GLN cc_start: 0.8268 (tp40) cc_final: 0.8038 (mm110) outliers start: 9 outliers final: 6 residues processed: 61 average time/residue: 1.7865 time to fit residues: 118.4014 Evaluate side-chains 60 residues out of total 1217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1062 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A1261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15079 Z= 0.252 Angle : 0.514 6.898 21044 Z= 0.277 Chirality : 0.038 0.175 2410 Planarity : 0.003 0.045 2107 Dihedral : 20.678 171.364 3634 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.99 % Allowed : 7.22 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.23), residues: 1351 helix: 1.17 (0.20), residues: 646 sheet: -0.64 (0.44), residues: 123 loop : -0.14 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.003 0.001 HIS A1241 PHE 0.019 0.001 PHE A1327 TYR 0.013 0.001 TYR A 155 ARG 0.007 0.000 ARG A1058 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 1.726 Fit side-chains REVERT: A 43 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8725 (tt) REVERT: A 674 GLN cc_start: 0.8243 (tp40) cc_final: 0.8004 (mm110) REVERT: A 830 ILE cc_start: 0.8029 (mm) cc_final: 0.7743 (mm) outliers start: 11 outliers final: 5 residues processed: 66 average time/residue: 1.8027 time to fit residues: 129.1857 Evaluate side-chains 62 residues out of total 1217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1062 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.0870 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15079 Z= 0.223 Angle : 0.509 7.245 21044 Z= 0.275 Chirality : 0.037 0.169 2410 Planarity : 0.003 0.051 2107 Dihedral : 20.620 171.897 3634 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.07 % Allowed : 7.31 % Favored : 91.63 % 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 (0.23), residues: 1351 helix: 1.26 (0.20), residues: 646 sheet: -0.72 (0.44), residues: 125 loop : -0.11 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.003 0.001 HIS A 328 PHE 0.018 0.001 PHE A1327 TYR 0.013 0.001 TYR A 155 ARG 0.011 0.000 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 1.572 Fit side-chains REVERT: A 627 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6970 (pt0) REVERT: A 674 GLN cc_start: 0.8253 (tp40) cc_final: 0.8028 (mm110) REVERT: A 830 ILE cc_start: 0.8052 (mm) cc_final: 0.7848 (mm) REVERT: A 1029 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7599 (pp) outliers start: 12 outliers final: 6 residues processed: 68 average time/residue: 1.8623 time to fit residues: 137.2134 Evaluate side-chains 63 residues out of total 1217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15079 Z= 0.316 Angle : 0.540 7.940 21044 Z= 0.288 Chirality : 0.039 0.180 2410 Planarity : 0.004 0.059 2107 Dihedral : 20.634 170.541 3634 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.07 % Allowed : 7.55 % Favored : 91.38 % 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: 0.62 (0.23), residues: 1351 helix: 1.20 (0.20), residues: 646 sheet: -0.71 (0.44), residues: 125 loop : -0.12 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.004 0.001 HIS A1241 PHE 0.018 0.001 PHE A1327 TYR 0.015 0.001 TYR A 155 ARG 0.011 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 1.443 Fit side-chains REVERT: A 627 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6959 (tp30) REVERT: A 674 GLN cc_start: 0.8255 (tp40) cc_final: 0.8020 (mm110) REVERT: A 879 MET cc_start: 0.7132 (mmt) cc_final: 0.6458 (mtt) REVERT: A 1029 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7658 (pp) outliers start: 12 outliers final: 9 residues processed: 65 average time/residue: 1.8017 time to fit residues: 127.0601 Evaluate side-chains 66 residues out of total 1217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 71 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 112 optimal weight: 0.0470 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15079 Z= 0.174 Angle : 0.502 8.331 21044 Z= 0.270 Chirality : 0.036 0.166 2410 Planarity : 0.003 0.055 2107 Dihedral : 20.595 172.581 3634 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.82 % Allowed : 7.88 % Favored : 91.30 % 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: 0.77 (0.23), residues: 1351 helix: 1.34 (0.21), residues: 647 sheet: -0.65 (0.44), residues: 125 loop : -0.05 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.003 0.001 HIS A 328 PHE 0.017 0.001 PHE A1327 TYR 0.011 0.001 TYR A 155 ARG 0.013 0.000 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 1.476 Fit side-chains REVERT: A 627 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6929 (pt0) REVERT: A 674 GLN cc_start: 0.8243 (tp40) cc_final: 0.8012 (mm110) REVERT: A 879 MET cc_start: 0.7014 (mmt) cc_final: 0.6377 (mtt) REVERT: A 1029 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7514 (pp) outliers start: 9 outliers final: 6 residues processed: 64 average time/residue: 1.7947 time to fit residues: 124.5268 Evaluate side-chains 63 residues out of total 1217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15079 Z= 0.192 Angle : 0.498 7.812 21044 Z= 0.268 Chirality : 0.037 0.164 2410 Planarity : 0.003 0.059 2107 Dihedral : 20.527 172.156 3634 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.82 % Allowed : 8.13 % Favored : 91.05 % 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: 0.86 (0.23), residues: 1351 helix: 1.42 (0.20), residues: 647 sheet: -0.53 (0.45), residues: 123 loop : -0.04 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 476 HIS 0.003 0.001 HIS A 328 PHE 0.016 0.001 PHE A1327 TYR 0.012 0.001 TYR A 155 ARG 0.013 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 1.445 Fit side-chains REVERT: A 627 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6923 (tp30) REVERT: A 674 GLN cc_start: 0.8228 (tp40) cc_final: 0.7997 (mm110) REVERT: A 1029 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7493 (pp) outliers start: 9 outliers final: 4 residues processed: 67 average time/residue: 1.7996 time to fit residues: 130.6877 Evaluate side-chains 62 residues out of total 1217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15079 Z= 0.288 Angle : 0.535 8.490 21044 Z= 0.286 Chirality : 0.039 0.173 2410 Planarity : 0.004 0.063 2107 Dihedral : 20.573 170.535 3634 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.66 % Allowed : 8.37 % Favored : 90.97 % 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: 0.76 (0.23), residues: 1351 helix: 1.32 (0.20), residues: 647 sheet: -0.54 (0.45), residues: 123 loop : -0.07 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 476 HIS 0.004 0.001 HIS A1241 PHE 0.017 0.001 PHE A1327 TYR 0.014 0.001 TYR A 155 ARG 0.013 0.001 ARG A 653 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 1.472 Fit side-chains REVERT: A 627 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6979 (tp30) REVERT: A 674 GLN cc_start: 0.8258 (tp40) cc_final: 0.8022 (mm110) REVERT: A 1029 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7562 (pp) outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 1.8900 time to fit residues: 120.6586 Evaluate side-chains 62 residues out of total 1217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 3.9990 chunk 36 optimal weight: 0.0030 chunk 108 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 118 optimal weight: 0.0980 chunk 49 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.103055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.067507 restraints weight = 47694.469| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.69 r_work: 0.2801 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15079 Z= 0.152 Angle : 0.492 8.082 21044 Z= 0.266 Chirality : 0.036 0.197 2410 Planarity : 0.003 0.058 2107 Dihedral : 20.543 172.559 3634 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.66 % Allowed : 8.54 % Favored : 90.80 % 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: 0.88 (0.23), residues: 1351 helix: 1.45 (0.21), residues: 647 sheet: -0.53 (0.45), residues: 123 loop : -0.05 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.003 0.001 HIS A 328 PHE 0.016 0.001 PHE A1327 TYR 0.010 0.001 TYR A 155 ARG 0.013 0.000 ARG A 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3800.74 seconds wall clock time: 68 minutes 9.09 seconds (4089.09 seconds total)