Starting phenix.real_space_refine on Thu Aug 6 08:42:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pjb_17703/08_2026/8pjb_17703.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pjb_17703/08_2026/8pjb_17703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8pjb_17703/08_2026/8pjb_17703.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pjb_17703/08_2026/8pjb_17703.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pjb_17703/08_2026/8pjb_17703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pjb_17703/08_2026/8pjb_17703.map" model { file = "/net/cci-nas-00/data/ceres_data/8pjb_17703/08_2026/8pjb_17703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pjb_17703/08_2026/8pjb_17703.cif" } resolution = 3.62 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 7765 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 P 11 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 4933 2.51 5 N 1357 2.21 5 O 1490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7840 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7632 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 962, 7621 Classifications: {'peptide': 962} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 915} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 962, 7621 Classifications: {'peptide': 962} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 915} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 7754 Chain: "C" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'RNAv2': 9} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 7} Link IDs: {'rna2p': 1, 'rna3p': 7} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.26, per 1000 atoms: 0.29 Number of scatterers: 7840 At special positions: 0 Unit cell: (87.132, 96.174, 104.394, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 11 15.00 Mg 1 11.99 O 1490 8.00 N 1357 7.00 C 4933 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=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 493.8 milliseconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1840 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 7 sheets defined 52.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 146 through 154 removed outlier: 3.812A pdb=" N ASN A 150 " --> pdb=" O GLN A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 181 removed outlier: 4.085A pdb=" N LYS A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLU A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 242 removed outlier: 3.581A pdb=" N ALA A 227 " --> pdb=" O ASN A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 282 Processing helix chain 'A' and resid 352 through 371 Processing helix chain 'A' and resid 371 through 382 removed outlier: 3.702A pdb=" N ARG A 375 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 400 removed outlier: 4.132A pdb=" N ALA A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 428 removed outlier: 4.281A pdb=" N ALA A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLN A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 487 through 494 Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 509 through 512 removed outlier: 3.589A pdb=" N ARG A 512 " --> pdb=" O ILE A 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 512' Processing helix chain 'A' and resid 513 through 530 Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.567A pdb=" N PHE A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 579 Processing helix chain 'A' and resid 583 through 590 Processing helix chain 'A' and resid 610 through 614 removed outlier: 3.554A pdb=" N LYS A 613 " --> pdb=" O ASN A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 removed outlier: 3.614A pdb=" N LEU A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 651 removed outlier: 3.587A pdb=" N ASN A 651 " --> pdb=" O ILE A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 676 removed outlier: 3.705A pdb=" N THR A 676 " --> pdb=" O PHE A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 701 Processing helix chain 'A' and resid 718 through 721 Processing helix chain 'A' and resid 758 through 768 Processing helix chain 'A' and resid 782 through 789 Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 802 through 813 Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 829 through 843 Processing helix chain 'A' and resid 853 through 862 Processing helix chain 'A' and resid 865 through 878 Processing helix chain 'A' and resid 880 through 890 Processing helix chain 'A' and resid 910 through 915 removed outlier: 3.881A pdb=" N LEU A 914 " --> pdb=" O HIS A 910 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 910 through 915' Processing helix chain 'A' and resid 916 through 919 Processing helix chain 'A' and resid 920 through 939 removed outlier: 3.505A pdb=" N ARG A 934 " --> pdb=" O GLN A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 951 Processing helix chain 'A' and resid 953 through 975 removed outlier: 3.639A pdb=" N GLY A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 removed outlier: 4.125A pdb=" N ILE A 982 " --> pdb=" O GLU A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1008 removed outlier: 3.822A pdb=" N CYS A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1078 Processing helix chain 'A' and resid 1086 through 1088 No H-bonds generated for 'chain 'A' and resid 1086 through 1088' Processing helix chain 'A' and resid 1101 through 1110 Processing helix chain 'A' and resid 1110 through 1125 removed outlier: 4.088A pdb=" N ALA A1114 " --> pdb=" O ALA A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1129 removed outlier: 3.870A pdb=" N ILE A1129 " --> pdb=" O PRO A1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1126 through 1129' Processing helix chain 'A' and resid 1133 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 202 removed outlier: 3.545A pdb=" N PHE A 200 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 221 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 264 removed outlier: 5.911A pdb=" N TYR A 263 " --> pdb=" O ASP A1099 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 329 removed outlier: 4.206A pdb=" N ALA A 329 " --> pdb=" O LEU A 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 474 removed outlier: 3.986A pdb=" N THR A 486 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE A 436 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N CYS A 485 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL A 438 " --> pdb=" O CYS A 485 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASN A 435 " --> pdb=" O HIS A 503 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE A 505 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TYR A 437 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASP A 507 " --> pdb=" O TYR A 437 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR A 439 " --> pdb=" O ASP A 507 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE A 504 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N MET A 538 " --> pdb=" O ILE A 504 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL A 506 " --> pdb=" O MET A 538 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 407 " --> pdb=" O SER A 539 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 567 through 569 removed outlier: 6.504A pdb=" N GLN A 567 " --> pdb=" O CYS A 777 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR A 779 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N PHE A 569 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL A 730 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE A 778 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL A 732 " --> pdb=" O PHE A 778 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA A 655 " --> pdb=" O PHE A 731 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ILE A 733 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 657 " --> pdb=" O ILE A 733 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 737 through 744 Processing sheet with id=AA7, first strand: chain 'A' and resid 1054 through 1056 removed outlier: 8.236A pdb=" N CYS A1063 " --> pdb=" O ALA A1028 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU A1030 " --> pdb=" O CYS A1063 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A1017 " --> pdb=" O LYS A1020 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU A1022 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N HIS A1015 " --> pdb=" O LEU A1022 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 1017 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1295 1.30 - 1.43: 1991 1.43 - 1.56: 4627 1.56 - 1.69: 20 1.69 - 1.81: 73 Bond restraints: 8006 Sorted by residual: bond pdb=" CA SER A 222 " pdb=" CB SER A 222 " ideal model delta sigma weight residual 1.533 1.458 0.075 1.60e-02 3.91e+03 2.17e+01 bond pdb=" CA SER A 892 " pdb=" CB SER A 892 " ideal model delta sigma weight residual 1.530 1.453 0.077 1.69e-02 3.50e+03 2.08e+01 bond pdb=" C PRO A 191 " pdb=" O PRO A 191 " ideal model delta sigma weight residual 1.233 1.177 0.056 1.24e-02 6.50e+03 2.06e+01 bond pdb=" CA ALA A 202 " pdb=" CB ALA A 202 " ideal model delta sigma weight residual 1.533 1.455 0.078 1.72e-02 3.38e+03 2.03e+01 bond pdb=" CA SER A 891 " pdb=" CB SER A 891 " ideal model delta sigma weight residual 1.528 1.469 0.058 1.35e-02 5.49e+03 1.85e+01 ... (remaining 8001 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 10662 3.26 - 6.52: 198 6.52 - 9.78: 16 9.78 - 13.04: 3 13.04 - 16.30: 2 Bond angle restraints: 10881 Sorted by residual: angle pdb=" C3' U C 9 " pdb=" O3' U C 9 " pdb=" P U C 10 " ideal model delta sigma weight residual 119.70 103.40 16.30 1.20e+00 6.94e-01 1.84e+02 angle pdb=" C3' U C 3 " pdb=" O3' U C 3 " pdb=" P C C 4 " ideal model delta sigma weight residual 119.70 107.33 12.37 1.20e+00 6.94e-01 1.06e+02 angle pdb=" C3' C C 2 " pdb=" O3' C C 2 " pdb=" P U C 3 " ideal model delta sigma weight residual 119.70 108.63 11.07 1.20e+00 6.94e-01 8.51e+01 angle pdb=" N ARG A1059 " pdb=" CA ARG A1059 " pdb=" C ARG A1059 " ideal model delta sigma weight residual 112.72 104.35 8.37 1.14e+00 7.69e-01 5.39e+01 angle pdb=" CA GLY A 221 " pdb=" C GLY A 221 " pdb=" N SER A 222 " ideal model delta sigma weight residual 114.58 120.82 -6.24 8.60e-01 1.35e+00 5.26e+01 ... (remaining 10876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4124 17.99 - 35.98: 536 35.98 - 53.97: 186 53.97 - 71.96: 45 71.96 - 89.95: 10 Dihedral angle restraints: 4901 sinusoidal: 2075 harmonic: 2826 Sorted by residual: dihedral pdb=" C4' U C 9 " pdb=" C3' U C 9 " pdb=" C2' U C 9 " pdb=" C1' U C 9 " ideal model delta sinusoidal sigma weight residual 36.34 -37.22 73.56 1 3.10e+00 1.04e-01 7.16e+02 dihedral pdb=" C4' U C 10 " pdb=" C3' U C 10 " pdb=" C2' U C 10 " pdb=" C1' U C 10 " ideal model delta sinusoidal sigma weight residual 36.34 -30.74 67.08 1 3.10e+00 1.04e-01 6.10e+02 dihedral pdb=" O4' U C 10 " pdb=" C4' U C 10 " pdb=" C3' U C 10 " pdb=" C2' U C 10 " ideal model delta sinusoidal sigma weight residual -35.15 29.50 -64.65 1 4.00e+00 6.25e-02 3.43e+02 ... (remaining 4898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 1214 0.160 - 0.319: 29 0.319 - 0.479: 3 0.479 - 0.638: 4 0.638 - 0.798: 1 Chirality restraints: 1251 Sorted by residual: chirality pdb=" P C C 2 " pdb=" OP1 C C 2 " pdb=" OP2 C C 2 " pdb=" O5' C C 2 " both_signs ideal model delta sigma weight residual True 2.17 -2.97 -0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" P C C 4 " pdb=" OP1 C C 4 " pdb=" OP2 C C 4 " pdb=" O5' C C 4 " both_signs ideal model delta sigma weight residual True 2.17 -2.77 -0.60 2.00e-01 2.50e+01 9.01e+00 chirality pdb=" P U C 3 " pdb=" OP1 U C 3 " pdb=" OP2 U C 3 " pdb=" O5' U C 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.77 -0.60 2.00e-01 2.50e+01 9.00e+00 ... (remaining 1248 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 905 " 1.064 9.50e-02 1.11e+02 4.77e-01 1.37e+02 pdb=" NE ARG A 905 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG A 905 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 905 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 905 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 590 " -0.989 9.50e-02 1.11e+02 4.43e-01 1.19e+02 pdb=" NE ARG A 590 " 0.059 2.00e-02 2.50e+03 pdb=" CZ ARG A 590 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 590 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 590 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 198 " -0.881 9.50e-02 1.11e+02 3.95e-01 9.45e+01 pdb=" NE ARG A 198 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A 198 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 198 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 198 " -0.024 2.00e-02 2.50e+03 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 168 2.66 - 3.22: 7370 3.22 - 3.78: 12253 3.78 - 4.34: 16148 4.34 - 4.90: 26440 Nonbonded interactions: 62379 Sorted by model distance: nonbonded pdb=" OG1 THR A 414 " pdb=" OD2 ASP A 507 " model vdw 2.096 3.040 nonbonded pdb=" OE1 GLN A 621 " pdb=" NH2 ARG A 624 " model vdw 2.266 3.120 nonbonded pdb=" O GLN A 332 " pdb=" OH TYR A 479 " model vdw 2.282 3.040 nonbonded pdb=" OE1 GLN A 440 " pdb=" OG SER A 445 " model vdw 2.296 3.040 nonbonded pdb=" OG ASER A1070 " pdb=" NE2 GLN A1073 " model vdw 2.316 3.120 ... (remaining 62374 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=0.00 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.260 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 8006 Z= 0.354 Angle : 0.991 16.296 10881 Z= 0.618 Chirality : 0.072 0.798 1251 Planarity : 0.026 0.477 1371 Dihedral : 18.597 89.948 3061 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 1.15 % Allowed : 5.65 % Favored : 93.20 % Rotamer: Outliers : 4.25 % Allowed : 22.67 % Favored : 73.08 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 2.13 % 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: -0.17 (0.28), residues: 958 helix: 1.03 (0.25), residues: 443 sheet: -0.98 (0.43), residues: 148 loop : -1.08 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 867 TYR 0.015 0.002 TYR A 550 PHE 0.029 0.002 PHE A 240 TRP 0.014 0.001 TRP A 932 HIS 0.007 0.001 HIS A 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.35 ( 8006) covalent geometry : angle 0.99070 / 0.62 (10881) hydrogen bonds : bond 0.12888 / 8.41 ( 357) hydrogen bonds : angle 5.43823 / 3.90 ( 1017) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 10 residues processed: 194 average time/residue: 0.1005 time to fit residues: 26.2192 Evaluate side-chains 123 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1057 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 440 GLN A1037 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.073593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.057944 restraints weight = 47206.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.060700 restraints weight = 21314.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.062667 restraints weight = 12974.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.064063 restraints weight = 9138.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.065042 restraints weight = 7015.812| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8006 Z= 0.148 Angle : 0.824 14.409 10881 Z= 0.386 Chirality : 0.052 0.488 1251 Planarity : 0.006 0.135 1371 Dihedral : 7.715 67.699 1189 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.54 % Favored : 94.04 % Rotamer: Outliers : 3.19 % Allowed : 26.80 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.08 (0.27), residues: 958 helix: 0.95 (0.24), residues: 456 sheet: -0.58 (0.46), residues: 139 loop : -0.73 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 362 TYR 0.021 0.002 TYR A 420 PHE 0.034 0.001 PHE A 155 TRP 0.038 0.002 TRP A 328 HIS 0.010 0.002 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 8006) covalent geometry : angle 0.82418 / 0.39 (10881) hydrogen bonds : bond 0.03835 / 2.48 ( 357) hydrogen bonds : angle 4.47172 / 3.24 ( 1017) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8363 (p) REVERT: A 525 ASP cc_start: 0.8804 (t70) cc_final: 0.8551 (t0) REVERT: A 627 MET cc_start: 0.9197 (tmm) cc_final: 0.8188 (tpp) REVERT: A 645 MET cc_start: 0.8865 (tmm) cc_final: 0.8652 (tmm) REVERT: A 670 MET cc_start: 0.8925 (ttm) cc_final: 0.8422 (tmm) REVERT: A 697 ASP cc_start: 0.9003 (m-30) cc_final: 0.8680 (t0) REVERT: A 884 MET cc_start: 0.8998 (tpp) cc_final: 0.8409 (mmm) REVERT: A 954 MET cc_start: 0.8568 (ttm) cc_final: 0.8303 (tpp) REVERT: A 957 MET cc_start: 0.9178 (mmm) cc_final: 0.8724 (tpp) REVERT: A 969 ASP cc_start: 0.9434 (t0) cc_final: 0.9030 (m-30) REVERT: A 1005 CYS cc_start: 0.8530 (m) cc_final: 0.8312 (m) REVERT: A 1030 LEU cc_start: 0.9267 (mt) cc_final: 0.9045 (tp) REVERT: A 1054 GLU cc_start: 0.8690 (tt0) cc_final: 0.8346 (tt0) REVERT: A 1131 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8430 (ptp-110) outliers start: 26 outliers final: 17 residues processed: 148 average time/residue: 0.0747 time to fit residues: 15.8625 Evaluate side-chains 132 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 38 optimal weight: 0.0470 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 693 GLN A1094 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.073818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.058141 restraints weight = 52930.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.060954 restraints weight = 22457.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.062951 restraints weight = 13313.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.064325 restraints weight = 9268.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.065311 restraints weight = 7128.472| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8006 Z= 0.129 Angle : 0.730 10.931 10881 Z= 0.347 Chirality : 0.046 0.323 1251 Planarity : 0.005 0.115 1371 Dihedral : 7.137 57.473 1175 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.50 % Favored : 95.19 % Rotamer: Outliers : 3.90 % Allowed : 25.62 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.24 (0.28), residues: 958 helix: 1.11 (0.24), residues: 454 sheet: -0.27 (0.44), residues: 154 loop : -0.80 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1080 TYR 0.021 0.002 TYR A 189 PHE 0.024 0.001 PHE A 155 TRP 0.020 0.002 TRP A 328 HIS 0.005 0.001 HIS A 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 8006) covalent geometry : angle 0.72989 / 0.35 (10881) hydrogen bonds : bond 0.03455 / 2.25 ( 357) hydrogen bonds : angle 4.17179 / 3.05 ( 1017) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8713 (mmmt) REVERT: A 328 TRP cc_start: 0.8105 (t60) cc_final: 0.7745 (t60) REVERT: A 440 GLN cc_start: 0.8453 (mm110) cc_final: 0.7743 (mt0) REVERT: A 645 MET cc_start: 0.8772 (tmm) cc_final: 0.8507 (tmm) REVERT: A 663 TRP cc_start: 0.8996 (t-100) cc_final: 0.8680 (t-100) REVERT: A 670 MET cc_start: 0.8893 (ttm) cc_final: 0.8397 (tmm) REVERT: A 694 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.8995 (tt) REVERT: A 697 ASP cc_start: 0.8941 (OUTLIER) cc_final: 0.8620 (p0) REVERT: A 718 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.8163 (p0) REVERT: A 884 MET cc_start: 0.8863 (tpp) cc_final: 0.8499 (mmm) REVERT: A 957 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8733 (tpp) REVERT: A 998 ASP cc_start: 0.8602 (m-30) cc_final: 0.8311 (m-30) REVERT: A 1054 GLU cc_start: 0.8751 (tt0) cc_final: 0.8408 (tt0) REVERT: A 1064 LYS cc_start: 0.9288 (tptp) cc_final: 0.9059 (tppp) REVERT: A 1131 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8689 (ptp90) outliers start: 32 outliers final: 18 residues processed: 149 average time/residue: 0.0602 time to fit residues: 13.1029 Evaluate side-chains 139 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 957 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.0770 chunk 16 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 38 optimal weight: 0.1980 chunk 71 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1094 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.073847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.058610 restraints weight = 45080.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.061253 restraints weight = 20725.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.063135 restraints weight = 12773.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.064389 restraints weight = 9107.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.065384 restraints weight = 7136.850| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8006 Z= 0.124 Angle : 0.726 9.648 10881 Z= 0.345 Chirality : 0.046 0.268 1251 Planarity : 0.006 0.105 1371 Dihedral : 6.588 56.924 1171 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.39 % Favored : 95.29 % Rotamer: Outliers : 2.95 % Allowed : 26.80 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.28 (0.27), residues: 958 helix: 1.18 (0.24), residues: 453 sheet: -0.21 (0.43), residues: 152 loop : -0.87 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 587 TYR 0.033 0.001 TYR A 420 PHE 0.027 0.001 PHE A 898 TRP 0.027 0.002 TRP A 949 HIS 0.003 0.001 HIS A 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 8006) covalent geometry : angle 0.72559 / 0.34 (10881) hydrogen bonds : bond 0.03262 / 2.14 ( 357) hydrogen bonds : angle 4.16875 / 3.05 ( 1017) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9053 (mmmt) cc_final: 0.8446 (mmmt) REVERT: A 218 ARG cc_start: 0.8638 (mpt-90) cc_final: 0.8411 (mpt-90) REVERT: A 414 THR cc_start: 0.8840 (m) cc_final: 0.8212 (p) REVERT: A 440 GLN cc_start: 0.8419 (mm110) cc_final: 0.7683 (mt0) REVERT: A 538 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7582 (tmm) REVERT: A 627 MET cc_start: 0.9162 (tmm) cc_final: 0.8605 (tmm) REVERT: A 645 MET cc_start: 0.8870 (tmm) cc_final: 0.8617 (tmm) REVERT: A 663 TRP cc_start: 0.9004 (t-100) cc_final: 0.8716 (t-100) REVERT: A 670 MET cc_start: 0.8823 (ttm) cc_final: 0.8369 (tmm) REVERT: A 697 ASP cc_start: 0.8992 (m-30) cc_final: 0.8647 (p0) REVERT: A 789 LEU cc_start: 0.9381 (mt) cc_final: 0.9157 (mt) REVERT: A 884 MET cc_start: 0.8830 (tpp) cc_final: 0.8507 (mmm) REVERT: A 954 MET cc_start: 0.8276 (tpp) cc_final: 0.7744 (tpp) REVERT: A 957 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8839 (tpp) REVERT: A 969 ASP cc_start: 0.9398 (t0) cc_final: 0.8992 (m-30) REVERT: A 998 ASP cc_start: 0.8427 (m-30) cc_final: 0.8191 (m-30) REVERT: A 1054 GLU cc_start: 0.8860 (tt0) cc_final: 0.8522 (tt0) REVERT: A 1131 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8725 (ptp90) outliers start: 24 outliers final: 18 residues processed: 137 average time/residue: 0.0622 time to fit residues: 12.3280 Evaluate side-chains 132 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 957 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1094 ASN Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 6 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 0.0010 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 693 GLN A1094 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.070264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.053722 restraints weight = 76654.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.056644 restraints weight = 27867.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.058683 restraints weight = 15899.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.060170 restraints weight = 10931.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.061155 restraints weight = 8309.371| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 0.048 8006 Z= 0.194 Angle : 0.736 9.392 10881 Z= 0.353 Chirality : 0.046 0.249 1251 Planarity : 0.005 0.101 1371 Dihedral : 6.478 56.402 1170 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.81 % Favored : 94.98 % Rotamer: Outliers : 3.66 % Allowed : 25.62 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.29 (0.28), residues: 958 helix: 1.23 (0.24), residues: 453 sheet: -0.42 (0.41), residues: 168 loop : -0.83 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 587 TYR 0.015 0.002 TYR A 420 PHE 0.018 0.001 PHE A 898 TRP 0.043 0.003 TRP A 328 HIS 0.006 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 ( 8006) covalent geometry : angle 0.73561 / 0.35 (10881) hydrogen bonds : bond 0.03509 / 2.30 ( 357) hydrogen bonds : angle 4.33542 / 3.19 ( 1017) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.8953 (mmmt) cc_final: 0.8705 (mmmt) REVERT: A 219 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7576 (mm-30) REVERT: A 440 GLN cc_start: 0.8550 (mm110) cc_final: 0.7726 (mt0) REVERT: A 627 MET cc_start: 0.9192 (tmm) cc_final: 0.8612 (tmm) REVERT: A 634 ASP cc_start: 0.9081 (p0) cc_final: 0.8871 (t0) REVERT: A 645 MET cc_start: 0.8868 (tmm) cc_final: 0.8600 (tmm) REVERT: A 663 TRP cc_start: 0.9231 (t-100) cc_final: 0.8875 (t-100) REVERT: A 697 ASP cc_start: 0.8994 (m-30) cc_final: 0.8695 (p0) REVERT: A 718 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8159 (p0) REVERT: A 789 LEU cc_start: 0.9494 (mt) cc_final: 0.9256 (mt) REVERT: A 884 MET cc_start: 0.8927 (tpp) cc_final: 0.8605 (mmm) REVERT: A 898 PHE cc_start: 0.8856 (m-80) cc_final: 0.8539 (m-80) REVERT: A 905 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7811 (pmt-80) REVERT: A 998 ASP cc_start: 0.8541 (m-30) cc_final: 0.8297 (m-30) REVERT: A 1131 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8775 (ptp90) outliers start: 30 outliers final: 17 residues processed: 123 average time/residue: 0.0639 time to fit residues: 11.3744 Evaluate side-chains 121 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1094 ASN Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 65 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1094 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.071574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.055612 restraints weight = 58354.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.058388 restraints weight = 24276.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.060383 restraints weight = 14395.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.061791 restraints weight = 10057.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.062667 restraints weight = 7729.978| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8006 Z= 0.135 Angle : 0.712 9.257 10881 Z= 0.341 Chirality : 0.045 0.232 1251 Planarity : 0.005 0.098 1371 Dihedral : 6.271 56.561 1168 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.92 % Favored : 94.87 % Rotamer: Outliers : 3.90 % Allowed : 25.38 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.35 (0.28), residues: 958 helix: 1.31 (0.24), residues: 453 sheet: -0.38 (0.42), residues: 163 loop : -0.83 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 470 TYR 0.015 0.001 TYR A 420 PHE 0.034 0.001 PHE A 155 TRP 0.038 0.002 TRP A 328 HIS 0.006 0.001 HIS A 922 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 8006) covalent geometry : angle 0.71196 / 0.34 (10881) hydrogen bonds : bond 0.03267 / 2.13 ( 357) hydrogen bonds : angle 4.20716 / 3.10 ( 1017) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8764 (mmmt) REVERT: A 218 ARG cc_start: 0.8608 (mpt-90) cc_final: 0.8392 (mpt-90) REVERT: A 440 GLN cc_start: 0.8545 (mm110) cc_final: 0.7764 (mt0) REVERT: A 472 GLU cc_start: 0.6905 (mp0) cc_final: 0.6608 (mp0) REVERT: A 508 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8012 (mm-30) REVERT: A 526 MET cc_start: 0.9318 (mmm) cc_final: 0.8986 (mmm) REVERT: A 538 MET cc_start: 0.7872 (tmm) cc_final: 0.6845 (tmm) REVERT: A 627 MET cc_start: 0.9184 (tmm) cc_final: 0.8547 (tmm) REVERT: A 645 MET cc_start: 0.8832 (tmm) cc_final: 0.8599 (tmm) REVERT: A 663 TRP cc_start: 0.9155 (t-100) cc_final: 0.8865 (t-100) REVERT: A 697 ASP cc_start: 0.9007 (m-30) cc_final: 0.8697 (p0) REVERT: A 718 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.8132 (p0) REVERT: A 789 LEU cc_start: 0.9508 (mt) cc_final: 0.9236 (mt) REVERT: A 884 MET cc_start: 0.8902 (tpp) cc_final: 0.8580 (mmm) REVERT: A 898 PHE cc_start: 0.8828 (m-80) cc_final: 0.8543 (m-80) REVERT: A 905 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7826 (pmt-80) REVERT: A 954 MET cc_start: 0.8569 (tpp) cc_final: 0.8026 (tpp) REVERT: A 969 ASP cc_start: 0.9388 (t0) cc_final: 0.8995 (m-30) REVERT: A 998 ASP cc_start: 0.8445 (m-30) cc_final: 0.8192 (m-30) REVERT: A 1131 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8760 (ptp90) outliers start: 32 outliers final: 20 residues processed: 132 average time/residue: 0.0622 time to fit residues: 11.5291 Evaluate side-chains 131 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1094 ASN Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 82 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 chunk 20 optimal weight: 0.0970 chunk 70 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 89 optimal weight: 0.0000 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 GLN A 966 GLN A1094 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.072292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.055918 restraints weight = 72732.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.058953 restraints weight = 26693.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.061079 restraints weight = 15072.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.062564 restraints weight = 10235.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.063589 restraints weight = 7760.202| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8006 Z= 0.121 Angle : 0.721 9.440 10881 Z= 0.345 Chirality : 0.045 0.240 1251 Planarity : 0.005 0.097 1371 Dihedral : 6.166 56.744 1168 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.67 % Rotamer: Outliers : 3.66 % Allowed : 26.21 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.43 (0.28), residues: 958 helix: 1.39 (0.24), residues: 452 sheet: -0.37 (0.43), residues: 156 loop : -0.80 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 524 TYR 0.012 0.001 TYR A 420 PHE 0.032 0.001 PHE A 155 TRP 0.016 0.001 TRP A 949 HIS 0.006 0.001 HIS A 922 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 8006) covalent geometry : angle 0.72095 / 0.35 (10881) hydrogen bonds : bond 0.03074 / 2.01 ( 357) hydrogen bonds : angle 4.15761 / 3.08 ( 1017) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 TYR cc_start: 0.8317 (m-80) cc_final: 0.7626 (m-10) REVERT: A 440 GLN cc_start: 0.8504 (mm110) cc_final: 0.7756 (mt0) REVERT: A 508 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7938 (mm-30) REVERT: A 538 MET cc_start: 0.7914 (tmm) cc_final: 0.6918 (tmm) REVERT: A 541 THR cc_start: 0.9395 (OUTLIER) cc_final: 0.9149 (p) REVERT: A 627 MET cc_start: 0.9147 (tmm) cc_final: 0.8492 (tmm) REVERT: A 645 MET cc_start: 0.8847 (tmm) cc_final: 0.8593 (tmm) REVERT: A 663 TRP cc_start: 0.9128 (t-100) cc_final: 0.8849 (t-100) REVERT: A 697 ASP cc_start: 0.9011 (m-30) cc_final: 0.8713 (p0) REVERT: A 789 LEU cc_start: 0.9474 (mt) cc_final: 0.9117 (mt) REVERT: A 884 MET cc_start: 0.8834 (tpp) cc_final: 0.8493 (mmm) REVERT: A 898 PHE cc_start: 0.8821 (m-80) cc_final: 0.8538 (m-80) REVERT: A 905 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7828 (pmt-80) REVERT: A 998 ASP cc_start: 0.8382 (m-30) cc_final: 0.8123 (m-30) REVERT: A 1054 GLU cc_start: 0.8720 (tt0) cc_final: 0.8327 (tm-30) REVERT: A 1131 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8780 (ptp90) outliers start: 30 outliers final: 18 residues processed: 131 average time/residue: 0.0696 time to fit residues: 13.1430 Evaluate side-chains 127 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 718 ASN A1037 ASN A1094 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.069585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.053571 restraints weight = 67720.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.056384 restraints weight = 25449.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.058404 restraints weight = 14606.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.059758 restraints weight = 10038.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.060730 restraints weight = 7698.733| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8006 Z= 0.180 Angle : 0.757 9.264 10881 Z= 0.362 Chirality : 0.046 0.222 1251 Planarity : 0.005 0.096 1371 Dihedral : 6.142 56.654 1168 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.92 % Favored : 94.87 % Rotamer: Outliers : 3.54 % Allowed : 26.09 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.46 (0.28), residues: 958 helix: 1.45 (0.24), residues: 453 sheet: -0.49 (0.41), residues: 168 loop : -0.75 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 524 TYR 0.016 0.001 TYR A1009 PHE 0.027 0.001 PHE A 155 TRP 0.025 0.002 TRP A 932 HIS 0.005 0.001 HIS A 922 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 8006) covalent geometry : angle 0.75711 / 0.36 (10881) hydrogen bonds : bond 0.03360 / 2.22 ( 357) hydrogen bonds : angle 4.29109 / 3.17 ( 1017) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 TYR cc_start: 0.8378 (m-80) cc_final: 0.8094 (m-80) REVERT: A 440 GLN cc_start: 0.8617 (mm110) cc_final: 0.7736 (mt0) REVERT: A 508 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7981 (mm-30) REVERT: A 526 MET cc_start: 0.9360 (mmm) cc_final: 0.9100 (mmm) REVERT: A 538 MET cc_start: 0.7934 (tmm) cc_final: 0.7010 (tmm) REVERT: A 541 THR cc_start: 0.9452 (OUTLIER) cc_final: 0.9243 (p) REVERT: A 627 MET cc_start: 0.9139 (tmm) cc_final: 0.8487 (tmm) REVERT: A 645 MET cc_start: 0.8873 (tmm) cc_final: 0.8660 (tmm) REVERT: A 663 TRP cc_start: 0.9203 (t-100) cc_final: 0.8900 (t-100) REVERT: A 697 ASP cc_start: 0.9004 (m-30) cc_final: 0.8718 (p0) REVERT: A 789 LEU cc_start: 0.9535 (mt) cc_final: 0.9203 (mt) REVERT: A 843 MET cc_start: 0.8668 (ttp) cc_final: 0.8287 (ttm) REVERT: A 884 MET cc_start: 0.9072 (tpp) cc_final: 0.8562 (mmm) REVERT: A 898 PHE cc_start: 0.8921 (m-80) cc_final: 0.8697 (m-80) REVERT: A 905 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7830 (pmt-80) REVERT: A 954 MET cc_start: 0.8329 (mmt) cc_final: 0.7669 (tpp) REVERT: A 998 ASP cc_start: 0.8434 (m-30) cc_final: 0.8180 (m-30) REVERT: A 1131 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8811 (ptp90) outliers start: 29 outliers final: 22 residues processed: 132 average time/residue: 0.0694 time to fit residues: 13.0270 Evaluate side-chains 130 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1094 ASN Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 0.0470 chunk 74 optimal weight: 4.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 718 ASN A1094 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.071301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.055568 restraints weight = 58544.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.058371 restraints weight = 23910.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.060317 restraints weight = 14062.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.061719 restraints weight = 9788.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.062623 restraints weight = 7504.126| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8006 Z= 0.126 Angle : 0.757 10.697 10881 Z= 0.359 Chirality : 0.045 0.208 1251 Planarity : 0.005 0.095 1371 Dihedral : 6.151 55.682 1168 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.60 % Favored : 95.19 % Rotamer: Outliers : 3.31 % Allowed : 26.45 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.47 (0.28), residues: 958 helix: 1.42 (0.24), residues: 453 sheet: -0.40 (0.42), residues: 168 loop : -0.76 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 390 TYR 0.017 0.001 TYR A 420 PHE 0.026 0.001 PHE A 155 TRP 0.020 0.002 TRP A 932 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 8006) covalent geometry : angle 0.75742 / 0.36 (10881) hydrogen bonds : bond 0.03138 / 2.07 ( 357) hydrogen bonds : angle 4.27497 / 3.16 ( 1017) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 389 MET cc_start: 0.9224 (mmm) cc_final: 0.8897 (mmm) REVERT: A 420 TYR cc_start: 0.8316 (m-80) cc_final: 0.7681 (m-10) REVERT: A 440 GLN cc_start: 0.8554 (mm110) cc_final: 0.7730 (mt0) REVERT: A 508 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7867 (mm-30) REVERT: A 526 MET cc_start: 0.9270 (mmm) cc_final: 0.9035 (mmm) REVERT: A 538 MET cc_start: 0.7969 (tmm) cc_final: 0.7085 (tmm) REVERT: A 627 MET cc_start: 0.9131 (tmm) cc_final: 0.8474 (tmm) REVERT: A 645 MET cc_start: 0.8840 (tmm) cc_final: 0.8591 (tmm) REVERT: A 663 TRP cc_start: 0.9100 (t-100) cc_final: 0.8849 (t-100) REVERT: A 697 ASP cc_start: 0.8983 (m-30) cc_final: 0.8695 (p0) REVERT: A 789 LEU cc_start: 0.9510 (mt) cc_final: 0.9198 (mt) REVERT: A 843 MET cc_start: 0.8631 (ttp) cc_final: 0.8197 (ttm) REVERT: A 884 MET cc_start: 0.9117 (tpp) cc_final: 0.8307 (mmm) REVERT: A 905 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7784 (pmt-80) REVERT: A 954 MET cc_start: 0.8287 (mmt) cc_final: 0.7599 (tpp) REVERT: A 998 ASP cc_start: 0.8361 (m-30) cc_final: 0.8095 (m-30) REVERT: A 1064 LYS cc_start: 0.9087 (tptm) cc_final: 0.8704 (tppt) REVERT: A 1131 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8786 (ptp90) outliers start: 27 outliers final: 22 residues processed: 127 average time/residue: 0.0648 time to fit residues: 12.1410 Evaluate side-chains 127 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1094 ASN Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.0050 chunk 69 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 14 optimal weight: 0.0020 chunk 29 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1037 ASN A1094 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.071430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.056016 restraints weight = 50975.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.058734 restraints weight = 22184.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.060662 restraints weight = 13293.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.061961 restraints weight = 9351.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.062854 restraints weight = 7269.225| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.261 8006 Z= 0.322 Angle : 1.221 58.995 10881 Z= 0.733 Chirality : 0.056 1.049 1251 Planarity : 0.006 0.095 1371 Dihedral : 5.969 55.661 1164 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.39 % Favored : 95.19 % Rotamer: Outliers : 3.19 % Allowed : 26.68 % Favored : 70.13 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.13 % 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: 0.46 (0.28), residues: 958 helix: 1.41 (0.24), residues: 453 sheet: -0.40 (0.42), residues: 168 loop : -0.77 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 390 TYR 0.016 0.001 TYR A 420 PHE 0.025 0.001 PHE A 155 TRP 0.018 0.002 TRP A 932 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.32 ( 8006) covalent geometry : angle 1.22133 / 0.73 (10881) hydrogen bonds : bond 0.03143 / 2.07 ( 357) hydrogen bonds : angle 4.29085 / 3.18 ( 1017) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 389 MET cc_start: 0.9216 (mmm) cc_final: 0.8888 (mmm) REVERT: A 420 TYR cc_start: 0.8311 (m-80) cc_final: 0.7677 (m-10) REVERT: A 440 GLN cc_start: 0.8561 (mm110) cc_final: 0.7728 (mt0) REVERT: A 508 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7863 (mm-30) REVERT: A 526 MET cc_start: 0.9264 (mmm) cc_final: 0.9031 (mmm) REVERT: A 538 MET cc_start: 0.7970 (tmm) cc_final: 0.7088 (tmm) REVERT: A 627 MET cc_start: 0.9121 (tmm) cc_final: 0.8467 (tmm) REVERT: A 645 MET cc_start: 0.8828 (tmm) cc_final: 0.8571 (tmm) REVERT: A 663 TRP cc_start: 0.9106 (t-100) cc_final: 0.8857 (t-100) REVERT: A 697 ASP cc_start: 0.8987 (m-30) cc_final: 0.8696 (p0) REVERT: A 789 LEU cc_start: 0.9509 (mt) cc_final: 0.9201 (mt) REVERT: A 843 MET cc_start: 0.8617 (ttp) cc_final: 0.8159 (ttm) REVERT: A 884 MET cc_start: 0.9041 (tpp) cc_final: 0.8318 (mmm) REVERT: A 905 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7789 (pmt-80) REVERT: A 954 MET cc_start: 0.8280 (mmt) cc_final: 0.7603 (tpp) REVERT: A 998 ASP cc_start: 0.8357 (m-30) cc_final: 0.8093 (m-30) REVERT: A 1054 GLU cc_start: 0.8805 (tt0) cc_final: 0.8399 (tm-30) REVERT: A 1064 LYS cc_start: 0.9081 (tptm) cc_final: 0.8316 (tppt) REVERT: A 1131 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8789 (ptp90) outliers start: 26 outliers final: 23 residues processed: 117 average time/residue: 0.0671 time to fit residues: 11.4595 Evaluate side-chains 124 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1056 ILE Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 0.0570 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1094 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 = 0.3302 r_free = 0.3302 target = 0.071517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.056470 restraints weight = 44278.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.059042 restraints weight = 20650.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.060864 restraints weight = 12833.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.062064 restraints weight = 9197.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.062969 restraints weight = 7280.358| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.261 8006 Z= 0.321 Angle : 1.221 58.997 10881 Z= 0.733 Chirality : 0.056 1.048 1251 Planarity : 0.006 0.095 1371 Dihedral : 5.969 55.661 1164 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.39 % Favored : 95.19 % Rotamer: Outliers : 3.07 % Allowed : 26.80 % Favored : 70.13 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.13 % 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: 0.46 (0.28), residues: 958 helix: 1.41 (0.24), residues: 453 sheet: -0.40 (0.42), residues: 168 loop : -0.77 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 390 TYR 0.016 0.001 TYR A 420 PHE 0.025 0.001 PHE A 155 TRP 0.018 0.002 TRP A 932 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.32 ( 8006) covalent geometry : angle 1.22122 / 0.73 (10881) hydrogen bonds : bond 0.03143 / 2.07 ( 357) hydrogen bonds : angle 4.29085 / 3.18 ( 1017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1432.36 seconds wall clock time: 25 minutes 19.37 seconds (1519.37 seconds total)