Starting phenix.real_space_refine (version: dev) on Mon Feb 20 09:23:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0y_0584/02_2023/6o0y_0584.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0y_0584/02_2023/6o0y_0584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0y_0584/02_2023/6o0y_0584.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0y_0584/02_2023/6o0y_0584.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0y_0584/02_2023/6o0y_0584.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0y_0584/02_2023/6o0y_0584.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ASP 95": "OD1" <-> "OD2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ARG 467": "NH1" <-> "NH2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ASP 850": "OD1" <-> "OD2" Residue "A ARG 859": "NH1" <-> "NH2" Residue "A ASP 861": "OD1" <-> "OD2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A PHE 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 936": "OD1" <-> "OD2" Residue "A ARG 967": "NH1" <-> "NH2" Residue "A ASP 1135": "OD1" <-> "OD2" Residue "A GLU 1162": "OE1" <-> "OE2" Residue "A ARG 1210": "NH1" <-> "NH2" Residue "A GLU 1225": "OE1" <-> "OE2" Residue "A GLU 1260": "OE1" <-> "OE2" Residue "A ARG 1279": "NH1" <-> "NH2" Residue "A ARG 1298": "NH1" <-> "NH2" Residue "A TYR 1336": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11828 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 8669 Classifications: {'peptide': 1146} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 29, 'TRANS': 1116} Chain breaks: 4 Unresolved non-hydrogen bonds: 761 Unresolved non-hydrogen angles: 916 Unresolved non-hydrogen dihedrals: 609 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 37, 'GLU:plan': 63, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 490 Chain: "B" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2104 Classifications: {'RNA': 98} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 53, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 86} Chain: "C" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 261 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 331 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain breaks: 1 Chain: "c" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 463 Classifications: {'DNA': 23} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 22} Time building chain proxies: 7.60, per 1000 atoms: 0.64 Number of scatterers: 11828 At special positions: 0 Unit cell: (137.104, 126.236, 88.616, 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 15 16.00 P 149 15.00 O 2513 8.00 N 2092 7.00 C 7059 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: 5.62 Conformation dependent library (CDL) restraints added in 1.6 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2182 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 7 sheets defined 51.7% alpha, 7.6% beta 52 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'A' and resid 59 through 92 removed outlier: 3.720A pdb=" N ARG A 70 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 removed outlier: 4.005A pdb=" N GLU A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.590A pdb=" N PHE A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.737A pdb=" N ILE A 350 " --> pdb=" O LYS A 346 " (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: 3.600A pdb=" N MET A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.756A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.411A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.943A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.527A pdb=" N ILE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 444 " --> pdb=" O ILE A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.779A 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 552 Processing helix chain 'A' and resid 560 through 567 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 Processing helix chain 'A' and resid 631 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 652 removed outlier: 3.559A pdb=" N LYS A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.520A pdb=" N ILE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.530A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 776 Processing helix chain 'A' and resid 779 through 791 removed outlier: 4.053A pdb=" N ARG A 783 " --> pdb=" O GLU A 779 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 785 " --> pdb=" O MET A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 798 removed outlier: 3.983A pdb=" N GLU A 798 " --> pdb=" O ILE A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 817 removed outlier: 3.755A pdb=" N LEU A 813 " --> pdb=" O GLU A 809 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR A 814 " --> pdb=" O LYS A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 866 removed outlier: 3.649A pdb=" N ASN A 863 " --> pdb=" O ARG A 859 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 889 removed outlier: 6.169A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A 888 " --> pdb=" O ARG A 884 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA A 889 " --> pdb=" O GLN A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 902 through 905 Processing helix chain 'A' and resid 917 through 940 removed outlier: 4.035A pdb=" N LEU A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A 925 " --> pdb=" O LEU A 921 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.647A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1000 Processing helix chain 'A' and resid 1080 through 1087 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 4.102A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 removed outlier: 3.632A pdb=" N PHE A1181 " --> pdb=" O ASN A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1195 removed outlier: 3.836A pdb=" N ILE A1195 " --> pdb=" O LYS A1192 " (cutoff:3.500A) 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 removed outlier: 3.508A pdb=" N VAL A1233 " --> pdb=" O PRO A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1261 Processing helix chain 'A' and resid 1263 through 1278 removed outlier: 3.825A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A1276 " --> pdb=" O GLN A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1296 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.808A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1317 removed outlier: 4.072A pdb=" N ASN A1317 " --> pdb=" O THR A1314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1314 through 1317' Processing helix chain 'A' and resid 1341 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: 4.459A pdb=" N GLU A 762 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE A 11 " --> pdb=" O GLU A 762 " (cutoff:3.500A) removed outlier: 3.582A 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 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.827A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 528 through 530 removed outlier: 3.694A pdb=" N LYS A 528 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA6, first strand: chain 'A' and resid 1157 through 1167 removed outlier: 3.545A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 3.722A 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 392 hydrogen bonds defined for protein. 1143 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 130 hydrogen bonds 252 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 7.70 Time building geometry restraints manager: 6.04 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: 1912 1.33 - 1.44: 3845 1.44 - 1.56: 6290 1.56 - 1.68: 294 1.68 - 1.80: 28 Bond restraints: 12369 Sorted by residual: bond pdb=" C3' DC C 1 " pdb=" O3' DC C 1 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.87e+00 bond pdb=" C3' A B 38 " pdb=" O3' A B 38 " ideal model delta sigma weight residual 1.417 1.436 -0.019 1.50e-02 4.44e+03 1.67e+00 bond pdb=" C3' A B 8 " pdb=" O3' A B 8 " ideal model delta sigma weight residual 1.417 1.436 -0.019 1.50e-02 4.44e+03 1.64e+00 bond pdb=" O5' DT c 21 " pdb=" C5' DT c 21 " ideal model delta sigma weight residual 1.423 1.385 0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CB ILE A 733 " pdb=" CG2 ILE A 733 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.58e+00 ... (remaining 12364 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.51: 1038 106.51 - 113.36: 6920 113.36 - 120.21: 4657 120.21 - 127.06: 4416 127.06 - 133.91: 409 Bond angle restraints: 17440 Sorted by residual: angle pdb=" O3' A B 42 " pdb=" C3' A B 42 " pdb=" C2' A B 42 " ideal model delta sigma weight residual 113.70 119.97 -6.27 1.50e+00 4.44e-01 1.75e+01 angle pdb=" C3' A B 8 " pdb=" O3' A B 8 " pdb=" P A B 9 " ideal model delta sigma weight residual 120.20 126.00 -5.80 1.50e+00 4.44e-01 1.49e+01 angle pdb=" C3' A B 38 " pdb=" O3' A B 38 " pdb=" P G B 39 " ideal model delta sigma weight residual 120.20 125.78 -5.58 1.50e+00 4.44e-01 1.39e+01 angle pdb=" O3' A B 38 " pdb=" C3' A B 38 " pdb=" C2' A B 38 " ideal model delta sigma weight residual 113.70 119.06 -5.36 1.50e+00 4.44e-01 1.27e+01 angle pdb=" C3' A B 42 " pdb=" O3' A B 42 " pdb=" P G B 43 " ideal model delta sigma weight residual 120.20 125.54 -5.34 1.50e+00 4.44e-01 1.27e+01 ... (remaining 17435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.17: 6633 31.17 - 62.34: 340 62.34 - 93.51: 15 93.51 - 124.68: 0 124.68 - 155.86: 5 Dihedral angle restraints: 6993 sinusoidal: 3624 harmonic: 3369 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 57.44 142.56 1 1.50e+01 4.44e-03 7.65e+01 dihedral pdb=" O4' U B 97 " pdb=" C1' U B 97 " pdb=" N1 U B 97 " pdb=" C2 U B 97 " ideal model delta sinusoidal sigma weight residual -160.00 -73.39 -86.61 1 1.50e+01 4.44e-03 4.01e+01 dihedral pdb=" CA ASN A 612 " pdb=" C ASN A 612 " pdb=" N GLU A 613 " pdb=" CA GLU A 613 " ideal model delta harmonic sigma weight residual -180.00 -155.40 -24.60 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 6990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1810 0.067 - 0.133: 246 0.133 - 0.200: 28 0.200 - 0.266: 4 0.266 - 0.333: 3 Chirality restraints: 2091 Sorted by residual: chirality pdb=" C3' A B 42 " pdb=" C4' A B 42 " pdb=" O3' A B 42 " pdb=" C2' A B 42 " both_signs ideal model delta sigma weight residual False -2.48 -2.14 -0.33 2.00e-01 2.50e+01 2.77e+00 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 -2.17 -0.31 2.00e-01 2.50e+01 2.43e+00 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 -2.17 -0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 2088 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 622 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.35e+00 pdb=" C THR A 622 " 0.053 2.00e-02 2.50e+03 pdb=" O THR A 622 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU A 623 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 617 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.74e+00 pdb=" C GLU A 617 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU A 617 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP A 618 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 619 " -0.015 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" C ILE A 619 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE A 619 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL A 620 " -0.017 2.00e-02 2.50e+03 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3093 2.80 - 3.32: 9597 3.32 - 3.85: 20409 3.85 - 4.37: 22751 4.37 - 4.90: 35911 Nonbonded interactions: 91761 Sorted by model distance: nonbonded pdb=" O2 DC C 1 " pdb=" N2 DG D 40 " model vdw 2.272 2.496 nonbonded pdb=" O TYR A 521 " pdb=" OG1 THR A 525 " model vdw 2.306 2.440 nonbonded pdb=" OG SER A 512 " pdb=" OE2 GLU A 617 " model vdw 2.317 2.440 nonbonded pdb=" O TYR A 25 " pdb=" OH TYR A 988 " model vdw 2.330 2.440 nonbonded pdb=" OH TYR A 373 " pdb=" O LEU A 398 " model vdw 2.352 2.440 ... (remaining 91756 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 149 5.49 5 S 15 5.16 5 C 7059 2.51 5 N 2092 2.21 5 O 2513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 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: 1.640 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: 6.900 Check model and map are aligned: 0.170 Process input model: 40.620 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.130 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 12369 Z= 0.343 Angle : 0.737 10.478 17440 Z= 0.406 Chirality : 0.048 0.333 2091 Planarity : 0.005 0.055 1656 Dihedral : 16.705 155.856 4811 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer Outliers : 0.37 % 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: -4.11 (0.19), residues: 1136 helix: -2.75 (0.15), residues: 537 sheet: -1.14 (0.48), residues: 117 loop : -3.01 (0.22), residues: 482 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 1.637 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 75 average time/residue: 0.2541 time to fit residues: 27.9606 Evaluate side-chains 51 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 1.164 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1033 time to fit residues: 1.8564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 77 ASN A 113 HIS A 402 GLN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 ASN A1177 ASN A1252 ASN A1295 ASN A1308 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 12369 Z= 0.207 Angle : 0.501 7.022 17440 Z= 0.279 Chirality : 0.037 0.193 2091 Planarity : 0.003 0.037 1656 Dihedral : 16.063 157.016 2918 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 0.87 % 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: -2.18 (0.23), residues: 1136 helix: -0.72 (0.20), residues: 558 sheet: -0.66 (0.50), residues: 105 loop : -2.49 (0.25), residues: 473 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 1.273 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 62 average time/residue: 0.2400 time to fit residues: 22.7279 Evaluate side-chains 56 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1176 time to fit residues: 2.5410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 0.0980 chunk 95 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 39 optimal weight: 0.0470 chunk 92 optimal weight: 10.0000 overall best weight: 2.0284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS A 817 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 12369 Z= 0.199 Angle : 0.482 7.466 17440 Z= 0.266 Chirality : 0.036 0.188 2091 Planarity : 0.003 0.030 1656 Dihedral : 15.984 155.009 2918 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 1.12 % 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: -1.32 (0.24), residues: 1136 helix: 0.19 (0.22), residues: 561 sheet: -0.60 (0.48), residues: 114 loop : -2.31 (0.26), residues: 461 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 1.200 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 63 average time/residue: 0.2110 time to fit residues: 21.3511 Evaluate side-chains 54 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 1.210 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1209 time to fit residues: 2.6418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 77 optimal weight: 0.0870 chunk 115 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 12369 Z= 0.195 Angle : 0.480 7.379 17440 Z= 0.262 Chirality : 0.036 0.178 2091 Planarity : 0.003 0.028 1656 Dihedral : 15.921 155.143 2918 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.25), residues: 1136 helix: 0.65 (0.22), residues: 563 sheet: -0.52 (0.48), residues: 114 loop : -2.16 (0.26), residues: 459 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 1.316 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 60 average time/residue: 0.2222 time to fit residues: 21.1985 Evaluate side-chains 56 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1249 time to fit residues: 2.8931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 30.0000 chunk 110 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 12369 Z= 0.322 Angle : 0.552 13.047 17440 Z= 0.296 Chirality : 0.038 0.190 2091 Planarity : 0.003 0.027 1656 Dihedral : 16.073 156.697 2918 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 1.12 % 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: -0.71 (0.25), residues: 1136 helix: 0.79 (0.23), residues: 564 sheet: -0.28 (0.50), residues: 99 loop : -2.13 (0.26), residues: 473 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 1.316 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 60 average time/residue: 0.2044 time to fit residues: 19.6184 Evaluate side-chains 56 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1003 time to fit residues: 2.5075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 102 optimal weight: 0.0470 chunk 56 optimal weight: 7.9990 chunk 10 optimal weight: 0.2980 chunk 40 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 overall best weight: 3.0684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 12369 Z= 0.279 Angle : 0.531 12.005 17440 Z= 0.287 Chirality : 0.038 0.189 2091 Planarity : 0.003 0.027 1656 Dihedral : 16.055 156.456 2918 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer Outliers : 1.49 % 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: -0.58 (0.25), residues: 1136 helix: 0.89 (0.23), residues: 564 sheet: -0.37 (0.49), residues: 106 loop : -2.02 (0.27), residues: 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 1.188 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 58 average time/residue: 0.2309 time to fit residues: 21.3855 Evaluate side-chains 57 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 1.225 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1651 time to fit residues: 3.3933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 76 optimal weight: 40.0000 chunk 74 optimal weight: 0.1980 chunk 56 optimal weight: 8.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 12369 Z= 0.276 Angle : 0.542 14.461 17440 Z= 0.290 Chirality : 0.038 0.189 2091 Planarity : 0.003 0.026 1656 Dihedral : 16.052 156.506 2918 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 0.50 % 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: -0.52 (0.25), residues: 1136 helix: 0.91 (0.23), residues: 564 sheet: -0.30 (0.50), residues: 101 loop : -1.97 (0.27), residues: 471 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 1.371 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 0.2520 time to fit residues: 22.4113 Evaluate side-chains 51 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1116 time to fit residues: 1.8776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 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 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 12369 Z= 0.150 Angle : 0.484 13.194 17440 Z= 0.259 Chirality : 0.036 0.171 2091 Planarity : 0.002 0.027 1656 Dihedral : 15.817 154.085 2918 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.50 % 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: -0.24 (0.25), residues: 1136 helix: 1.16 (0.23), residues: 563 sheet: -0.21 (0.49), residues: 117 loop : -1.90 (0.27), residues: 456 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 1.518 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 58 average time/residue: 0.2426 time to fit residues: 22.3338 Evaluate side-chains 55 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 1.219 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1266 time to fit residues: 2.2637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 103 optimal weight: 0.0870 chunk 107 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 12369 Z= 0.229 Angle : 0.517 12.527 17440 Z= 0.277 Chirality : 0.037 0.176 2091 Planarity : 0.003 0.026 1656 Dihedral : 15.907 155.708 2918 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 0.25 % 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: -0.15 (0.26), residues: 1136 helix: 1.22 (0.23), residues: 563 sheet: -0.13 (0.49), residues: 115 loop : -1.81 (0.28), residues: 458 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 1.178 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 54 average time/residue: 0.2213 time to fit residues: 19.2561 Evaluate side-chains 51 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1199 time to fit residues: 1.8561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 12369 Z= 0.322 Angle : 0.567 12.214 17440 Z= 0.301 Chirality : 0.039 0.187 2091 Planarity : 0.003 0.028 1656 Dihedral : 16.034 156.791 2918 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 0.12 % 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: -0.23 (0.25), residues: 1136 helix: 1.13 (0.23), residues: 563 sheet: 0.06 (0.51), residues: 106 loop : -1.85 (0.27), residues: 467 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 1.213 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 50 average time/residue: 0.2155 time to fit residues: 17.5645 Evaluate side-chains 50 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1066 time to fit residues: 1.6475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 0.0770 chunk 42 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.076471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.055764 restraints weight = 39334.451| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.93 r_work: 0.2695 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 12369 Z= 0.253 Angle : 0.538 12.184 17440 Z= 0.288 Chirality : 0.038 0.186 2091 Planarity : 0.003 0.027 1656 Dihedral : 16.003 156.562 2918 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 0.50 % 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: -0.15 (0.25), residues: 1136 helix: 1.18 (0.23), residues: 563 sheet: 0.17 (0.52), residues: 106 loop : -1.82 (0.27), residues: 467 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: