Starting phenix.real_space_refine on Sat Oct 24 01:37:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mb6_63767/10_2026/9mb6_63767.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mb6_63767/10_2026/9mb6_63767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mb6_63767/10_2026/9mb6_63767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mb6_63767/10_2026/9mb6_63767.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mb6_63767/10_2026/9mb6_63767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mb6_63767/10_2026/9mb6_63767.map" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 162 5.49 5 S 23 5.16 5 C 6800 2.51 5 N 2058 2.21 5 O 2602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11645 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 306 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "C" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 486 Unusual residues: {' AS': 2, ' GS': 2, ' SC': 3} Classifications: {'DNA': 17, 'undetermined': 7} Link IDs: {'rna3p': 16, None: 7} Not linked: pdbres=" SC C 13 " pdbres=" SC C 14 " Not linked: pdbres=" SC C 14 " pdbres=" AS C 15 " Not linked: pdbres=" AS C 15 " pdbres=" AS C 16 " Not linked: pdbres=" AS C 16 " pdbres=" GS C 17 " Not linked: pdbres=" GS C 17 " pdbres=" SC C 18 " ... (remaining 2 not shown) Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Chain: "A" Number of atoms: 8222 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 988, 8214 Classifications: {'peptide': 988} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 963} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 988, 8214 Classifications: {'peptide': 988} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 963} Chain breaks: 3 bond proxies already assigned to first conformer: 8346 Chain: "B" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2092 Classifications: {'RNA': 98} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 49, 'rna3p_pyr': 40} Link IDs: {'rna2p': 9, 'rna3p': 88} Chain: "D" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "D" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 350 Unusual residues: {' GS': 2} Classifications: {'DNA': 15, 'undetermined': 2} Link IDs: {'rna3p': 14, None: 2} Not linked: pdbres=" GS D -2 " pdbres=" GS D -1 " Not linked: pdbres=" GS D -1 " pdbres=" DC D 0 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 4.28, per 1000 atoms: 0.37 Number of scatterers: 11645 At special positions: 0 Unit cell: (91.7706, 128.052, 126.985, 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 162 15.00 O 2602 8.00 N 2058 7.00 C 6800 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 - 3.00 Amino acid : True - 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 769.1 milliseconds 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1894 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 8 sheets defined 50.4% alpha, 10.8% beta 58 base pairs and 91 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 40 through 74 removed outlier: 4.187A pdb=" N ASN A 44 " --> pdb=" O ASN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 101 through 115 removed outlier: 3.510A pdb=" N ARG A 115 " --> pdb=" O HIS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 172 through 191 removed outlier: 4.446A pdb=" N ALA A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 207 Processing helix chain 'A' and resid 225 through 234 Processing helix chain 'A' and resid 250 through 265 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 295 through 304 removed outlier: 3.505A pdb=" N GLU A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 326 through 336 removed outlier: 3.878A pdb=" N HIS A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 344 through 358 Processing helix chain 'A' and resid 360 through 370 removed outlier: 3.628A pdb=" N GLU A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 384 Processing helix chain 'A' and resid 396 through 410 removed outlier: 3.576A pdb=" N ILE A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLU A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 438 through 445 removed outlier: 4.361A pdb=" N ASP A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 469 Processing helix chain 'A' and resid 484 through 513 Processing helix chain 'A' and resid 517 through 530 removed outlier: 3.518A pdb=" N ILE A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 549 Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 577 through 584 Processing helix chain 'A' and resid 587 through 593 Processing helix chain 'A' and resid 600 through 613 Processing helix chain 'A' and resid 619 through 627 Processing helix chain 'A' and resid 635 through 640 removed outlier: 4.251A pdb=" N LYS A 639 " --> pdb=" O PHE A 635 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 635 through 640' Processing helix chain 'A' and resid 649 through 668 Processing helix chain 'A' and resid 677 through 688 removed outlier: 3.888A pdb=" N THR A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 717 removed outlier: 4.015A pdb=" N ALA A 702 " --> pdb=" O TYR A 698 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASP A 712 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N PHE A 713 " --> pdb=" O ALA A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 766 Processing helix chain 'A' and resid 814 through 823 Processing helix chain 'A' and resid 824 through 826 No H-bonds generated for 'chain 'A' and resid 824 through 826' Processing helix chain 'A' and resid 827 through 833 removed outlier: 4.072A pdb=" N HIS A 831 " --> pdb=" O LEU A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 847 removed outlier: 3.889A pdb=" N ILE A 843 " --> pdb=" O LYS A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 862 removed outlier: 3.628A pdb=" N LYS A 856 " --> pdb=" O ASN A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 897 Processing helix chain 'A' and resid 943 through 954 Processing helix chain 'A' and resid 1000 through 1009 Processing sheet with id=AA1, first strand: chain 'A' and resid 672 through 673 removed outlier: 4.108A pdb=" N ASP A 473 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A 16 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL A 33 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR A 18 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA A 31 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 20 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267 Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 315 removed outlier: 4.231A pdb=" N ARG A 314 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 553 through 557 Processing sheet with id=AA5, first strand: chain 'A' and resid 880 through 886 removed outlier: 4.854A pdb=" N ILE A 801 " --> pdb=" O GLY A 884 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYS A 886 " --> pdb=" O THR A 799 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N THR A 799 " --> pdb=" O LYS A 886 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N SER A 790 " --> pdb=" O VAL A 802 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 922 through 929 removed outlier: 6.471A pdb=" N PHE A 914 " --> pdb=" O SER A 965 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER A 965 " --> pdb=" O PHE A 914 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL A 916 " --> pdb=" O ILE A 963 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 933 through 935 Processing sheet with id=AA8, first strand: chain 'A' and resid 1016 through 1019 removed outlier: 4.283A pdb=" N ILE A1016 " --> pdb=" O VAL A 994 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG A 991 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL A 984 " --> pdb=" O ARG A 991 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU A 993 " --> pdb=" O ILE A 982 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 971 " --> pdb=" O TYR A1030 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1088 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 137 hydrogen bonds 270 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 91 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 4533 1.39 - 1.56: 7302 1.56 - 1.74: 317 1.74 - 1.91: 25 1.91 - 2.09: 9 Bond restraints: 12186 Sorted by residual: bond pdb=" OP1 SC C 14 " pdb=" P SC C 14 " ideal model delta sigma weight residual 1.600 1.491 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" OP1 SC C 13 " pdb=" P SC C 13 " ideal model delta sigma weight residual 1.600 1.495 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" N1 DT D 2 " pdb=" C2 DT D 2 " ideal model delta sigma weight residual 1.376 1.417 -0.041 8.00e-03 1.56e+04 2.61e+01 bond pdb=" OP1 SC C 18 " pdb=" P SC C 18 " ideal model delta sigma weight residual 1.600 1.500 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" OP1 AS C 15 " pdb=" P AS C 15 " ideal model delta sigma weight residual 1.588 1.489 0.099 2.00e-02 2.50e+03 2.43e+01 ... (remaining 12181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 16415 4.03 - 8.05: 667 8.05 - 12.08: 47 12.08 - 16.11: 7 16.11 - 20.13: 1 Bond angle restraints: 17137 Sorted by residual: angle pdb=" C4' DA D 4 " pdb=" O4' DA D 4 " pdb=" C1' DA D 4 " ideal model delta sigma weight residual 110.10 101.00 9.10 1.00e+00 1.00e+00 8.29e+01 angle pdb=" O4' DG D 3 " pdb=" C1' DG D 3 " pdb=" C2' DG D 3 " ideal model delta sigma weight residual 105.90 100.27 5.63 8.00e-01 1.56e+00 4.95e+01 angle pdb=" C4' DG C 32 " pdb=" O4' DG C 32 " pdb=" C1' DG C 32 " ideal model delta sigma weight residual 110.10 103.08 7.02 1.00e+00 1.00e+00 4.93e+01 angle pdb=" O5' SC C 18 " pdb=" P SC C 18 " pdb=" S2P SC C 18 " ideal model delta sigma weight residual 112.93 92.80 20.13 3.00e+00 1.11e-01 4.50e+01 angle pdb=" O3' DT D 2 " pdb=" P DG D 3 " pdb=" O5' DG D 3 " ideal model delta sigma weight residual 104.00 91.68 12.32 1.90e+00 2.77e-01 4.20e+01 ... (remaining 17132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 6210 17.66 - 35.33: 788 35.33 - 52.99: 290 52.99 - 70.65: 177 70.65 - 88.31: 33 Dihedral angle restraints: 7498 sinusoidal: 4559 harmonic: 2939 Sorted by residual: dihedral pdb=" O4' U B 89 " pdb=" C2' U B 89 " pdb=" C1' U B 89 " pdb=" C3' U B 89 " ideal model delta sinusoidal sigma weight residual 25.00 -19.87 44.87 1 8.00e+00 1.56e-02 4.37e+01 dihedral pdb=" C4' U B 89 " pdb=" O4' U B 89 " pdb=" C1' U B 89 " pdb=" C2' U B 89 " ideal model delta sinusoidal sigma weight residual 3.00 -39.19 42.19 1 8.00e+00 1.56e-02 3.89e+01 dihedral pdb=" O4' U B 44 " pdb=" C4' U B 44 " pdb=" C3' U B 44 " pdb=" C2' U B 44 " ideal model delta sinusoidal sigma weight residual 24.00 -11.30 35.30 1 8.00e+00 1.56e-02 2.76e+01 ... (remaining 7495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1684 0.129 - 0.258: 260 0.258 - 0.388: 14 0.388 - 0.517: 0 0.517 - 0.646: 3 Chirality restraints: 1961 Sorted by residual: chirality pdb=" P DA D -24 " pdb=" OP1 DA D -24 " pdb=" OP2 DA D -24 " pdb=" O5' DA D -24 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P C B 20 " pdb=" OP1 C B 20 " pdb=" OP2 C B 20 " pdb=" O5' C B 20 " both_signs ideal model delta sigma weight residual True 2.41 -1.82 0.59 2.00e-01 2.50e+01 8.78e+00 chirality pdb=" P G B 0 " pdb=" OP1 G B 0 " pdb=" OP2 G B 0 " pdb=" O5' G B 0 " both_signs ideal model delta sigma weight residual True 2.41 2.98 -0.57 2.00e-01 2.50e+01 8.00e+00 ... (remaining 1958 not shown) Planarity restraints: 1602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1015 " 0.670 9.50e-02 1.11e+02 3.01e-01 6.01e+01 pdb=" NE ARG A1015 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG A1015 " -0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG A1015 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A1015 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA D 4 " -0.083 2.00e-02 2.50e+03 3.71e-02 3.79e+01 pdb=" N9 DA D 4 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DA D 4 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DA D 4 " 0.026 2.00e-02 2.50e+03 pdb=" C5 DA D 4 " 0.016 2.00e-02 2.50e+03 pdb=" C6 DA D 4 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA D 4 " -0.036 2.00e-02 2.50e+03 pdb=" N1 DA D 4 " -0.044 2.00e-02 2.50e+03 pdb=" C2 DA D 4 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DA D 4 " 0.046 2.00e-02 2.50e+03 pdb=" C4 DA D 4 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 165 " -0.432 9.50e-02 1.11e+02 1.95e-01 2.76e+01 pdb=" NE ARG A 165 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 165 " 0.041 2.00e-02 2.50e+03 pdb=" NH1 ARG A 165 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 165 " -0.027 2.00e-02 2.50e+03 ... (remaining 1599 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 903 2.74 - 3.28: 10628 3.28 - 3.82: 20521 3.82 - 4.36: 26502 4.36 - 4.90: 39103 Nonbonded interactions: 97657 Sorted by model distance: nonbonded pdb=" NH2 ARG A1015 " pdb=" O6 DG D 3 " model vdw 2.201 3.120 nonbonded pdb=" OD2 ASP A 412 " pdb=" NH2 ARG A 420 " model vdw 2.256 3.120 nonbonded pdb=" OP1 DA C 25 " pdb=" NH2 ARG A 650 " model vdw 2.262 3.120 nonbonded pdb=" NH2 ARG A 48 " pdb=" OP2 C B 13 " model vdw 2.310 3.120 nonbonded pdb=" OP2 DG C 12 " pdb=" OG1 THR A 787 " model vdw 2.332 3.040 ... (remaining 97652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.240 Find NCS groups from input model: 0.070 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:1.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 0.010 0.109 12196 Z= 0.657 Angle : 1.800 20.135 17137 Z= 1.154 Chirality : 0.091 0.646 1961 Planarity : 0.015 0.301 1602 Dihedral : 19.609 88.313 5604 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.74 % Allowed : 5.81 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.23), residues: 981 helix: -1.00 (0.21), residues: 444 sheet: -1.39 (0.50), residues: 80 loop : -1.44 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.005 ARG A1015 TYR 0.032 0.005 TYR A 698 PHE 0.026 0.005 PHE A 925 TRP 0.023 0.006 TRP A 688 HIS 0.010 0.003 HIS A 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00960 / 0.64 (12186) covalent geometry : angle 1.79969 / 1.15 (17137) hydrogen bonds : bond 0.18208 / 18.20 ( 510) hydrogen bonds : angle 7.43029 / 9.05 ( 1358) Misc. bond : bond 0.04702 / 4.34 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7876 (m-30) cc_final: 0.7625 (t0) REVERT: A 606 LYS cc_start: 0.7943 (ttmm) cc_final: 0.7714 (mtmm) REVERT: A 668 ASN cc_start: 0.7927 (t0) cc_final: 0.7576 (t0) REVERT: A 693 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6458 (tm-30) REVERT: A 855 TYR cc_start: 0.7640 (t80) cc_final: 0.7383 (t80) REVERT: A 943 ASN cc_start: 0.7573 (t0) cc_final: 0.7121 (t0) REVERT: A 955 LYS cc_start: 0.8597 (mttt) cc_final: 0.8123 (tttm) REVERT: A 993 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8004 (tt0) REVERT: A 1004 TYR cc_start: 0.8145 (t80) cc_final: 0.7941 (t80) outliers start: 25 outliers final: 5 residues processed: 241 average time/residue: 0.1433 time to fit residues: 45.6282 Evaluate side-chains 129 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 PRO Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain A residue 993 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106] chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 382 GLN A 394 ASN A 585 ASN A 658 ASN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 HIS A 863 ASN A 986 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.158912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121715 restraints weight = 21211.674| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.42 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12196 Z= 0.204 Angle : 0.694 13.398 17137 Z= 0.392 Chirality : 0.047 0.231 1961 Planarity : 0.005 0.043 1602 Dihedral : 20.433 81.200 3442 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.86 % Allowed : 10.75 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.25), residues: 981 helix: 1.22 (0.24), residues: 449 sheet: -0.79 (0.54), residues: 83 loop : -0.78 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 157 TYR 0.016 0.002 TYR A 882 PHE 0.025 0.002 PHE A 240 TRP 0.015 0.002 TRP A 229 HIS 0.007 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.20 (12186) covalent geometry : angle 0.69436 / 0.39 (17137) hydrogen bonds : bond 0.05585 / 5.24 ( 510) hydrogen bonds : angle 4.73872 / 5.82 ( 1358) Misc. bond : bond 0.00294 / 0.25 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7450 (m-30) cc_final: 0.7125 (m-30) REVERT: A 668 ASN cc_start: 0.7185 (t0) cc_final: 0.6902 (t0) REVERT: A 693 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6754 (tp30) outliers start: 17 outliers final: 8 residues processed: 143 average time/residue: 0.1415 time to fit residues: 27.1346 Evaluate side-chains 113 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain A residue 953 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [52, 85, 11, 107, 1, 27, 39, 0, 29, 74, 87] chunk 52 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 107 optimal weight: 50.0000 chunk 1 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 29 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 943 ASN A 986 ASN A1007 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.157246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.121324 restraints weight = 20043.010| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.89 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12196 Z= 0.180 Angle : 0.619 13.782 17137 Z= 0.350 Chirality : 0.043 0.234 1961 Planarity : 0.004 0.045 1602 Dihedral : 20.291 79.650 3431 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.64 % Allowed : 10.75 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.26), residues: 981 helix: 1.60 (0.24), residues: 452 sheet: -0.46 (0.56), residues: 83 loop : -0.51 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1012 TYR 0.024 0.002 TYR A 855 PHE 0.026 0.002 PHE A 240 TRP 0.015 0.002 TRP A 229 HIS 0.006 0.001 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (12186) covalent geometry : angle 0.61931 / 0.35 (17137) hydrogen bonds : bond 0.04847 / 4.60 ( 510) hydrogen bonds : angle 4.42972 / 5.41 ( 1358) Misc. bond : bond 0.00124 / 0.14 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7415 (m-30) cc_final: 0.7131 (m-30) REVERT: A 668 ASN cc_start: 0.7220 (t0) cc_final: 0.6973 (t0) REVERT: A 693 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6875 (tp30) outliers start: 15 outliers final: 9 residues processed: 123 average time/residue: 0.1381 time to fit residues: 22.6885 Evaluate side-chains 113 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [62, 96, 19, 64, 27, 81, 13, 57, 92, 58, 23] chunk 62 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 13 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN A 695 ASN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 ASN A 888 ASN A1007 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.157540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.120884 restraints weight = 21421.679| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.16 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12196 Z= 0.170 Angle : 0.581 11.610 17137 Z= 0.329 Chirality : 0.041 0.233 1961 Planarity : 0.004 0.044 1602 Dihedral : 20.257 78.574 3431 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.75 % Allowed : 11.29 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.26), residues: 981 helix: 1.72 (0.24), residues: 451 sheet: -0.45 (0.55), residues: 90 loop : -0.46 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 338 TYR 0.023 0.002 TYR A 855 PHE 0.014 0.002 PHE A 925 TRP 0.010 0.001 TRP A 229 HIS 0.005 0.001 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (12186) covalent geometry : angle 0.58061 / 0.33 (17137) hydrogen bonds : bond 0.04428 / 4.12 ( 510) hydrogen bonds : angle 4.33764 / 5.29 ( 1358) Misc. bond : bond 0.00101 / 0.09 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 116 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7006 (ptt-90) REVERT: A 497 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7585 (ttp-110) REVERT: A 668 ASN cc_start: 0.7266 (t0) cc_final: 0.6945 (t0) REVERT: A 693 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6903 (tp30) outliers start: 16 outliers final: 11 residues processed: 123 average time/residue: 0.1388 time to fit residues: 23.0802 Evaluate side-chains 116 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 677 ASN Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [22, 93, 55, 34, 97, 100, 58, 30, 26, 23, 94] chunk 22 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.154866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.118833 restraints weight = 22653.376| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.23 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12196 Z= 0.277 Angle : 0.662 10.599 17137 Z= 0.362 Chirality : 0.046 0.264 1961 Planarity : 0.005 0.046 1602 Dihedral : 20.286 77.458 3431 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.97 % Allowed : 11.73 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.26), residues: 981 helix: 1.35 (0.23), residues: 452 sheet: -0.48 (0.52), residues: 99 loop : -0.58 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 55 TYR 0.025 0.002 TYR A 855 PHE 0.023 0.002 PHE A 925 TRP 0.015 0.002 TRP A 229 HIS 0.009 0.002 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.28 (12186) covalent geometry : angle 0.66182 / 0.36 (17137) hydrogen bonds : bond 0.04972 / 4.61 ( 510) hydrogen bonds : angle 4.43018 / 5.36 ( 1358) Misc. bond : bond 0.00138 / 0.14 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7540 (m-30) cc_final: 0.7298 (m-30) REVERT: A 116 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.6944 (ptt-90) REVERT: A 668 ASN cc_start: 0.7288 (t0) cc_final: 0.7001 (t0) REVERT: A 693 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6964 (tp30) outliers start: 18 outliers final: 9 residues processed: 122 average time/residue: 0.1409 time to fit residues: 23.2945 Evaluate side-chains 114 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 677 ASN Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [77, 34, 69, 38, 41, 5, 67, 97, 43, 66, 57] chunk 77 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.158250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121016 restraints weight = 18233.159| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.04 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12196 Z= 0.130 Angle : 0.538 13.311 17137 Z= 0.309 Chirality : 0.039 0.230 1961 Planarity : 0.004 0.043 1602 Dihedral : 20.226 76.499 3431 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.10 % Allowed : 12.61 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.27), residues: 981 helix: 1.72 (0.24), residues: 452 sheet: -0.44 (0.56), residues: 90 loop : -0.42 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 420 TYR 0.021 0.001 TYR A 855 PHE 0.010 0.001 PHE A 914 TRP 0.008 0.001 TRP A 408 HIS 0.003 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (12186) covalent geometry : angle 0.53839 / 0.31 (17137) hydrogen bonds : bond 0.03996 / 3.68 ( 510) hydrogen bonds : angle 4.23617 / 5.14 ( 1358) Misc. bond : bond 0.00066 / 0.06 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7476 (m-30) cc_final: 0.7224 (m-30) REVERT: A 116 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7045 (ptt-90) REVERT: A 420 ARG cc_start: 0.7192 (mtm110) cc_final: 0.6904 (ttm110) REVERT: A 668 ASN cc_start: 0.7218 (t0) cc_final: 0.6934 (t0) REVERT: A 693 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6946 (tp30) REVERT: A 958 ASN cc_start: 0.8152 (m110) cc_final: 0.7899 (m110) outliers start: 10 outliers final: 7 residues processed: 113 average time/residue: 0.1420 time to fit residues: 21.4938 Evaluate side-chains 108 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain A residue 1007 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [48, 38, 94, 78, 107, 63, 12, 56, 15, 57, 52] chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 107 optimal weight: 50.0000 chunk 63 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.156796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.119557 restraints weight = 21299.816| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.36 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12196 Z= 0.179 Angle : 0.560 11.699 17137 Z= 0.316 Chirality : 0.041 0.236 1961 Planarity : 0.004 0.042 1602 Dihedral : 20.197 75.859 3431 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.43 % Allowed : 12.72 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.26), residues: 981 helix: 1.56 (0.24), residues: 460 sheet: -0.46 (0.55), residues: 90 loop : -0.48 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 420 TYR 0.021 0.002 TYR A 855 PHE 0.015 0.002 PHE A 925 TRP 0.010 0.002 TRP A 408 HIS 0.005 0.001 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (12186) covalent geometry : angle 0.56042 / 0.32 (17137) hydrogen bonds : bond 0.04141 / 3.78 ( 510) hydrogen bonds : angle 4.21521 / 5.13 ( 1358) Misc. bond : bond 0.00091 / 0.09 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7492 (m-30) cc_final: 0.7249 (m-30) REVERT: A 116 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.6988 (ptt-90) REVERT: A 668 ASN cc_start: 0.7260 (t0) cc_final: 0.6964 (t0) REVERT: A 693 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6969 (tp30) outliers start: 13 outliers final: 10 residues processed: 110 average time/residue: 0.1401 time to fit residues: 20.7826 Evaluate side-chains 110 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1034 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [89, 26, 31, 21, 62, 54, 99, 78, 47, 57, 39] chunk 89 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 99 optimal weight: 30.0000 chunk 78 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.156913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121221 restraints weight = 16163.105| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.60 r_work: 0.2818 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12196 Z= 0.176 Angle : 0.563 12.123 17137 Z= 0.315 Chirality : 0.041 0.237 1961 Planarity : 0.004 0.041 1602 Dihedral : 20.195 75.224 3431 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.75 % Allowed : 12.72 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.26), residues: 981 helix: 1.54 (0.24), residues: 460 sheet: -0.50 (0.55), residues: 90 loop : -0.45 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 420 TYR 0.021 0.002 TYR A 855 PHE 0.015 0.001 PHE A 925 TRP 0.010 0.002 TRP A 408 HIS 0.005 0.001 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (12186) covalent geometry : angle 0.56255 / 0.32 (17137) hydrogen bonds : bond 0.04106 / 3.76 ( 510) hydrogen bonds : angle 4.19519 / 5.12 ( 1358) Misc. bond : bond 0.00089 / 0.08 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.8304 (m-30) cc_final: 0.7985 (m-30) REVERT: A 116 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.7301 (ptt-90) REVERT: A 668 ASN cc_start: 0.8045 (t0) cc_final: 0.7638 (t0) REVERT: A 693 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6856 (tp30) REVERT: A 762 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.7460 (t-90) REVERT: A 958 ASN cc_start: 0.8743 (m110) cc_final: 0.8519 (m110) outliers start: 16 outliers final: 10 residues processed: 112 average time/residue: 0.1341 time to fit residues: 20.1813 Evaluate side-chains 112 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain A residue 762 HIS Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1034 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [1, 8, 23, 87, 50, 97, 62, 70, 89, 28, 22] chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 62 optimal weight: 0.0000 chunk 70 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.158253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.121411 restraints weight = 30913.496| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 4.02 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12196 Z= 0.136 Angle : 0.527 12.165 17137 Z= 0.299 Chirality : 0.038 0.215 1961 Planarity : 0.003 0.039 1602 Dihedral : 20.126 74.106 3431 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.32 % Allowed : 13.27 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.27), residues: 981 helix: 1.67 (0.24), residues: 461 sheet: -0.49 (0.54), residues: 90 loop : -0.40 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 420 TYR 0.015 0.001 TYR A 837 PHE 0.011 0.001 PHE A 914 TRP 0.010 0.001 TRP A 408 HIS 0.004 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (12186) covalent geometry : angle 0.52708 / 0.30 (17137) hydrogen bonds : bond 0.03786 / 3.45 ( 510) hydrogen bonds : angle 4.13214 / 4.99 ( 1358) Misc. bond : bond 0.00066 / 0.06 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7135 (ptt-90) REVERT: A 529 MET cc_start: 0.7958 (mmm) cc_final: 0.7706 (mmm) REVERT: A 668 ASN cc_start: 0.7292 (t0) cc_final: 0.6974 (t0) REVERT: A 693 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7006 (tp30) outliers start: 12 outliers final: 6 residues processed: 111 average time/residue: 0.1407 time to fit residues: 21.0531 Evaluate side-chains 105 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1034 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [101, 8, 83, 100, 37, 45, 35, 63, 41, 74, 49] chunk 101 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 ASN A 986 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.156722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.119380 restraints weight = 17813.907| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.00 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12196 Z= 0.184 Angle : 0.570 12.231 17137 Z= 0.316 Chirality : 0.041 0.231 1961 Planarity : 0.004 0.040 1602 Dihedral : 20.130 74.534 3427 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.99 % Allowed : 14.14 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.27), residues: 981 helix: 1.52 (0.24), residues: 463 sheet: -0.46 (0.55), residues: 90 loop : -0.44 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 420 TYR 0.057 0.002 TYR A 855 PHE 0.016 0.001 PHE A 925 TRP 0.010 0.001 TRP A 408 HIS 0.005 0.001 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (12186) covalent geometry : angle 0.57035 / 0.32 (17137) hydrogen bonds : bond 0.04056 / 3.71 ( 510) hydrogen bonds : angle 4.14919 / 5.00 ( 1358) Misc. bond : bond 0.00088 / 0.08 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7136 (ptt-90) REVERT: A 668 ASN cc_start: 0.7271 (t0) cc_final: 0.6960 (t0) REVERT: A 693 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7017 (tp30) outliers start: 9 outliers final: 7 residues processed: 105 average time/residue: 0.1366 time to fit residues: 19.3649 Evaluate side-chains 103 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1034 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [95, 35, 97, 8, 13, 54, 11, 9, 25, 29, 46] chunk 95 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.157274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.119871 restraints weight = 18161.131| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.01 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12196 Z= 0.142 Angle : 0.781 54.717 17137 Z= 0.459 Chirality : 0.040 0.224 1961 Planarity : 0.004 0.044 1602 Dihedral : 20.131 74.573 3427 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.10 % Allowed : 14.14 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.27), residues: 981 helix: 1.56 (0.24), residues: 463 sheet: -0.46 (0.55), residues: 90 loop : -0.42 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 420 TYR 0.030 0.001 TYR A 855 PHE 0.014 0.001 PHE A 925 TRP 0.009 0.001 TRP A 408 HIS 0.004 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (12186) covalent geometry : angle 0.78111 / 0.46 (17137) hydrogen bonds : bond 0.03930 / 3.59 ( 510) hydrogen bonds : angle 4.14513 / 4.99 ( 1358) Misc. bond : bond 0.00073 / 0.06 ( 10) =============================================================================== Job complete usr+sys time: 2342.67 seconds wall clock time: 41 minutes 4.45 seconds (2464.45 seconds total)