Starting phenix.real_space_refine on Mon Dec 11 12:15:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4e_14494/12_2023/7z4e_14494.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4e_14494/12_2023/7z4e_14494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4e_14494/12_2023/7z4e_14494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4e_14494/12_2023/7z4e_14494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4e_14494/12_2023/7z4e_14494.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4e_14494/12_2023/7z4e_14494.pdb" } resolution = 4.14 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= 0.003 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3728 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 138 5.49 5 S 23 5.16 5 C 8436 2.51 5 N 2467 2.21 5 O 3005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 1131": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 14069 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 11089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1357, 11089 Classifications: {'peptide': 1357} Link IDs: {'PTRANS': 35, 'TRANS': 1321} Chain breaks: 1 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1884 Classifications: {'RNA': 88} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 46, 'rna3p_pyr': 28} Link IDs: {'rna2p': 14, 'rna3p': 73} Chain: "C" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 587 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 509 Inner-chain residues flagged as termini: ['pdbres=" DT D -3 "'] Classifications: {'DNA': 25} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 24} Time building chain proxies: 8.04, per 1000 atoms: 0.57 Number of scatterers: 14069 At special positions: 0 Unit cell: (94.9, 131.95, 122.2, 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 23 16.00 P 138 15.00 O 3005 8.00 N 2467 7.00 C 8436 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: 7.06 Conformation dependent library (CDL) restraints added in 2.1 seconds 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 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: 65 helices and 10 sheets defined 53.6% alpha, 8.0% beta 50 base pairs and 85 stacking pairs defined. Time for finding SS restraints: 5.57 Creating SS restraints... Processing helix chain 'B' and resid 59 through 94 removed outlier: 4.121A pdb=" N ARG B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ASN B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLU B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 103 Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 134 through 145 removed outlier: 3.737A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.737A pdb=" N PHE B 164 " --> pdb=" O HIS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 217 through 228 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 270 through 283 Processing helix chain 'B' and resid 286 through 303 Processing helix chain 'B' and resid 317 through 343 Processing helix chain 'B' and resid 346 through 353 removed outlier: 3.727A pdb=" N ASP B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 368 through 383 Proline residue: B 378 - end of helix Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 406 through 410 removed outlier: 4.097A pdb=" N SER B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 removed outlier: 4.269A pdb=" N HIS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'B' and resid 477 through 482 removed outlier: 3.525A pdb=" N VAL B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 495 Processing helix chain 'B' and resid 512 through 525 Processing helix chain 'B' and resid 541 through 552 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.686A pdb=" N TYR B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 612 through 626 removed outlier: 3.604A pdb=" N PHE B 626 " --> pdb=" O THR B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 637 Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 644 through 654 Processing helix chain 'B' and resid 664 through 669 Processing helix chain 'B' and resid 678 through 685 Processing helix chain 'B' and resid 692 through 698 Processing helix chain 'B' and resid 702 through 713 removed outlier: 4.450A pdb=" N GLU B 706 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 727 removed outlier: 3.769A pdb=" N HIS B 723 " --> pdb=" O SER B 719 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 727 " --> pdb=" O HIS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 751 Processing helix chain 'B' and resid 776 through 792 Processing helix chain 'B' and resid 794 through 799 Processing helix chain 'B' and resid 803 through 807 Processing helix chain 'B' and resid 808 through 817 Processing helix chain 'B' and resid 832 through 836 Processing helix chain 'B' and resid 860 through 865 removed outlier: 3.577A pdb=" N GLY B 865 " --> pdb=" O LYS B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 889 removed outlier: 5.950A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N TYR B 882 " --> pdb=" O LYS B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 901 Processing helix chain 'B' and resid 909 through 922 Processing helix chain 'B' and resid 926 through 940 Processing helix chain 'B' and resid 959 through 970 removed outlier: 3.950A pdb=" N VAL B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.345A pdb=" N ALA B 984 " --> pdb=" O ASN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1009 Processing helix chain 'B' and resid 1078 through 1088 Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1152 through 1155 Processing helix chain 'B' and resid 1170 through 1177 Processing helix chain 'B' and resid 1177 through 1186 Processing helix chain 'B' and resid 1191 through 1195 Processing helix chain 'B' and resid 1207 through 1209 No H-bonds generated for 'chain 'B' and resid 1207 through 1209' Processing helix chain 'B' and resid 1229 through 1240 Processing helix chain 'B' and resid 1248 through 1262 Processing helix chain 'B' and resid 1264 through 1281 Processing helix chain 'B' and resid 1283 through 1297 Processing helix chain 'B' and resid 1301 through 1313 Processing helix chain 'B' and resid 1314 through 1316 No H-bonds generated for 'chain 'B' and resid 1314 through 1316' Processing helix chain 'B' and resid 1340 through 1344 Processing sheet with id=AA1, first strand: chain 'B' and resid 954 through 957 Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 46 removed outlier: 3.519A pdb=" N ILE B 43 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 45 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 30 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N GLU B1357 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS B 33 " --> pdb=" O GLU B1357 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ARG B1359 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEU B 35 " --> pdb=" O ARG B1359 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ASP B1361 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B1203 " --> pdb=" O ILE B1348 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER B1202 " --> pdb=" O LEU B1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 507 through 509 removed outlier: 5.541A pdb=" N LEU B 508 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.604A pdb=" N TYR B 529 " --> pdb=" O ALA B 538 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 837 through 840 Processing sheet with id=AA6, first strand: chain 'B' and resid 1049 through 1050 Processing sheet with id=AA7, first strand: chain 'B' and resid 1063 through 1065 Processing sheet with id=AA8, first strand: chain 'B' and resid 1107 through 1111 removed outlier: 6.668A pdb=" N SER B1109 " --> pdb=" O ASP B1135 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ASP B1135 " --> pdb=" O SER B1109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1157 through 1167 removed outlier: 3.516A pdb=" N GLU B1162 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B1166 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR B1141 " --> pdb=" O ILE B1166 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B1196 " --> pdb=" O LEU B1144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1324 through 1326 517 hydrogen bonds defined for protein. 1485 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 123 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 85 stacking parallelities Total time for adding SS restraints: 7.54 Time building geometry restraints manager: 6.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 4323 1.35 - 1.50: 4657 1.50 - 1.65: 5599 1.65 - 1.80: 29 1.80 - 1.95: 15 Bond restraints: 14623 Sorted by residual: bond pdb=" SD MET B1021 " pdb=" CE MET B1021 " ideal model delta sigma weight residual 1.791 1.951 -0.160 2.50e-02 1.60e+03 4.10e+01 bond pdb=" CG MET B1021 " pdb=" SD MET B1021 " ideal model delta sigma weight residual 1.803 1.950 -0.147 2.50e-02 1.60e+03 3.46e+01 bond pdb=" O3' G A 43 " pdb=" P U A 44 " ideal model delta sigma weight residual 1.607 1.651 -0.044 1.50e-02 4.44e+03 8.51e+00 bond pdb=" N LYS B 163 " pdb=" CA LYS B 163 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.54e+00 bond pdb=" N GLU B 102 " pdb=" CA GLU B 102 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.33e-02 5.65e+03 6.69e+00 ... (remaining 14618 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.86: 879 105.86 - 112.88: 8028 112.88 - 119.90: 4934 119.90 - 126.91: 6053 126.91 - 133.93: 447 Bond angle restraints: 20341 Sorted by residual: angle pdb=" N GLU B 627 " pdb=" CA GLU B 627 " pdb=" C GLU B 627 " ideal model delta sigma weight residual 114.75 107.53 7.22 1.26e+00 6.30e-01 3.28e+01 angle pdb=" C ARG B 403 " pdb=" CA ARG B 403 " pdb=" CB ARG B 403 " ideal model delta sigma weight residual 109.53 116.08 -6.55 1.65e+00 3.67e-01 1.58e+01 angle pdb=" N GLN B 402 " pdb=" CA GLN B 402 " pdb=" C GLN B 402 " ideal model delta sigma weight residual 111.14 107.16 3.98 1.08e+00 8.57e-01 1.36e+01 angle pdb=" N ARG B 100 " pdb=" CA ARG B 100 " pdb=" C ARG B 100 " ideal model delta sigma weight residual 110.97 107.40 3.57 1.09e+00 8.42e-01 1.08e+01 angle pdb=" CA LEU B1206 " pdb=" C LEU B1206 " pdb=" N GLU B1207 " ideal model delta sigma weight residual 115.75 120.02 -4.27 1.34e+00 5.57e-01 1.02e+01 ... (remaining 20336 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.26: 7884 21.26 - 42.52: 531 42.52 - 63.78: 320 63.78 - 85.04: 45 85.04 - 106.30: 6 Dihedral angle restraints: 8786 sinusoidal: 4796 harmonic: 3990 Sorted by residual: dihedral pdb=" O4' U A 59 " pdb=" C1' U A 59 " pdb=" N1 U A 59 " pdb=" C2 U A 59 " ideal model delta sinusoidal sigma weight residual -128.00 -66.06 -61.94 1 1.70e+01 3.46e-03 1.76e+01 dihedral pdb=" O4' G A 33 " pdb=" C1' G A 33 " pdb=" N9 G A 33 " pdb=" C4 G A 33 " ideal model delta sinusoidal sigma weight residual 70.00 -2.44 72.44 1 2.00e+01 2.50e-03 1.68e+01 dihedral pdb=" O4' G A 82 " pdb=" C1' G A 82 " pdb=" N9 G A 82 " pdb=" C4 G A 82 " ideal model delta sinusoidal sigma weight residual -90.00 -33.97 -56.03 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 8783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1783 0.039 - 0.077: 411 0.077 - 0.116: 109 0.116 - 0.155: 12 0.155 - 0.194: 4 Chirality restraints: 2319 Sorted by residual: chirality pdb=" C1' U A 23 " pdb=" O4' U A 23 " pdb=" C2' U A 23 " pdb=" N1 U A 23 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.19 2.00e-01 2.50e+01 9.38e-01 chirality pdb=" C1' U A 66 " pdb=" O4' U A 66 " pdb=" C2' U A 66 " pdb=" N1 U A 66 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" C3' C A 20 " pdb=" C4' C A 20 " pdb=" O3' C A 20 " pdb=" C2' C A 20 " both_signs ideal model delta sigma weight residual False -2.48 -2.64 0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 2316 not shown) Planarity restraints: 2088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 21 " -0.009 2.00e-02 2.50e+03 1.41e-02 5.97e+00 pdb=" N9 G A 21 " 0.004 2.00e-02 2.50e+03 pdb=" C8 G A 21 " 0.019 2.00e-02 2.50e+03 pdb=" N7 G A 21 " 0.018 2.00e-02 2.50e+03 pdb=" C5 G A 21 " -0.008 2.00e-02 2.50e+03 pdb=" C6 G A 21 " -0.009 2.00e-02 2.50e+03 pdb=" O6 G A 21 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G A 21 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G A 21 " -0.009 2.00e-02 2.50e+03 pdb=" N2 G A 21 " 0.030 2.00e-02 2.50e+03 pdb=" N3 G A 21 " -0.011 2.00e-02 2.50e+03 pdb=" C4 G A 21 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 20 " -0.024 2.00e-02 2.50e+03 1.47e-02 4.85e+00 pdb=" N1 C A 20 " 0.004 2.00e-02 2.50e+03 pdb=" C2 C A 20 " 0.014 2.00e-02 2.50e+03 pdb=" O2 C A 20 " -0.001 2.00e-02 2.50e+03 pdb=" N3 C A 20 " 0.006 2.00e-02 2.50e+03 pdb=" C4 C A 20 " 0.014 2.00e-02 2.50e+03 pdb=" N4 C A 20 " -0.028 2.00e-02 2.50e+03 pdb=" C5 C A 20 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C A 20 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 24 " -0.023 2.00e-02 2.50e+03 1.30e-02 3.83e+00 pdb=" N1 U A 24 " 0.031 2.00e-02 2.50e+03 pdb=" C2 U A 24 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U A 24 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U A 24 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U A 24 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U A 24 " -0.003 2.00e-02 2.50e+03 pdb=" C5 U A 24 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U A 24 " 0.003 2.00e-02 2.50e+03 ... (remaining 2085 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1078 2.74 - 3.28: 13990 3.28 - 3.82: 25029 3.82 - 4.36: 29663 4.36 - 4.90: 45961 Nonbonded interactions: 115721 Sorted by model distance: nonbonded pdb=" O2' U A 59 " pdb=" OP1 C A 60 " model vdw 2.196 2.440 nonbonded pdb=" OD1 ASP B1267 " pdb=" OH TYR B1294 " model vdw 2.217 2.440 nonbonded pdb=" O ALA B1227 " pdb=" N2 G A 89 " model vdw 2.241 2.520 nonbonded pdb=" O2' U A 56 " pdb=" N2 G A 58 " model vdw 2.243 2.520 nonbonded pdb=" O LYS B 209 " pdb=" OG SER B 213 " model vdw 2.252 2.440 ... (remaining 115716 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 12.070 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 46.760 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 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 : 0.004 0.160 14623 Z= 0.224 Angle : 0.547 7.220 20341 Z= 0.329 Chirality : 0.037 0.194 2319 Planarity : 0.003 0.044 2088 Dihedral : 17.526 106.299 6206 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.64 % Allowed : 5.02 % Favored : 93.34 % 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: 1353 helix: 1.29 (0.21), residues: 667 sheet: -0.28 (0.50), residues: 111 loop : -0.33 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 464 HIS 0.003 0.001 HIS B 328 PHE 0.006 0.001 PHE B 97 TYR 0.007 0.001 TYR B1141 ARG 0.004 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 194 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 5 residues processed: 213 average time/residue: 0.3320 time to fit residues: 97.9268 Evaluate side-chains 99 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 1.771 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4247 time to fit residues: 4.7488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 59 optimal weight: 0.0030 chunk 115 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 341 GLN B 726 ASN ** B 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14623 Z= 0.159 Angle : 0.502 8.674 20341 Z= 0.271 Chirality : 0.035 0.163 2319 Planarity : 0.003 0.052 2088 Dihedral : 20.180 105.983 3323 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.16 % Allowed : 1.81 % Favored : 98.03 % 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: 1.03 (0.23), residues: 1353 helix: 1.50 (0.20), residues: 682 sheet: -0.07 (0.48), residues: 112 loop : -0.07 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 18 HIS 0.004 0.001 HIS B1262 PHE 0.016 0.001 PHE B1313 TYR 0.011 0.001 TYR B1016 ARG 0.004 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 122 average time/residue: 0.2847 time to fit residues: 51.8323 Evaluate side-chains 78 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 1.524 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1731 time to fit residues: 2.2780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 144 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS B 175 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 612 ASN B 726 ASN ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1027 GLN ** B1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1297 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14623 Z= 0.201 Angle : 0.511 7.241 20341 Z= 0.277 Chirality : 0.035 0.150 2319 Planarity : 0.004 0.049 2088 Dihedral : 20.309 105.963 3323 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.08 % Allowed : 2.30 % Favored : 97.62 % 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: 1.16 (0.23), residues: 1353 helix: 1.66 (0.21), residues: 681 sheet: -0.16 (0.58), residues: 77 loop : -0.07 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 18 HIS 0.006 0.001 HIS B1262 PHE 0.016 0.001 PHE B 966 TYR 0.022 0.001 TYR B 136 ARG 0.004 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.2588 time to fit residues: 39.7935 Evaluate side-chains 71 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.376 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 30.0000 chunk 100 optimal weight: 40.0000 chunk 69 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 89 optimal weight: 30.0000 chunk 134 optimal weight: 4.9990 chunk 142 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 overall best weight: 9.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 HIS B 224 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 ASN B 920 GLN ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 14623 Z= 0.468 Angle : 0.774 11.630 20341 Z= 0.414 Chirality : 0.043 0.214 2319 Planarity : 0.005 0.061 2088 Dihedral : 21.393 109.594 3323 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 29.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % 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: 0.09 (0.22), residues: 1353 helix: 0.76 (0.19), residues: 675 sheet: -0.93 (0.49), residues: 90 loop : -0.49 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 464 HIS 0.009 0.003 HIS B1262 PHE 0.024 0.003 PHE B 966 TYR 0.024 0.003 TYR B 373 ARG 0.009 0.001 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2779 time to fit residues: 29.9786 Evaluate side-chains 57 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.498 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 105 optimal weight: 30.0000 chunk 58 optimal weight: 50.0000 chunk 121 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN B 854 ASN B 863 ASN ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1264 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14623 Z= 0.209 Angle : 0.526 7.225 20341 Z= 0.286 Chirality : 0.036 0.161 2319 Planarity : 0.004 0.047 2088 Dihedral : 20.752 105.923 3323 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.08 % Allowed : 1.32 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.23), residues: 1353 helix: 1.28 (0.20), residues: 684 sheet: -0.57 (0.60), residues: 72 loop : -0.34 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 464 HIS 0.004 0.001 HIS B 328 PHE 0.013 0.001 PHE B 375 TYR 0.014 0.001 TYR B1265 ARG 0.006 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 87 average time/residue: 0.2819 time to fit residues: 37.3144 Evaluate side-chains 59 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.492 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 0.9980 chunk 127 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN B 863 ASN ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 14623 Z= 0.349 Angle : 0.645 10.559 20341 Z= 0.347 Chirality : 0.039 0.184 2319 Planarity : 0.004 0.060 2088 Dihedral : 21.063 108.120 3323 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 24.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1353 helix: 1.02 (0.20), residues: 683 sheet: -0.52 (0.60), residues: 72 loop : -0.45 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 464 HIS 0.006 0.002 HIS B 412 PHE 0.020 0.002 PHE B 966 TYR 0.019 0.002 TYR B1265 ARG 0.008 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2803 time to fit residues: 32.6254 Evaluate side-chains 57 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.559 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN B 863 ASN B1252 ASN ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14623 Z= 0.304 Angle : 0.594 9.374 20341 Z= 0.322 Chirality : 0.037 0.169 2319 Planarity : 0.004 0.051 2088 Dihedral : 20.905 107.243 3323 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: 0.35 (0.23), residues: 1353 helix: 1.01 (0.20), residues: 691 sheet: -0.59 (0.60), residues: 75 loop : -0.52 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 464 HIS 0.005 0.002 HIS B 595 PHE 0.015 0.002 PHE B 970 TYR 0.018 0.002 TYR B1265 ARG 0.006 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2660 time to fit residues: 31.3037 Evaluate side-chains 59 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.559 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 30.0000 chunk 84 optimal weight: 40.0000 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 128 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN B 863 ASN ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14623 Z= 0.321 Angle : 0.617 11.233 20341 Z= 0.332 Chirality : 0.038 0.178 2319 Planarity : 0.004 0.075 2088 Dihedral : 20.994 107.773 3323 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 23.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: 0.25 (0.23), residues: 1353 helix: 0.92 (0.20), residues: 691 sheet: -0.81 (0.61), residues: 70 loop : -0.52 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 464 HIS 0.006 0.002 HIS B 595 PHE 0.016 0.002 PHE B 966 TYR 0.019 0.002 TYR B 373 ARG 0.007 0.001 ARG B1122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2577 time to fit residues: 29.5416 Evaluate side-chains 54 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.488 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 79 optimal weight: 50.0000 chunk 57 optimal weight: 30.0000 chunk 103 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN B 863 ASN ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14623 Z= 0.176 Angle : 0.510 8.616 20341 Z= 0.276 Chirality : 0.035 0.174 2319 Planarity : 0.004 0.066 2088 Dihedral : 20.513 104.474 3323 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.23), residues: 1353 helix: 1.40 (0.20), residues: 690 sheet: -0.63 (0.60), residues: 77 loop : -0.36 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 464 HIS 0.005 0.001 HIS B 595 PHE 0.012 0.001 PHE B 105 TYR 0.022 0.001 TYR B1265 ARG 0.004 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2813 time to fit residues: 34.6734 Evaluate side-chains 59 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.624 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 10.0000 chunk 85 optimal weight: 40.0000 chunk 66 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN B 863 ASN ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.6167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14623 Z= 0.287 Angle : 0.593 12.436 20341 Z= 0.318 Chirality : 0.037 0.163 2319 Planarity : 0.004 0.068 2088 Dihedral : 20.742 106.924 3323 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.23), residues: 1353 helix: 1.20 (0.20), residues: 694 sheet: -0.60 (0.60), residues: 75 loop : -0.45 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 464 HIS 0.007 0.002 HIS B 595 PHE 0.020 0.002 PHE B 86 TYR 0.023 0.002 TYR B1265 ARG 0.005 0.000 ARG B 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2746 time to fit residues: 31.3683 Evaluate side-chains 55 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 2.538 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 20.0000 chunk 102 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN B 863 ASN ** B1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.053727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.038878 restraints weight = 128349.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.040051 restraints weight = 70887.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.040744 restraints weight = 49516.804| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14623 Z= 0.273 Angle : 0.579 9.003 20341 Z= 0.313 Chirality : 0.037 0.198 2319 Planarity : 0.004 0.062 2088 Dihedral : 20.708 107.162 3323 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: 0.49 (0.23), residues: 1353 helix: 1.15 (0.20), residues: 694 sheet: -0.63 (0.60), residues: 75 loop : -0.47 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 464 HIS 0.006 0.001 HIS B 595 PHE 0.015 0.002 PHE B 966 TYR 0.022 0.002 TYR B1265 ARG 0.006 0.000 ARG B 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2439.24 seconds wall clock time: 47 minutes 27.87 seconds (2847.87 seconds total)