Starting phenix.real_space_refine on Thu Mar 14 21:38:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibw_35347/03_2024/8ibw_35347.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibw_35347/03_2024/8ibw_35347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibw_35347/03_2024/8ibw_35347.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibw_35347/03_2024/8ibw_35347.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibw_35347/03_2024/8ibw_35347.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibw_35347/03_2024/8ibw_35347.pdb" } resolution = 3.6 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= 0.002 sd= 0.058 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 24 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 125 5.49 5 S 38 5.16 5 C 5750 2.51 5 N 1874 2.21 5 O 2059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ASP 874": "OD1" <-> "OD2" Residue "C TYR 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9848 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 891 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "B" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 872 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "C" Number of atoms: 7250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 922, 7250 Classifications: {'peptide': 922} Link IDs: {'PTRANS': 44, 'TRANS': 877} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 833 Classifications: {'RNA': 39} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 15} Link IDs: {'rna2p': 6, 'rna3p': 32} Chain breaks: 2 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1794 SG CYS C 114 13.182 85.010 80.553 1.00 94.26 S ATOM 1820 SG CYS C 117 12.830 83.352 84.085 1.00 94.75 S ATOM 7643 SG CYS C 934 46.425 52.273 131.118 1.00104.45 S ATOM 7669 SG CYS C 938 49.604 51.093 132.882 1.00108.40 S ATOM 7774 SG CYS C 951 49.287 50.685 129.072 1.00 96.27 S Time building chain proxies: 5.80, per 1000 atoms: 0.59 Number of scatterers: 9848 At special positions: 0 Unit cell: (99.9089, 118.573, 152.608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 38 16.00 P 125 15.00 O 2059 8.00 N 1874 7.00 C 5750 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: 4.89 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1201 " pdb="ZN ZN C1201 " - pdb=" NE2 HIS C 130 " pdb="ZN ZN C1201 " - pdb=" NE2 HIS C 135 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 114 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 117 " pdb=" ZN C1202 " pdb="ZN ZN C1202 " - pdb=" NE2 HIS C 946 " pdb="ZN ZN C1202 " - pdb=" SG CYS C 938 " pdb="ZN ZN C1202 " - pdb=" SG CYS C 934 " pdb="ZN ZN C1202 " - pdb=" SG CYS C 951 " Number of angles added : 5 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 60.2% alpha, 5.4% beta 46 base pairs and 77 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'C' and resid 135 through 143 removed outlier: 3.616A pdb=" N THR C 139 " --> pdb=" O HIS C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 172 Processing helix chain 'C' and resid 175 through 183 removed outlier: 4.023A pdb=" N GLY C 181 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 187 removed outlier: 4.470A pdb=" N GLY C 187 " --> pdb=" O PRO C 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 184 through 187' Processing helix chain 'C' and resid 189 through 198 removed outlier: 3.656A pdb=" N LYS C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 214 Processing helix chain 'C' and resid 261 through 283 Processing helix chain 'C' and resid 306 through 322 Processing helix chain 'C' and resid 324 through 334 removed outlier: 3.612A pdb=" N ALA C 328 " --> pdb=" O CYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 357 removed outlier: 6.173A pdb=" N THR C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Proline residue: C 353 - end of helix Processing helix chain 'C' and resid 365 through 373 Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 413 through 420 removed outlier: 3.520A pdb=" N VAL C 420 " --> pdb=" O GLN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 436 Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.609A pdb=" N GLN C 444 " --> pdb=" O ILE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 469 through 487 removed outlier: 3.595A pdb=" N ILE C 478 " --> pdb=" O HIS C 474 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 479 " --> pdb=" O PHE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 520 Processing helix chain 'C' and resid 532 through 536 removed outlier: 3.513A pdb=" N ASP C 535 " --> pdb=" O LYS C 532 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR C 536 " --> pdb=" O ALA C 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 532 through 536' Processing helix chain 'C' and resid 538 through 549 removed outlier: 4.345A pdb=" N GLU C 544 " --> pdb=" O GLU C 540 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 565 Processing helix chain 'C' and resid 592 through 608 removed outlier: 3.603A pdb=" N ASN C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 599 " --> pdb=" O ILE C 595 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 608 " --> pdb=" O ILE C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 655 Processing helix chain 'C' and resid 719 through 730 Processing helix chain 'C' and resid 733 through 744 Processing helix chain 'C' and resid 744 through 756 removed outlier: 4.234A pdb=" N GLY C 752 " --> pdb=" O ARG C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 779 Processing helix chain 'C' and resid 785 through 791 removed outlier: 4.210A pdb=" N TYR C 789 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS C 790 " --> pdb=" O LYS C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 817 Proline residue: C 808 - end of helix removed outlier: 4.478A pdb=" N GLY C 817 " --> pdb=" O ARG C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 821 Processing helix chain 'C' and resid 823 through 831 removed outlier: 3.714A pdb=" N LYS C 831 " --> pdb=" O ARG C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 849 Processing helix chain 'C' and resid 861 through 870 Processing helix chain 'C' and resid 872 through 877 removed outlier: 4.599A pdb=" N GLU C 877 " --> pdb=" O VAL C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 885 through 889 removed outlier: 3.908A pdb=" N THR C 888 " --> pdb=" O PRO C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 911 Processing helix chain 'C' and resid 916 through 921 Processing helix chain 'C' and resid 943 through 950 Processing helix chain 'C' and resid 953 through 974 removed outlier: 4.421A pdb=" N GLY C 957 " --> pdb=" O ARG C 953 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA C 972 " --> pdb=" O PHE C 968 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1032 removed outlier: 3.614A pdb=" N LYS C1029 " --> pdb=" O GLU C1025 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR C1030 " --> pdb=" O LYS C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1045 Processing helix chain 'C' and resid 1048 through 1052 removed outlier: 3.651A pdb=" N VAL C1052 " --> pdb=" O ALA C1049 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1076 Processing helix chain 'C' and resid 1080 through 1105 removed outlier: 3.797A pdb=" N LEU C1084 " --> pdb=" O ARG C1080 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C1087 " --> pdb=" O THR C1083 " (cutoff:3.500A) Proline residue: C1088 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 112 through 113 removed outlier: 3.763A pdb=" N TRP C 112 " --> pdb=" O PHE C 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 448 through 451 Processing sheet with id=AA3, first strand: chain 'C' and resid 629 through 634 Processing sheet with id=AA4, first strand: chain 'C' and resid 567 through 568 Processing sheet with id=AA5, first strand: chain 'C' and resid 571 through 572 Processing sheet with id=AA6, first strand: chain 'C' and resid 614 through 616 Processing sheet with id=AA7, first strand: chain 'C' and resid 701 through 702 Processing sheet with id=AA8, first strand: chain 'C' and resid 851 through 852 Processing sheet with id=AA9, first strand: chain 'C' and resid 981 through 982 Processing sheet with id=AB1, first strand: chain 'C' and resid 1007 through 1013 removed outlier: 5.932A pdb=" N ILE C1007 " --> pdb=" O THR C1055 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N CYS C1057 " --> pdb=" O ILE C1007 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP C1009 " --> pdb=" O CYS C1057 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE C1059 " --> pdb=" O ASP C1009 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN C1011 " --> pdb=" O ILE C1059 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 371 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 77 stacking parallelities Total time for adding SS restraints: 5.00 Time building geometry restraints manager: 5.25 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: 2673 1.33 - 1.45: 2366 1.45 - 1.57: 4964 1.57 - 1.70: 245 1.70 - 1.82: 54 Bond restraints: 10302 Sorted by residual: bond pdb=" CA LEU C 344 " pdb=" C LEU C 344 " ideal model delta sigma weight residual 1.524 1.484 0.040 1.27e-02 6.20e+03 9.77e+00 bond pdb=" N GLY C 111 " pdb=" CA GLY C 111 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.16e+00 bond pdb=" CA VAL C 340 " pdb=" C VAL C 340 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.27e-02 6.20e+03 4.10e+00 bond pdb=" CA GLY C 341 " pdb=" C GLY C 341 " ideal model delta sigma weight residual 1.514 1.486 0.028 1.41e-02 5.03e+03 4.01e+00 bond pdb=" C4' G D 244 " pdb=" O4' G D 244 " ideal model delta sigma weight residual 1.454 1.429 0.025 1.50e-02 4.44e+03 2.73e+00 ... (remaining 10297 not shown) Histogram of bond angle deviations from ideal: 98.88 - 105.92: 846 105.92 - 112.95: 5573 112.95 - 119.98: 3775 119.98 - 127.02: 3887 127.02 - 134.05: 389 Bond angle restraints: 14470 Sorted by residual: angle pdb=" N LEU C 344 " pdb=" CA LEU C 344 " pdb=" C LEU C 344 " ideal model delta sigma weight residual 111.07 100.88 10.19 1.07e+00 8.73e-01 9.08e+01 angle pdb=" CA GLU C 200 " pdb=" CB GLU C 200 " pdb=" CG GLU C 200 " ideal model delta sigma weight residual 114.10 121.60 -7.50 2.00e+00 2.50e-01 1.41e+01 angle pdb=" O4' G D 244 " pdb=" C4' G D 244 " pdb=" C3' G D 244 " ideal model delta sigma weight residual 106.10 102.40 3.70 1.00e+00 1.00e+00 1.37e+01 angle pdb=" C4' G D 244 " pdb=" O4' G D 244 " pdb=" C1' G D 244 " ideal model delta sigma weight residual 109.70 106.00 3.70 1.00e+00 1.00e+00 1.37e+01 angle pdb=" CB MET C1097 " pdb=" CG MET C1097 " pdb=" SD MET C1097 " ideal model delta sigma weight residual 112.70 122.73 -10.03 3.00e+00 1.11e-01 1.12e+01 ... (remaining 14465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.59: 5324 32.59 - 65.18: 666 65.18 - 97.77: 42 97.77 - 130.36: 1 130.36 - 162.95: 3 Dihedral angle restraints: 6036 sinusoidal: 3404 harmonic: 2632 Sorted by residual: dihedral pdb=" O4' G D 244 " pdb=" C4' G D 244 " pdb=" C3' G D 244 " pdb=" C2' G D 244 " ideal model delta sinusoidal sigma weight residual 24.00 -40.21 64.21 1 8.00e+00 1.56e-02 8.47e+01 dihedral pdb=" C5' G D 244 " pdb=" C4' G D 244 " pdb=" C3' G D 244 " pdb=" O3' G D 244 " ideal model delta sinusoidal sigma weight residual 147.00 85.24 61.76 1 8.00e+00 1.56e-02 7.90e+01 dihedral pdb=" C4' G D 244 " pdb=" C3' G D 244 " pdb=" C2' G D 244 " pdb=" C1' G D 244 " ideal model delta sinusoidal sigma weight residual -35.00 20.94 -55.94 1 8.00e+00 1.56e-02 6.60e+01 ... (remaining 6033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1403 0.058 - 0.115: 211 0.115 - 0.173: 18 0.173 - 0.231: 0 0.231 - 0.289: 1 Chirality restraints: 1633 Sorted by residual: chirality pdb=" CA GLU C 200 " pdb=" N GLU C 200 " pdb=" C GLU C 200 " pdb=" CB GLU C 200 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CB ILE C 746 " pdb=" CA ILE C 746 " pdb=" CG1 ILE C 746 " pdb=" CG2 ILE C 746 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA SER C 343 " pdb=" N SER C 343 " pdb=" C SER C 343 " pdb=" CB SER C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.46e-01 ... (remaining 1630 not shown) Planarity restraints: 1419 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 503 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C LEU C 503 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU C 503 " -0.022 2.00e-02 2.50e+03 pdb=" N GLU C 504 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 904 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.18e+00 pdb=" C VAL C 904 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL C 904 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN C 905 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 123 " -0.025 2.00e-02 2.50e+03 1.55e-02 6.59e+00 pdb=" N9 A D 123 " 0.042 2.00e-02 2.50e+03 pdb=" C8 A D 123 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A D 123 " -0.004 2.00e-02 2.50e+03 pdb=" C5 A D 123 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A D 123 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A D 123 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A D 123 " -0.000 2.00e-02 2.50e+03 pdb=" C2 A D 123 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A D 123 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A D 123 " -0.015 2.00e-02 2.50e+03 ... (remaining 1416 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 119 2.59 - 3.17: 8555 3.17 - 3.75: 17113 3.75 - 4.32: 21764 4.32 - 4.90: 33206 Nonbonded interactions: 80757 Sorted by model distance: nonbonded pdb=" OG SER C 989 " pdb=" OE1 GLU C1035 " model vdw 2.018 2.440 nonbonded pdb=" OD1 ASP C 515 " pdb=" NZ LYS C 519 " model vdw 2.049 2.520 nonbonded pdb=" OP1 DT B 49 " pdb=" NH1 ARG C 188 " model vdw 2.151 2.520 nonbonded pdb=" NH2 ARG C 443 " pdb=" OG1 THR C 565 " model vdw 2.169 2.520 nonbonded pdb=" O ARG C 661 " pdb=" NH2 ARG C 693 " model vdw 2.172 2.520 ... (remaining 80752 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 2.260 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 35.990 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 0.040 10302 Z= 0.274 Angle : 0.729 10.194 14470 Z= 0.415 Chirality : 0.040 0.289 1633 Planarity : 0.006 0.055 1419 Dihedral : 23.494 162.948 4338 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.13 % Favored : 93.54 % Rotamer: Outliers : 0.39 % Allowed : 29.08 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.28), residues: 914 helix: 0.33 (0.24), residues: 503 sheet: -0.60 (0.66), residues: 65 loop : -1.39 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 351 HIS 0.010 0.001 HIS C 673 PHE 0.013 0.001 PHE C 496 TYR 0.027 0.002 TYR C 626 ARG 0.015 0.001 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 1.050 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 69 average time/residue: 0.2185 time to fit residues: 22.1577 Evaluate side-chains 60 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 751 HIS ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10302 Z= 0.211 Angle : 0.614 10.072 14470 Z= 0.329 Chirality : 0.037 0.191 1633 Planarity : 0.004 0.059 1419 Dihedral : 23.865 172.155 2569 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.58 % Favored : 94.09 % Rotamer: Outliers : 2.76 % Allowed : 28.29 % Favored : 68.95 % 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: 0.01 (0.28), residues: 914 helix: 0.91 (0.23), residues: 518 sheet: -0.32 (0.69), residues: 59 loop : -1.30 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 823 HIS 0.006 0.001 HIS C1096 PHE 0.011 0.001 PHE C 496 TYR 0.007 0.001 TYR C 679 ARG 0.008 0.000 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: C 194 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8788 (tttp) REVERT: C 948 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8790 (mp) REVERT: C 1097 MET cc_start: 0.7706 (tmm) cc_final: 0.7424 (tmm) outliers start: 21 outliers final: 7 residues processed: 88 average time/residue: 0.2065 time to fit residues: 26.6579 Evaluate side-chains 76 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 980 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 31 optimal weight: 0.0870 chunk 75 optimal weight: 3.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 641 GLN ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10302 Z= 0.277 Angle : 0.628 8.773 14470 Z= 0.337 Chirality : 0.039 0.185 1633 Planarity : 0.004 0.055 1419 Dihedral : 23.770 169.082 2569 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.13 % Favored : 93.54 % Rotamer: Outliers : 5.13 % Allowed : 26.05 % Favored : 68.82 % 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: 0.12 (0.29), residues: 914 helix: 1.01 (0.24), residues: 516 sheet: -0.26 (0.69), residues: 59 loop : -1.27 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 351 HIS 0.008 0.001 HIS C 751 PHE 0.009 0.001 PHE C 496 TYR 0.019 0.002 TYR C 626 ARG 0.005 0.000 ARG C 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 67 time to evaluate : 0.993 Fit side-chains REVERT: C 167 LEU cc_start: 0.9109 (tp) cc_final: 0.8763 (tp) REVERT: C 194 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8824 (tttp) REVERT: C 410 ASP cc_start: 0.7231 (p0) cc_final: 0.6707 (p0) REVERT: C 948 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8764 (mp) REVERT: C 961 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7993 (ptm160) REVERT: C 1097 MET cc_start: 0.7933 (tmm) cc_final: 0.7565 (tmm) outliers start: 39 outliers final: 21 residues processed: 99 average time/residue: 0.2160 time to fit residues: 31.1797 Evaluate side-chains 85 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 61 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 370 HIS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 686 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 899 THR Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 961 ARG Chi-restraints excluded: chain C residue 1000 SER Chi-restraints excluded: chain C residue 1006 VAL Chi-restraints excluded: chain C residue 1051 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 44 optimal weight: 0.1980 chunk 62 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 641 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10302 Z= 0.156 Angle : 0.564 8.410 14470 Z= 0.302 Chirality : 0.037 0.185 1633 Planarity : 0.004 0.057 1419 Dihedral : 23.638 170.590 2569 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.92 % Favored : 94.75 % Rotamer: Outliers : 2.89 % Allowed : 26.58 % Favored : 70.53 % 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: 0.43 (0.29), residues: 914 helix: 1.28 (0.24), residues: 513 sheet: -0.08 (0.69), residues: 59 loop : -1.16 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 351 HIS 0.008 0.001 HIS C 751 PHE 0.010 0.001 PHE C 496 TYR 0.015 0.001 TYR C 626 ARG 0.005 0.000 ARG C 151 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 71 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: C 194 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8709 (tttp) REVERT: C 410 ASP cc_start: 0.6952 (p0) cc_final: 0.6268 (p0) REVERT: C 948 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8813 (mp) REVERT: C 973 MET cc_start: 0.8092 (mmp) cc_final: 0.7669 (tpp) REVERT: C 1097 MET cc_start: 0.7863 (tmm) cc_final: 0.7461 (tmm) outliers start: 22 outliers final: 16 residues processed: 87 average time/residue: 0.2094 time to fit residues: 26.7530 Evaluate side-chains 80 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 62 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 686 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 1006 VAL Chi-restraints excluded: chain C residue 1051 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 10.0000 chunk 56 optimal weight: 0.0070 chunk 1 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 GLN C 598 ASN ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10302 Z= 0.191 Angle : 0.565 9.110 14470 Z= 0.302 Chirality : 0.036 0.179 1633 Planarity : 0.004 0.054 1419 Dihedral : 23.627 169.381 2569 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.92 % Favored : 94.75 % Rotamer: Outliers : 4.47 % Allowed : 25.26 % Favored : 70.26 % 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: 0.52 (0.29), residues: 914 helix: 1.35 (0.24), residues: 512 sheet: 0.02 (0.70), residues: 59 loop : -1.13 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 351 HIS 0.008 0.001 HIS C 751 PHE 0.011 0.001 PHE C 496 TYR 0.016 0.001 TYR C 626 ARG 0.006 0.000 ARG C1101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 66 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: C 167 LEU cc_start: 0.8988 (tp) cc_final: 0.8685 (tp) REVERT: C 194 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8814 (tttt) REVERT: C 196 GLN cc_start: 0.8343 (tm130) cc_final: 0.8022 (tm-30) REVERT: C 267 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7592 (mm) REVERT: C 472 LEU cc_start: 0.8440 (tp) cc_final: 0.8240 (tp) REVERT: C 948 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8837 (mp) REVERT: C 1097 MET cc_start: 0.7797 (tmm) cc_final: 0.7345 (tmm) outliers start: 34 outliers final: 24 residues processed: 95 average time/residue: 0.2000 time to fit residues: 28.3208 Evaluate side-chains 91 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 64 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 370 HIS Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 686 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 899 THR Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 1000 SER Chi-restraints excluded: chain C residue 1006 VAL Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1051 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 58 optimal weight: 0.0570 chunk 24 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 overall best weight: 2.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10302 Z= 0.271 Angle : 0.613 8.756 14470 Z= 0.326 Chirality : 0.038 0.174 1633 Planarity : 0.004 0.054 1419 Dihedral : 23.720 167.973 2569 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.80 % Favored : 93.87 % Rotamer: Outliers : 4.47 % Allowed : 26.58 % Favored : 68.95 % 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 (0.29), residues: 914 helix: 1.31 (0.24), residues: 508 sheet: -0.15 (0.68), residues: 59 loop : -1.05 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 701 HIS 0.009 0.001 HIS C 751 PHE 0.008 0.001 PHE C 496 TYR 0.026 0.002 TYR C 626 ARG 0.005 0.000 ARG C1101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 67 time to evaluate : 1.008 Fit side-chains REVERT: C 167 LEU cc_start: 0.9031 (tp) cc_final: 0.8724 (tp) REVERT: C 194 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8773 (tttp) REVERT: C 410 ASP cc_start: 0.7505 (p0) cc_final: 0.6808 (p0) REVERT: C 948 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8823 (mp) REVERT: C 1097 MET cc_start: 0.7823 (tmm) cc_final: 0.7293 (tmm) outliers start: 34 outliers final: 25 residues processed: 97 average time/residue: 0.2066 time to fit residues: 29.1260 Evaluate side-chains 91 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 64 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 370 HIS Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 686 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 899 THR Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1000 SER Chi-restraints excluded: chain C residue 1006 VAL Chi-restraints excluded: chain C residue 1051 CYS Chi-restraints excluded: chain C residue 1059 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 83 optimal weight: 0.0670 chunk 55 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10302 Z= 0.183 Angle : 0.578 14.581 14470 Z= 0.306 Chirality : 0.037 0.185 1633 Planarity : 0.004 0.054 1419 Dihedral : 23.662 169.742 2569 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.03 % Favored : 94.64 % Rotamer: Outliers : 3.82 % Allowed : 26.32 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.29), residues: 914 helix: 1.43 (0.24), residues: 506 sheet: -0.13 (0.68), residues: 58 loop : -0.98 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 351 HIS 0.011 0.001 HIS C 751 PHE 0.009 0.001 PHE C 496 TYR 0.022 0.001 TYR C 626 ARG 0.005 0.000 ARG C1101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 69 time to evaluate : 0.971 Fit side-chains REVERT: C 167 LEU cc_start: 0.9001 (tp) cc_final: 0.8720 (tp) REVERT: C 194 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8750 (tttp) REVERT: C 196 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7775 (tm-30) REVERT: C 410 ASP cc_start: 0.7343 (p0) cc_final: 0.6651 (p0) REVERT: C 948 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8926 (mp) REVERT: C 1097 MET cc_start: 0.7893 (tmm) cc_final: 0.7461 (tmm) outliers start: 29 outliers final: 25 residues processed: 94 average time/residue: 0.1929 time to fit residues: 27.3321 Evaluate side-chains 91 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 64 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 370 HIS Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 686 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1000 SER Chi-restraints excluded: chain C residue 1006 VAL Chi-restraints excluded: chain C residue 1059 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.0770 chunk 59 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 GLN ** C 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10302 Z= 0.157 Angle : 0.569 14.613 14470 Z= 0.298 Chirality : 0.036 0.181 1633 Planarity : 0.004 0.055 1419 Dihedral : 23.596 171.220 2569 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.49 % Favored : 95.19 % Rotamer: Outliers : 3.16 % Allowed : 27.50 % Favored : 69.34 % 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: 0.69 (0.29), residues: 914 helix: 1.51 (0.24), residues: 508 sheet: -0.11 (0.67), residues: 59 loop : -1.02 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 152 HIS 0.009 0.001 HIS C 751 PHE 0.008 0.001 PHE C 496 TYR 0.020 0.001 TYR C 626 ARG 0.004 0.000 ARG C1101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 72 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 188 ARG cc_start: 0.7792 (mmt-90) cc_final: 0.7495 (mmm-85) REVERT: C 194 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8675 (tttp) REVERT: C 410 ASP cc_start: 0.7112 (p0) cc_final: 0.6478 (p0) REVERT: C 948 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8754 (mp) REVERT: C 1097 MET cc_start: 0.7889 (tmm) cc_final: 0.7477 (tmm) outliers start: 24 outliers final: 19 residues processed: 94 average time/residue: 0.1922 time to fit residues: 27.1763 Evaluate side-chains 91 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 70 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 686 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1006 VAL Chi-restraints excluded: chain C residue 1059 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 97 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 GLN ** C 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 HIS ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10302 Z= 0.151 Angle : 0.569 14.590 14470 Z= 0.295 Chirality : 0.035 0.179 1633 Planarity : 0.004 0.054 1419 Dihedral : 23.557 171.617 2569 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.49 % Favored : 95.19 % Rotamer: Outliers : 3.03 % Allowed : 27.50 % Favored : 69.47 % 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 (0.29), residues: 914 helix: 1.51 (0.24), residues: 509 sheet: 0.05 (0.68), residues: 59 loop : -1.02 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 152 HIS 0.005 0.001 HIS C1096 PHE 0.008 0.001 PHE C 496 TYR 0.019 0.001 TYR C 626 ARG 0.004 0.000 ARG C1101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 73 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8690 (tttp) REVERT: C 196 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7918 (tm-30) REVERT: C 410 ASP cc_start: 0.7106 (p0) cc_final: 0.6516 (p0) REVERT: C 948 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8662 (mp) REVERT: C 1097 MET cc_start: 0.7982 (tmm) cc_final: 0.7608 (tmm) outliers start: 23 outliers final: 18 residues processed: 92 average time/residue: 0.1863 time to fit residues: 26.2241 Evaluate side-chains 92 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 71 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 686 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1006 VAL Chi-restraints excluded: chain C residue 1059 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 641 GLN ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10302 Z= 0.309 Angle : 0.664 13.087 14470 Z= 0.345 Chirality : 0.039 0.162 1633 Planarity : 0.005 0.055 1419 Dihedral : 23.690 170.255 2569 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.80 % Favored : 93.87 % Rotamer: Outliers : 3.16 % Allowed : 27.63 % Favored : 69.21 % 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: 0.43 (0.29), residues: 914 helix: 1.26 (0.24), residues: 510 sheet: -0.04 (0.70), residues: 59 loop : -1.11 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 701 HIS 0.010 0.001 HIS C 751 PHE 0.013 0.002 PHE C 186 TYR 0.040 0.002 TYR C 626 ARG 0.012 0.001 ARG C 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 64 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: C 167 LEU cc_start: 0.8914 (tp) cc_final: 0.8657 (tp) REVERT: C 410 ASP cc_start: 0.7416 (p0) cc_final: 0.6809 (p0) REVERT: C 948 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8875 (mp) outliers start: 24 outliers final: 22 residues processed: 85 average time/residue: 0.1695 time to fit residues: 22.3786 Evaluate side-chains 86 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 63 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 686 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 899 THR Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1000 SER Chi-restraints excluded: chain C residue 1006 VAL Chi-restraints excluded: chain C residue 1059 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 GLN ** C 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 HIS ** C1104 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 = 0.4074 r_free = 0.4074 target = 0.105948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.079107 restraints weight = 31604.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.081129 restraints weight = 17571.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.082361 restraints weight = 12625.346| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10302 Z= 0.200 Angle : 0.602 12.977 14470 Z= 0.314 Chirality : 0.037 0.175 1633 Planarity : 0.004 0.054 1419 Dihedral : 23.663 173.557 2569 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.14 % Favored : 94.53 % Rotamer: Outliers : 3.29 % Allowed : 27.24 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.29), residues: 914 helix: 1.35 (0.24), residues: 512 sheet: -0.11 (0.68), residues: 59 loop : -1.08 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 152 HIS 0.005 0.001 HIS C1096 PHE 0.016 0.001 PHE C 496 TYR 0.027 0.001 TYR C 626 ARG 0.004 0.000 ARG C1101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1755.76 seconds wall clock time: 32 minutes 37.95 seconds (1957.95 seconds total)