Starting phenix.real_space_refine on Sat Oct 11 12:03:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pjb_17703/10_2025/8pjb_17703.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pjb_17703/10_2025/8pjb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8pjb_17703/10_2025/8pjb_17703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pjb_17703/10_2025/8pjb_17703.map" model { file = "/net/cci-nas-00/data/ceres_data/8pjb_17703/10_2025/8pjb_17703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pjb_17703/10_2025/8pjb_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/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: {'RNA': 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: 3.06, per 1000 atoms: 0.39 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: 0.58 Conformation dependent library (CDL) restraints added in 430.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.34 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: 1.30 Time building geometry restraints manager: 0.81 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 - 3.36: 10682 3.36 - 6.72: 181 6.72 - 10.08: 14 10.08 - 13.44: 2 13.44 - 16.80: 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 120.20 103.40 16.80 1.50e+00 4.44e-01 1.25e+02 angle pdb=" C3' U C 3 " pdb=" O3' U C 3 " pdb=" P C C 4 " ideal model delta sigma weight residual 120.20 107.33 12.87 1.50e+00 4.44e-01 7.36e+01 angle pdb=" C3' C C 2 " pdb=" O3' C C 2 " pdb=" P U C 3 " ideal model delta sigma weight residual 120.20 108.63 11.57 1.50e+00 4.44e-01 5.95e+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 - 18.73: 4197 18.73 - 37.45: 521 37.45 - 56.18: 163 56.18 - 74.91: 48 74.91 - 93.63: 8 Dihedral angle restraints: 4937 sinusoidal: 2111 harmonic: 2826 Sorted by residual: dihedral pdb=" CD ARG A 905 " pdb=" NE ARG A 905 " pdb=" CZ ARG A 905 " pdb=" NH1 ARG A 905 " ideal model delta sinusoidal sigma weight residual 0.00 -77.76 77.76 1 1.00e+01 1.00e-02 7.56e+01 dihedral pdb=" CD ARG A 590 " pdb=" NE ARG A 590 " pdb=" CZ ARG A 590 " pdb=" NH1 ARG A 590 " ideal model delta sinusoidal sigma weight residual 0.00 -64.26 64.26 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" CD ARG A 198 " pdb=" NE ARG A 198 " pdb=" CZ ARG A 198 " pdb=" NH1 ARG A 198 " ideal model delta sinusoidal sigma weight residual 0.00 -53.38 53.38 1 1.00e+01 1.00e-02 3.87e+01 ... (remaining 4934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1171 0.112 - 0.224: 64 0.224 - 0.336: 11 0.336 - 0.448: 4 0.448 - 0.561: 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 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.86e+00 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 2.41 -2.77 -0.36 2.00e-01 2.50e+01 3.30e+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 2.41 -2.77 -0.36 2.00e-01 2.50e+01 3.30e+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: 1.010 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: 0.020 Process input model: 10.230 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 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= 0.356 Angle : 0.985 16.796 10881 Z= 0.618 Chirality : 0.063 0.561 1251 Planarity : 0.026 0.477 1371 Dihedral : 18.757 93.633 3097 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 aren 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 covalent geometry : bond 0.00551 ( 8006) covalent geometry : angle 0.98538 (10881) hydrogen bonds : bond 0.12888 ( 357) hydrogen bonds : angle 5.43823 ( 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 : 0.359 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: 0.0954 time to fit residues: 24.8654 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 : 0.306 ------------------------------------------------------------------------------- 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: 4.9990 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: 0.9980 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: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3324 r_free = 0.3324 target = 0.073474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.057905 restraints weight = 47159.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.060654 restraints weight = 21165.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.062634 restraints weight = 12855.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.063981 restraints weight = 9043.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.064975 restraints weight = 6990.369| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 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 = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8006 Z= 0.146 Angle : 0.789 14.663 10881 Z= 0.380 Chirality : 0.045 0.246 1251 Planarity : 0.006 0.135 1371 Dihedral : 10.179 77.949 1225 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.44 % Favored : 94.14 % Rotamer: Outliers : 3.42 % Allowed : 26.80 % Favored : 69.78 % 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 aren not related in a simple way. whole: 0.09 (0.27), residues: 958 helix: 0.94 (0.24), residues: 456 sheet: -0.51 (0.45), residues: 149 loop : -0.74 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 362 TYR 0.019 0.002 TYR A 420 PHE 0.033 0.001 PHE A 155 TRP 0.037 0.002 TRP A 328 HIS 0.009 0.002 HIS A 503 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8006) covalent geometry : angle 0.78860 (10881) hydrogen bonds : bond 0.03826 ( 357) hydrogen bonds : angle 4.46873 ( 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 157 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8488 (p) REVERT: A 525 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8566 (t0) REVERT: A 645 MET cc_start: 0.8872 (tmm) cc_final: 0.8655 (tmm) REVERT: A 670 MET cc_start: 0.8935 (ttm) cc_final: 0.8428 (tmm) REVERT: A 697 ASP cc_start: 0.9006 (m-30) cc_final: 0.8684 (t0) REVERT: A 718 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.8179 (p0) REVERT: A 884 MET cc_start: 0.8997 (tpp) cc_final: 0.8404 (mmm) REVERT: A 954 MET cc_start: 0.8576 (ttm) cc_final: 0.8326 (tpp) REVERT: A 957 MET cc_start: 0.9181 (mmm) cc_final: 0.8727 (tpp) REVERT: A 969 ASP cc_start: 0.9436 (t0) cc_final: 0.9029 (m-30) REVERT: A 1005 CYS cc_start: 0.8548 (m) cc_final: 0.8334 (m) REVERT: A 1030 LEU cc_start: 0.9270 (mt) cc_final: 0.9049 (tp) REVERT: A 1054 GLU cc_start: 0.8695 (tt0) cc_final: 0.8356 (tt0) REVERT: A 1131 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8431 (ptp-110) outliers start: 28 outliers final: 17 residues processed: 145 average time/residue: 0.0789 time to fit residues: 16.1901 Evaluate side-chains 134 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 525 ASP 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 718 ASN 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: 0.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1094 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.073368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.057771 restraints weight = 51484.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.060561 restraints weight = 22215.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.062541 restraints weight = 13297.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.063934 restraints weight = 9271.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.064914 restraints weight = 7083.663| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 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 = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 0.032 8006 Z= 0.135 Angle : 0.711 10.792 10881 Z= 0.344 Chirality : 0.043 0.218 1251 Planarity : 0.006 0.114 1371 Dihedral : 9.646 75.344 1213 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.50 % Favored : 95.19 % Rotamer: Outliers : 3.78 % Allowed : 25.74 % 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 aren not related in a simple way. whole: 0.28 (0.28), residues: 958 helix: 1.23 (0.25), residues: 447 sheet: -0.41 (0.43), residues: 158 loop : -0.78 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 362 TYR 0.023 0.002 TYR A 189 PHE 0.023 0.001 PHE A 155 TRP 0.020 0.002 TRP A 328 HIS 0.006 0.001 HIS A 910 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8006) covalent geometry : angle 0.71063 (10881) hydrogen bonds : bond 0.03487 ( 357) hydrogen bonds : angle 4.18121 ( 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 152 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9117 (mmmt) cc_final: 0.8859 (mmmt) REVERT: A 328 TRP cc_start: 0.8136 (t60) cc_final: 0.7769 (t60) REVERT: A 440 GLN cc_start: 0.8470 (mm110) cc_final: 0.7749 (mt0) REVERT: A 645 MET cc_start: 0.8800 (tmm) cc_final: 0.8553 (tmm) REVERT: A 663 TRP cc_start: 0.9027 (t-100) cc_final: 0.8805 (t-100) REVERT: A 670 MET cc_start: 0.8934 (ttm) cc_final: 0.8415 (tmm) REVERT: A 694 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8939 (tt) REVERT: A 697 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8628 (p0) REVERT: A 884 MET cc_start: 0.8922 (tpp) cc_final: 0.8496 (mmm) REVERT: A 954 MET cc_start: 0.8567 (ttm) cc_final: 0.8350 (tpp) REVERT: A 957 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8745 (tpp) REVERT: A 998 ASP cc_start: 0.8627 (m-30) cc_final: 0.8334 (m-30) REVERT: A 1054 GLU cc_start: 0.8771 (tt0) cc_final: 0.8414 (tt0) REVERT: A 1064 LYS cc_start: 0.9298 (tptp) cc_final: 0.9067 (tppp) REVERT: A 1131 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8704 (ptp90) outliers start: 31 outliers final: 16 residues processed: 141 average time/residue: 0.0789 time to fit residues: 15.9978 Evaluate side-chains 130 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 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 1131 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 38 optimal weight: 0.4980 chunk 71 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1094 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.073165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.057878 restraints weight = 45178.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.060532 restraints weight = 20832.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.062452 restraints weight = 12842.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.063693 restraints weight = 9130.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.064688 restraints weight = 7157.420| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 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 = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8006 Z= 0.126 Angle : 0.698 9.656 10881 Z= 0.338 Chirality : 0.043 0.205 1251 Planarity : 0.005 0.105 1371 Dihedral : 9.289 75.343 1207 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.71 % Favored : 94.98 % 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 aren not related in a simple way. whole: 0.34 (0.28), residues: 958 helix: 1.24 (0.24), residues: 453 sheet: -0.49 (0.42), residues: 169 loop : -0.69 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 587 TYR 0.031 0.001 TYR A 420 PHE 0.028 0.001 PHE A 898 TRP 0.033 0.002 TRP A 949 HIS 0.004 0.001 HIS A 922 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8006) covalent geometry : angle 0.69838 (10881) hydrogen bonds : bond 0.03223 ( 357) hydrogen bonds : angle 4.13296 ( 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 142 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9148 (mmmt) cc_final: 0.8854 (mmmt) REVERT: A 414 THR cc_start: 0.8816 (m) cc_final: 0.8221 (p) REVERT: A 440 GLN cc_start: 0.8423 (mm110) cc_final: 0.7676 (mt0) REVERT: A 627 MET cc_start: 0.9170 (tmm) cc_final: 0.8599 (tmm) REVERT: A 634 ASP cc_start: 0.9082 (p0) cc_final: 0.8864 (t0) REVERT: A 641 GLU cc_start: 0.9283 (tt0) cc_final: 0.9067 (pp20) REVERT: A 645 MET cc_start: 0.8867 (tmm) cc_final: 0.8583 (tmm) REVERT: A 663 TRP cc_start: 0.9027 (t-100) cc_final: 0.8714 (t-100) REVERT: A 670 MET cc_start: 0.8872 (ttm) cc_final: 0.8387 (tmm) REVERT: A 697 ASP cc_start: 0.9012 (m-30) cc_final: 0.8663 (p0) REVERT: A 789 LEU cc_start: 0.9397 (mt) cc_final: 0.9167 (mt) REVERT: A 884 MET cc_start: 0.8877 (tpp) cc_final: 0.8508 (mmm) REVERT: A 957 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8810 (tpp) REVERT: A 969 ASP cc_start: 0.9427 (t0) cc_final: 0.8990 (m-30) REVERT: A 998 ASP cc_start: 0.8486 (m-30) cc_final: 0.8250 (m-30) REVERT: A 1054 GLU cc_start: 0.8865 (tt0) cc_final: 0.8506 (tt0) REVERT: A 1131 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8745 (ptp90) outliers start: 24 outliers final: 17 residues processed: 132 average time/residue: 0.0733 time to fit residues: 13.8500 Evaluate side-chains 127 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 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 556 VAL Chi-restraints excluded: chain A residue 581 VAL 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 914 LEU Chi-restraints excluded: chain A residue 957 MET 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: 3.9990 chunk 22 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1094 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.070348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.053807 restraints weight = 76200.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.056716 restraints weight = 27950.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.058804 restraints weight = 15973.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.060247 restraints weight = 10903.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.061293 restraints weight = 8297.321| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 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 = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8006 Z= 0.190 Angle : 0.713 9.339 10881 Z= 0.348 Chirality : 0.044 0.198 1251 Planarity : 0.005 0.100 1371 Dihedral : 9.173 75.760 1204 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.81 % Favored : 94.98 % Rotamer: Outliers : 3.54 % Allowed : 25.03 % Favored : 71.43 % 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 aren not related in a simple way. whole: 0.36 (0.28), residues: 958 helix: 1.33 (0.24), residues: 453 sheet: -0.51 (0.41), residues: 173 loop : -0.76 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 524 TYR 0.014 0.002 TYR A 187 PHE 0.018 0.001 PHE A1045 TRP 0.044 0.003 TRP A 328 HIS 0.005 0.001 HIS A 922 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 8006) covalent geometry : angle 0.71309 (10881) hydrogen bonds : bond 0.03470 ( 357) hydrogen bonds : angle 4.25847 ( 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: 29 poor density : 108 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9132 (mmmt) cc_final: 0.8831 (mmmt) REVERT: A 440 GLN cc_start: 0.8394 (mm110) cc_final: 0.7719 (mt0) REVERT: A 508 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8053 (mm-30) REVERT: A 627 MET cc_start: 0.9205 (tmm) cc_final: 0.8593 (tmm) REVERT: A 641 GLU cc_start: 0.9276 (tt0) cc_final: 0.9032 (tt0) REVERT: A 645 MET cc_start: 0.8869 (tmm) cc_final: 0.8584 (tmm) REVERT: A 663 TRP cc_start: 0.9169 (t-100) cc_final: 0.8883 (t-100) REVERT: A 697 ASP cc_start: 0.9021 (m-30) cc_final: 0.8717 (p0) REVERT: A 789 LEU cc_start: 0.9492 (mt) cc_final: 0.9228 (mt) REVERT: A 884 MET cc_start: 0.8976 (tpp) cc_final: 0.8599 (mmm) REVERT: A 898 PHE cc_start: 0.8796 (m-80) cc_final: 0.8558 (m-80) REVERT: A 905 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7959 (pmt-80) REVERT: A 942 MET cc_start: 0.9214 (mmp) cc_final: 0.8452 (tpt) REVERT: A 954 MET cc_start: 0.8216 (tpp) cc_final: 0.7742 (tpp) REVERT: A 957 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.9017 (mmm) REVERT: A 998 ASP cc_start: 0.8524 (m-30) cc_final: 0.8252 (m-30) REVERT: A 1004 LEU cc_start: 0.9628 (tp) cc_final: 0.9396 (tt) REVERT: A 1054 GLU cc_start: 0.8833 (tt0) cc_final: 0.8544 (tt0) REVERT: A 1131 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8779 (ptp90) outliers start: 29 outliers final: 22 residues processed: 128 average time/residue: 0.0779 time to fit residues: 14.3524 Evaluate side-chains 128 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 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 702 VAL 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 891 SER Chi-restraints excluded: chain A residue 892 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 957 MET 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 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: 0.9990 chunk 6 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1094 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.070406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.054428 restraints weight = 58695.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.057196 restraints weight = 24490.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.059174 restraints weight = 14546.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.060543 restraints weight = 10149.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.061552 restraints weight = 7828.507| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 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 = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3496 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 : 0.698 9.332 10881 Z= 0.337 Chirality : 0.043 0.201 1251 Planarity : 0.005 0.097 1371 Dihedral : 9.087 74.316 1204 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.67 % Rotamer: Outliers : 3.31 % Allowed : 25.86 % Favored : 70.84 % 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 aren not related in a simple way. whole: 0.45 (0.28), residues: 958 helix: 1.40 (0.24), residues: 454 sheet: -0.36 (0.41), residues: 166 loop : -0.78 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 524 TYR 0.020 0.001 TYR A 420 PHE 0.034 0.001 PHE A 155 TRP 0.038 0.002 TRP A 328 HIS 0.008 0.001 HIS A1032 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8006) covalent geometry : angle 0.69758 (10881) hydrogen bonds : bond 0.03190 ( 357) hydrogen bonds : angle 4.10408 ( 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 136 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9141 (mmmt) cc_final: 0.8860 (mmmt) REVERT: A 440 GLN cc_start: 0.8447 (mm110) cc_final: 0.7752 (mt0) REVERT: A 508 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7949 (mm-30) REVERT: A 526 MET cc_start: 0.9285 (mmm) cc_final: 0.8942 (mmm) REVERT: A 627 MET cc_start: 0.9212 (tmm) cc_final: 0.8572 (tmm) REVERT: A 629 MET cc_start: 0.9059 (mtm) cc_final: 0.8733 (ptp) REVERT: A 641 GLU cc_start: 0.9249 (tt0) cc_final: 0.9015 (tt0) REVERT: A 645 MET cc_start: 0.8816 (tmm) cc_final: 0.8532 (tmm) REVERT: A 663 TRP cc_start: 0.9091 (t-100) cc_final: 0.8798 (t-100) REVERT: A 697 ASP cc_start: 0.9010 (m-30) cc_final: 0.8714 (p0) REVERT: A 789 LEU cc_start: 0.9488 (mt) cc_final: 0.9145 (mt) REVERT: A 884 MET cc_start: 0.8874 (tpp) cc_final: 0.8563 (mmm) REVERT: A 905 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7922 (pmt-80) REVERT: A 942 MET cc_start: 0.9185 (mmp) cc_final: 0.8376 (tpt) REVERT: A 954 MET cc_start: 0.8253 (tpp) cc_final: 0.7736 (tpp) REVERT: A 957 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.9019 (mmm) REVERT: A 998 ASP cc_start: 0.8409 (m-30) cc_final: 0.8115 (m-30) REVERT: A 1004 LEU cc_start: 0.9630 (tp) cc_final: 0.9427 (tt) REVERT: A 1032 HIS cc_start: 0.8852 (t-90) cc_final: 0.8412 (t-90) REVERT: A 1054 GLU cc_start: 0.8834 (tt0) cc_final: 0.8509 (tt0) REVERT: A 1131 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8760 (ptp90) outliers start: 27 outliers final: 19 residues processed: 125 average time/residue: 0.0744 time to fit residues: 13.4620 Evaluate side-chains 127 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 702 VAL 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 897 VAL Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 957 MET Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1034 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 82 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 0.0770 chunk 86 optimal weight: 0.0010 chunk 91 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 overall best weight: 0.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.072018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.055522 restraints weight = 73083.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.058525 restraints weight = 26520.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.060662 restraints weight = 15040.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.062175 restraints weight = 10193.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.063244 restraints weight = 7657.102| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 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 = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3716 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= 0.117 Angle : 0.686 9.493 10881 Z= 0.328 Chirality : 0.043 0.198 1251 Planarity : 0.005 0.096 1371 Dihedral : 9.015 73.740 1204 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.92 % Favored : 94.87 % Rotamer: Outliers : 3.19 % Allowed : 25.74 % Favored : 71.07 % 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 aren not related in a simple way. whole: 0.51 (0.28), residues: 958 helix: 1.46 (0.24), residues: 454 sheet: -0.23 (0.43), residues: 156 loop : -0.84 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 910 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8006) covalent geometry : angle 0.68624 (10881) hydrogen bonds : bond 0.03070 ( 357) hydrogen bonds : angle 4.04416 ( 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 140 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9121 (mmmt) cc_final: 0.8858 (mmmt) REVERT: A 219 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7425 (mm-30) REVERT: A 420 TYR cc_start: 0.8302 (m-80) cc_final: 0.7994 (m-10) REVERT: A 440 GLN cc_start: 0.8477 (mm110) cc_final: 0.7736 (mt0) REVERT: A 508 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7911 (mm-30) REVERT: A 541 THR cc_start: 0.9402 (OUTLIER) cc_final: 0.9156 (p) REVERT: A 627 MET cc_start: 0.9163 (tmm) cc_final: 0.8525 (tmm) REVERT: A 629 MET cc_start: 0.9052 (mtm) cc_final: 0.8730 (ptm) REVERT: A 641 GLU cc_start: 0.9259 (tt0) cc_final: 0.9018 (tt0) REVERT: A 645 MET cc_start: 0.8828 (tmm) cc_final: 0.8560 (tmm) REVERT: A 697 ASP cc_start: 0.9024 (m-30) cc_final: 0.8716 (p0) REVERT: A 789 LEU cc_start: 0.9456 (mt) cc_final: 0.9100 (mt) REVERT: A 884 MET cc_start: 0.8921 (tpp) cc_final: 0.8467 (mmm) REVERT: A 905 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7886 (pmt-80) REVERT: A 954 MET cc_start: 0.8253 (tpp) cc_final: 0.7696 (tpp) REVERT: A 969 ASP cc_start: 0.9376 (t0) cc_final: 0.8970 (m-30) REVERT: A 998 ASP cc_start: 0.8434 (m-30) cc_final: 0.8127 (m-30) REVERT: A 1032 HIS cc_start: 0.8793 (t-90) cc_final: 0.8413 (t-90) REVERT: A 1054 GLU cc_start: 0.8773 (tt0) cc_final: 0.8451 (tt0) REVERT: A 1131 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8781 (ptp90) outliers start: 26 outliers final: 20 residues processed: 133 average time/residue: 0.0859 time to fit residues: 16.1160 Evaluate side-chains 129 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 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 702 VAL 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 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 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: 5.9990 chunk 44 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.068557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.052489 restraints weight = 68817.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.055261 restraints weight = 26666.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.057217 restraints weight = 15506.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.058633 restraints weight = 10723.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.059602 restraints weight = 8180.451| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8006 Z= 0.239 Angle : 0.762 12.344 10881 Z= 0.373 Chirality : 0.045 0.199 1251 Planarity : 0.006 0.096 1371 Dihedral : 9.115 74.218 1204 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.67 % 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 aren not related in a simple way. whole: 0.44 (0.28), residues: 958 helix: 1.46 (0.24), residues: 448 sheet: -0.44 (0.40), residues: 167 loop : -0.81 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 524 TYR 0.011 0.002 TYR A 752 PHE 0.022 0.002 PHE A 155 TRP 0.042 0.003 TRP A 663 HIS 0.010 0.002 HIS A1032 Details of bonding type rmsd covalent geometry : bond 0.00540 ( 8006) covalent geometry : angle 0.76228 (10881) hydrogen bonds : bond 0.03508 ( 357) hydrogen bonds : angle 4.37500 ( 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 136 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9122 (mmmt) cc_final: 0.8896 (mmmt) REVERT: A 440 GLN cc_start: 0.8642 (mm110) cc_final: 0.7773 (mt0) REVERT: A 508 GLU cc_start: 0.8548 (mm-30) cc_final: 0.7941 (mm-30) REVERT: A 538 MET cc_start: 0.8009 (tmm) cc_final: 0.6959 (tmm) REVERT: A 629 MET cc_start: 0.9054 (mtm) cc_final: 0.8625 (ptm) REVERT: A 641 GLU cc_start: 0.9246 (tt0) cc_final: 0.9023 (tt0) REVERT: A 645 MET cc_start: 0.8851 (tmm) cc_final: 0.8624 (tmm) REVERT: A 665 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9186 (tt) REVERT: A 697 ASP cc_start: 0.9040 (m-30) cc_final: 0.8741 (p0) REVERT: A 721 GLU cc_start: 0.8861 (tt0) cc_final: 0.8639 (tm-30) REVERT: A 740 MET cc_start: 0.8593 (ptp) cc_final: 0.8305 (ptm) REVERT: A 789 LEU cc_start: 0.9534 (mt) cc_final: 0.9196 (mt) REVERT: A 843 MET cc_start: 0.8596 (ttp) cc_final: 0.8075 (ttm) REVERT: A 884 MET cc_start: 0.9107 (tpp) cc_final: 0.8611 (mmm) REVERT: A 905 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7880 (pmt-80) REVERT: A 954 MET cc_start: 0.8126 (tpp) cc_final: 0.7658 (tpp) REVERT: A 998 ASP cc_start: 0.8496 (m-30) cc_final: 0.8245 (m-30) REVERT: A 1032 HIS cc_start: 0.8871 (t-90) cc_final: 0.8427 (t-90) REVERT: A 1054 GLU cc_start: 0.8790 (tt0) cc_final: 0.8419 (tt0) REVERT: A 1131 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8797 (ptp90) outliers start: 29 outliers final: 23 residues processed: 127 average time/residue: 0.0846 time to fit residues: 15.3640 Evaluate side-chains 129 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 702 VAL 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 891 SER Chi-restraints excluded: chain A residue 892 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 1034 THR Chi-restraints excluded: chain A residue 1051 VAL 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: 2.9990 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.068903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.053168 restraints weight = 58690.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.055891 restraints weight = 24222.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.057851 restraints weight = 14380.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.059164 restraints weight = 10012.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.060134 restraints weight = 7754.555| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 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 = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8006 Z= 0.157 Angle : 0.731 12.855 10881 Z= 0.351 Chirality : 0.044 0.200 1251 Planarity : 0.005 0.095 1371 Dihedral : 9.050 73.710 1204 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.67 % Rotamer: Outliers : 3.07 % Allowed : 26.33 % Favored : 70.60 % 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 aren not related in a simple way. whole: 0.51 (0.28), residues: 958 helix: 1.52 (0.24), residues: 448 sheet: -0.41 (0.41), residues: 168 loop : -0.80 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 390 TYR 0.013 0.001 TYR A 420 PHE 0.026 0.001 PHE A 155 TRP 0.044 0.003 TRP A 663 HIS 0.007 0.001 HIS A1032 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8006) covalent geometry : angle 0.73128 (10881) hydrogen bonds : bond 0.03254 ( 357) hydrogen bonds : angle 4.29561 ( 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 133 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8883 (mmmt) REVERT: A 420 TYR cc_start: 0.8070 (m-80) cc_final: 0.7647 (m-10) REVERT: A 440 GLN cc_start: 0.8566 (mm110) cc_final: 0.7757 (mt0) REVERT: A 508 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7911 (mm-30) REVERT: A 538 MET cc_start: 0.8082 (tmm) cc_final: 0.6834 (tmm) REVERT: A 627 MET cc_start: 0.9210 (tmm) cc_final: 0.8343 (tpp) REVERT: A 629 MET cc_start: 0.9054 (mtm) cc_final: 0.8631 (ptm) REVERT: A 641 GLU cc_start: 0.9231 (tt0) cc_final: 0.8994 (tt0) REVERT: A 645 MET cc_start: 0.8842 (tmm) cc_final: 0.8608 (tmm) REVERT: A 697 ASP cc_start: 0.9048 (m-30) cc_final: 0.8747 (p0) REVERT: A 789 LEU cc_start: 0.9530 (mt) cc_final: 0.9240 (mt) REVERT: A 843 MET cc_start: 0.8569 (ttp) cc_final: 0.8007 (ttm) REVERT: A 884 MET cc_start: 0.9055 (tpp) cc_final: 0.8466 (mmm) REVERT: A 905 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7770 (pmt-80) REVERT: A 914 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8288 (tp) REVERT: A 954 MET cc_start: 0.8175 (tpp) cc_final: 0.7664 (tpp) REVERT: A 998 ASP cc_start: 0.8452 (m-30) cc_final: 0.8190 (m-30) REVERT: A 1032 HIS cc_start: 0.8813 (t-90) cc_final: 0.8461 (t-90) REVERT: A 1054 GLU cc_start: 0.8757 (tt0) cc_final: 0.8316 (tt0) REVERT: A 1131 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8784 (ptp90) outliers start: 25 outliers final: 21 residues processed: 124 average time/residue: 0.0804 time to fit residues: 14.2153 Evaluate side-chains 128 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 702 VAL 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 892 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 1034 THR Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1131 ARG Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 0.0870 chunk 29 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** 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 = 0.3282 r_free = 0.3282 target = 0.070696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.055544 restraints weight = 47963.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.058152 restraints weight = 21313.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.060019 restraints weight = 12983.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.061282 restraints weight = 9210.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.062128 restraints weight = 7179.882| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 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 = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4004 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= 0.135 Angle : 0.721 11.751 10881 Z= 0.345 Chirality : 0.044 0.200 1251 Planarity : 0.005 0.095 1371 Dihedral : 8.911 73.763 1200 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.33 % Favored : 94.46 % Rotamer: Outliers : 2.72 % Allowed : 27.15 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: 0.65 (0.28), residues: 958 helix: 1.62 (0.24), residues: 448 sheet: -0.31 (0.41), residues: 168 loop : -0.72 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 390 TYR 0.012 0.001 TYR A 420 PHE 0.026 0.001 PHE A 155 TRP 0.043 0.002 TRP A 663 HIS 0.006 0.001 HIS A1032 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8006) covalent geometry : angle 0.72075 (10881) hydrogen bonds : bond 0.03130 ( 357) hydrogen bonds : angle 4.20329 ( 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 125 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9133 (mmmt) cc_final: 0.8902 (mmmt) REVERT: A 420 TYR cc_start: 0.8122 (m-80) cc_final: 0.7635 (m-10) REVERT: A 440 GLN cc_start: 0.8540 (mm110) cc_final: 0.7708 (mt0) REVERT: A 508 GLU cc_start: 0.8512 (mm-30) cc_final: 0.7888 (mm-30) REVERT: A 526 MET cc_start: 0.9289 (mmm) cc_final: 0.9028 (mmm) REVERT: A 538 MET cc_start: 0.8104 (tmm) cc_final: 0.6827 (tmm) REVERT: A 627 MET cc_start: 0.9204 (tmm) cc_final: 0.8321 (tpp) REVERT: A 629 MET cc_start: 0.9080 (mtm) cc_final: 0.8633 (ptm) REVERT: A 641 GLU cc_start: 0.9234 (tt0) cc_final: 0.8995 (tt0) REVERT: A 645 MET cc_start: 0.8835 (tmm) cc_final: 0.8588 (tmm) REVERT: A 697 ASP cc_start: 0.9063 (m-30) cc_final: 0.8761 (p0) REVERT: A 789 LEU cc_start: 0.9524 (mt) cc_final: 0.9240 (mt) REVERT: A 884 MET cc_start: 0.9106 (tpp) cc_final: 0.8526 (mmm) REVERT: A 905 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7795 (pmt-80) REVERT: A 914 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8319 (tp) REVERT: A 954 MET cc_start: 0.8172 (tpp) cc_final: 0.7632 (tpp) REVERT: A 998 ASP cc_start: 0.8423 (m-30) cc_final: 0.8149 (m-30) REVERT: A 1032 HIS cc_start: 0.8765 (t-90) cc_final: 0.8433 (t-90) REVERT: A 1054 GLU cc_start: 0.8681 (tt0) cc_final: 0.8246 (tt0) REVERT: A 1131 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8788 (ptp90) outliers start: 22 outliers final: 19 residues processed: 118 average time/residue: 0.0856 time to fit residues: 14.3979 Evaluate side-chains 123 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 702 VAL 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 892 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 1051 VAL 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: 0.7980 chunk 14 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 0.0030 chunk 65 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.069986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.054943 restraints weight = 43584.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.057471 restraints weight = 20359.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.059295 restraints weight = 12663.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.060527 restraints weight = 9098.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.061348 restraints weight = 7152.738| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 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 = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4092 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= 0.138 Angle : 0.712 11.724 10881 Z= 0.341 Chirality : 0.044 0.200 1251 Planarity : 0.005 0.094 1371 Dihedral : 8.865 73.742 1200 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.23 % Favored : 94.56 % 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 aren not related in a simple way. whole: 0.67 (0.28), residues: 958 helix: 1.64 (0.24), residues: 448 sheet: -0.31 (0.41), residues: 169 loop : -0.69 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 390 TYR 0.010 0.001 TYR A 420 PHE 0.025 0.001 PHE A 155 TRP 0.040 0.002 TRP A 663 HIS 0.006 0.001 HIS A1032 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8006) covalent geometry : angle 0.71236 (10881) hydrogen bonds : bond 0.03140 ( 357) hydrogen bonds : angle 4.21110 ( 1017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1627.88 seconds wall clock time: 28 minutes 45.60 seconds (1725.60 seconds total)