Starting phenix.real_space_refine on Thu Jun 12 23:47:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pjb_17703/06_2025/8pjb_17703.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pjb_17703/06_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_17703/06_2025/8pjb_17703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pjb_17703/06_2025/8pjb_17703.map" model { file = "/net/cci-nas-00/data/ceres_data/8pjb_17703/06_2025/8pjb_17703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pjb_17703/06_2025/8pjb_17703.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.74, per 1000 atoms: 1.24 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: 2.29 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.20 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: 2.93 Time building geometry restraints manager: 2.69 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 29.800 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.920 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (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 TRP 0.014 0.001 TRP A 932 HIS 0.007 0.001 HIS A 910 PHE 0.029 0.002 PHE A 240 TYR 0.015 0.002 TYR A 550 ARG 0.008 0.001 ARG A 867 Details of bonding type rmsd hydrogen bonds : bond 0.12888 ( 357) hydrogen bonds : angle 5.43823 ( 1017) covalent geometry : bond 0.00551 ( 8006) covalent geometry : angle 0.98538 (10881) *********************** 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 : 0.865 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: 0.2153 time to fit residues: 55.9996 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 : 0.962 ------------------------------------------------------------------------------- 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 81 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 0.0170 chunk 87 optimal weight: 0.8980 overall best weight: 0.7218 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.072879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.056730 restraints weight = 57133.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.059668 restraints weight = 23415.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.061756 restraints weight = 13718.615| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 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 = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8006 Z= 0.152 Angle : 0.786 14.358 10881 Z= 0.379 Chirality : 0.045 0.260 1251 Planarity : 0.006 0.137 1371 Dihedral : 10.162 77.720 1225 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.44 % Favored : 94.14 % Rotamer: Outliers : 3.42 % Allowed : 26.92 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.27), residues: 958 helix: 0.96 (0.24), residues: 456 sheet: -0.51 (0.45), residues: 149 loop : -0.75 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 328 HIS 0.007 0.002 HIS A 503 PHE 0.034 0.001 PHE A 155 TYR 0.022 0.002 TYR A 420 ARG 0.008 0.001 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 357) hydrogen bonds : angle 4.46120 ( 1017) covalent geometry : bond 0.00332 ( 8006) covalent geometry : angle 0.78565 (10881) *********************** 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 156 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8544 (p) REVERT: A 253 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8520 (mmmt) REVERT: A 525 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8607 (t0) REVERT: A 670 MET cc_start: 0.8947 (ttm) cc_final: 0.8434 (tmm) REVERT: A 697 ASP cc_start: 0.9031 (m-30) cc_final: 0.8707 (t0) REVERT: A 718 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8193 (p0) REVERT: A 884 MET cc_start: 0.8979 (tpp) cc_final: 0.8394 (mmm) REVERT: A 954 MET cc_start: 0.8577 (ttm) cc_final: 0.8294 (tpp) REVERT: A 969 ASP cc_start: 0.9456 (t0) cc_final: 0.9040 (m-30) REVERT: A 1005 CYS cc_start: 0.8588 (m) cc_final: 0.8383 (m) REVERT: A 1030 LEU cc_start: 0.9286 (mt) cc_final: 0.9071 (tp) REVERT: A 1054 GLU cc_start: 0.8719 (tt0) cc_final: 0.8368 (tt0) REVERT: A 1131 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8479 (ptp-110) outliers start: 28 outliers final: 16 residues processed: 144 average time/residue: 0.1822 time to fit residues: 37.0849 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 : 0.904 ------------------------------------------------------------------------------- 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 66 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 95 optimal weight: 0.0770 chunk 52 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 overall best weight: 2.3744 ------------------------------------------------------------------------------- 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 = 0.3273 r_free = 0.3273 target = 0.070689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.055291 restraints weight = 47294.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.057891 restraints weight = 21325.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.059814 restraints weight = 13032.758| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 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 = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8006 Z= 0.197 Angle : 0.751 10.077 10881 Z= 0.366 Chirality : 0.045 0.225 1251 Planarity : 0.006 0.117 1371 Dihedral : 9.792 77.074 1213 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.23 % Favored : 94.46 % Rotamer: Outliers : 3.78 % Allowed : 26.09 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.28), residues: 958 helix: 1.03 (0.24), residues: 455 sheet: -0.45 (0.43), residues: 166 loop : -0.72 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 949 HIS 0.004 0.001 HIS A 910 PHE 0.024 0.002 PHE A 155 TYR 0.033 0.002 TYR A 420 ARG 0.007 0.001 ARG A1080 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 357) hydrogen bonds : angle 4.34987 ( 1017) covalent geometry : bond 0.00447 ( 8006) covalent geometry : angle 0.75073 (10881) *********************** 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 141 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 TRP cc_start: 0.8199 (t60) cc_final: 0.7790 (t60) REVERT: A 440 GLN cc_start: 0.8566 (mm110) cc_final: 0.7837 (mt0) REVERT: A 627 MET cc_start: 0.9231 (tmm) cc_final: 0.8712 (tmm) REVERT: A 694 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.9016 (tt) REVERT: A 697 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8668 (p0) REVERT: A 884 MET cc_start: 0.8950 (tpp) cc_final: 0.8572 (mmm) REVERT: A 898 PHE cc_start: 0.9112 (m-80) cc_final: 0.8856 (m-80) REVERT: A 954 MET cc_start: 0.8539 (ttm) cc_final: 0.8237 (tpp) REVERT: A 998 ASP cc_start: 0.8743 (m-30) cc_final: 0.8486 (m-30) REVERT: A 1030 LEU cc_start: 0.9309 (mt) cc_final: 0.9107 (tp) REVERT: A 1034 THR cc_start: 0.9266 (m) cc_final: 0.9031 (p) REVERT: A 1054 GLU cc_start: 0.8783 (tt0) cc_final: 0.8397 (tt0) REVERT: A 1064 LYS cc_start: 0.9356 (tptp) cc_final: 0.9092 (tppp) REVERT: A 1131 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8736 (ptp90) outliers start: 31 outliers final: 16 residues processed: 130 average time/residue: 0.1678 time to fit residues: 31.7014 Evaluate side-chains 121 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 249 SER Chi-restraints excluded: chain A residue 253 LYS 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 678 ILE 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 1004 LEU Chi-restraints excluded: chain A residue 1006 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 17 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A1094 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.071957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.055554 restraints weight = 71476.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.058539 restraints weight = 25705.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.060686 restraints weight = 14442.108| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8006 Z= 0.133 Angle : 0.700 9.365 10881 Z= 0.340 Chirality : 0.044 0.209 1251 Planarity : 0.006 0.107 1371 Dihedral : 9.222 75.101 1205 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.71 % Favored : 94.98 % Rotamer: Outliers : 3.19 % Allowed : 26.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.28), residues: 958 helix: 1.23 (0.24), residues: 455 sheet: -0.29 (0.44), residues: 160 loop : -0.71 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 949 HIS 0.003 0.001 HIS A 922 PHE 0.012 0.001 PHE A 518 TYR 0.035 0.001 TYR A 420 ARG 0.007 0.000 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 357) hydrogen bonds : angle 4.14221 ( 1017) covalent geometry : bond 0.00312 ( 8006) covalent geometry : angle 0.70004 (10881) *********************** 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: 26 poor density : 116 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9111 (mmmt) cc_final: 0.8851 (mmmt) REVERT: A 218 ARG cc_start: 0.8692 (mpt-90) cc_final: 0.8346 (mpt-90) REVERT: A 328 TRP cc_start: 0.7881 (t60) cc_final: 0.7348 (t60) REVERT: A 440 GLN cc_start: 0.8499 (mm110) cc_final: 0.7751 (mt0) REVERT: A 663 TRP cc_start: 0.9103 (t-100) cc_final: 0.8729 (t-100) REVERT: A 694 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8881 (tt) REVERT: A 697 ASP cc_start: 0.9044 (m-30) cc_final: 0.8709 (p0) REVERT: A 884 MET cc_start: 0.8865 (tpp) cc_final: 0.8528 (mmm) REVERT: A 898 PHE cc_start: 0.9055 (m-80) cc_final: 0.8812 (m-80) REVERT: A 905 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7928 (pmt-80) REVERT: A 998 ASP cc_start: 0.8583 (m-30) cc_final: 0.8357 (m-30) REVERT: A 1034 THR cc_start: 0.9307 (m) cc_final: 0.9055 (p) REVERT: A 1054 GLU cc_start: 0.8848 (tt0) cc_final: 0.8497 (tt0) REVERT: A 1064 LYS cc_start: 0.9351 (tptp) cc_final: 0.9098 (tppp) REVERT: A 1131 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8758 (ptp90) outliers start: 26 outliers final: 18 residues processed: 133 average time/residue: 0.1909 time to fit residues: 35.9261 Evaluate side-chains 125 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 694 ILE 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 900 LEU Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1094 ASN Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 29 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 82 optimal weight: 0.0670 chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 overall best weight: 1.4522 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.070578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.055777 restraints weight = 38629.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.058205 restraints weight = 19229.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.059957 restraints weight = 12266.879| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8006 Z= 0.146 Angle : 0.719 10.024 10881 Z= 0.343 Chirality : 0.044 0.201 1251 Planarity : 0.005 0.102 1371 Dihedral : 9.164 75.278 1204 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.81 % Favored : 94.98 % Rotamer: Outliers : 3.07 % Allowed : 26.92 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.28), residues: 958 helix: 1.30 (0.24), residues: 455 sheet: -0.39 (0.42), residues: 171 loop : -0.74 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 949 HIS 0.004 0.001 HIS A 503 PHE 0.017 0.001 PHE A1045 TYR 0.008 0.001 TYR A 752 ARG 0.004 0.000 ARG A 524 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 357) hydrogen bonds : angle 4.20539 ( 1017) covalent geometry : bond 0.00340 ( 8006) covalent geometry : angle 0.71869 (10881) *********************** 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 133 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9123 (mmmt) cc_final: 0.8826 (mmmt) REVERT: A 440 GLN cc_start: 0.8561 (mm110) cc_final: 0.7766 (mt0) REVERT: A 538 MET cc_start: 0.8280 (ttm) cc_final: 0.7936 (tmm) REVERT: A 627 MET cc_start: 0.9271 (tmm) cc_final: 0.8667 (tmm) REVERT: A 645 MET cc_start: 0.8844 (tmm) cc_final: 0.8564 (tmm) REVERT: A 663 TRP cc_start: 0.9151 (t-100) cc_final: 0.8807 (t-100) REVERT: A 694 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8978 (tt) REVERT: A 697 ASP cc_start: 0.9046 (m-30) cc_final: 0.8719 (p0) REVERT: A 789 LEU cc_start: 0.9437 (mt) cc_final: 0.9153 (mt) REVERT: A 884 MET cc_start: 0.8905 (tpp) cc_final: 0.8517 (mmm) REVERT: A 905 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7967 (pmt-80) REVERT: A 942 MET cc_start: 0.9229 (mmp) cc_final: 0.8432 (tpt) REVERT: A 954 MET cc_start: 0.7976 (tpp) cc_final: 0.7668 (tpp) REVERT: A 1034 THR cc_start: 0.9325 (m) cc_final: 0.9084 (p) REVERT: A 1064 LYS cc_start: 0.9317 (tptp) cc_final: 0.9058 (tppp) REVERT: A 1131 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8764 (ptp90) outliers start: 25 outliers final: 19 residues processed: 125 average time/residue: 0.1841 time to fit residues: 32.1575 Evaluate side-chains 124 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 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 678 ILE Chi-restraints excluded: chain A residue 694 ILE 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 897 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 0.0470 chunk 19 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- 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 = 0.3312 r_free = 0.3312 target = 0.072526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.057545 restraints weight = 43021.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.060132 restraints weight = 20156.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.061955 restraints weight = 12478.592| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 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 = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8006 Z= 0.124 Angle : 0.696 8.707 10881 Z= 0.335 Chirality : 0.043 0.202 1251 Planarity : 0.005 0.099 1371 Dihedral : 9.083 74.438 1204 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.02 % Favored : 94.77 % Rotamer: Outliers : 3.54 % Allowed : 25.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.28), residues: 958 helix: 1.35 (0.24), residues: 454 sheet: -0.32 (0.42), residues: 161 loop : -0.86 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 328 HIS 0.008 0.001 HIS A 910 PHE 0.033 0.001 PHE A 155 TYR 0.013 0.001 TYR A 187 ARG 0.006 0.000 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 357) hydrogen bonds : angle 4.16022 ( 1017) covalent geometry : bond 0.00291 ( 8006) covalent geometry : angle 0.69639 (10881) *********************** 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 140 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9115 (mmmt) cc_final: 0.8836 (mmmt) REVERT: A 440 GLN cc_start: 0.8585 (mm110) cc_final: 0.7810 (mt0) REVERT: A 577 MET cc_start: 0.8917 (tmm) cc_final: 0.8652 (tmm) REVERT: A 627 MET cc_start: 0.9269 (tmm) cc_final: 0.8675 (tmm) REVERT: A 645 MET cc_start: 0.8822 (tmm) cc_final: 0.8521 (tmm) REVERT: A 663 TRP cc_start: 0.9096 (t-100) cc_final: 0.8810 (t-100) REVERT: A 697 ASP cc_start: 0.9059 (m-30) cc_final: 0.8738 (p0) REVERT: A 789 LEU cc_start: 0.9454 (mt) cc_final: 0.9253 (mt) REVERT: A 884 MET cc_start: 0.8834 (tpp) cc_final: 0.8514 (mmm) REVERT: A 905 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7990 (pmt-80) REVERT: A 954 MET cc_start: 0.7976 (tpp) cc_final: 0.7714 (tpp) REVERT: A 1004 LEU cc_start: 0.9629 (tp) cc_final: 0.9411 (tt) REVERT: A 1034 THR cc_start: 0.9273 (m) cc_final: 0.9070 (p) REVERT: A 1064 LYS cc_start: 0.9271 (tptp) cc_final: 0.9060 (tppp) REVERT: A 1131 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8769 (ptp90) outliers start: 29 outliers final: 19 residues processed: 131 average time/residue: 0.1789 time to fit residues: 33.2128 Evaluate side-chains 125 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 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 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 1094 ASN Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 79 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.3251 r_free = 0.3251 target = 0.069395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.053682 restraints weight = 57466.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.056329 restraints weight = 24244.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.058250 restraints weight = 14527.412| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8006 Z= 0.206 Angle : 0.738 9.134 10881 Z= 0.360 Chirality : 0.045 0.239 1251 Planarity : 0.005 0.098 1371 Dihedral : 9.157 74.895 1204 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.33 % Favored : 94.46 % Rotamer: Outliers : 3.42 % Allowed : 26.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.28), residues: 958 helix: 1.40 (0.24), residues: 454 sheet: -0.45 (0.40), residues: 168 loop : -0.82 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1095 HIS 0.008 0.002 HIS A 910 PHE 0.029 0.002 PHE A 155 TYR 0.008 0.001 TYR A 890 ARG 0.005 0.001 ARG A 470 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 357) hydrogen bonds : angle 4.32865 ( 1017) covalent geometry : bond 0.00464 ( 8006) covalent geometry : angle 0.73804 (10881) *********************** 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 128 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9116 (mmmt) cc_final: 0.8852 (mmmt) REVERT: A 440 GLN cc_start: 0.8661 (mm110) cc_final: 0.7805 (mt0) REVERT: A 538 MET cc_start: 0.7952 (tmm) cc_final: 0.6983 (tmm) REVERT: A 541 THR cc_start: 0.9507 (OUTLIER) cc_final: 0.9305 (p) REVERT: A 627 MET cc_start: 0.9289 (tmm) cc_final: 0.8349 (tpp) REVERT: A 641 GLU cc_start: 0.9252 (tt0) cc_final: 0.8823 (tm-30) REVERT: A 645 MET cc_start: 0.8875 (tmm) cc_final: 0.8613 (tmm) REVERT: A 663 TRP cc_start: 0.9316 (t-100) cc_final: 0.8945 (t-100) REVERT: A 697 ASP cc_start: 0.9088 (m-30) cc_final: 0.8758 (p0) REVERT: A 789 LEU cc_start: 0.9514 (mt) cc_final: 0.9186 (mt) REVERT: A 884 MET cc_start: 0.9016 (tpp) cc_final: 0.8683 (mmm) REVERT: A 905 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7947 (pmt-80) REVERT: A 954 MET cc_start: 0.8001 (tpp) cc_final: 0.7532 (tpp) REVERT: A 1054 GLU cc_start: 0.8587 (tt0) cc_final: 0.8311 (tm-30) REVERT: A 1131 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8808 (ptp90) outliers start: 28 outliers final: 22 residues processed: 119 average time/residue: 0.1768 time to fit residues: 29.9912 Evaluate side-chains 124 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 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 571 LEU 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 724 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 93 optimal weight: 0.0770 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.071422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.055521 restraints weight = 63281.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.058378 restraints weight = 24616.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.060354 restraints weight = 14235.165| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3750 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= 0.122 Angle : 0.719 11.772 10881 Z= 0.342 Chirality : 0.043 0.202 1251 Planarity : 0.005 0.096 1371 Dihedral : 9.035 74.460 1204 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.81 % Favored : 94.98 % Rotamer: Outliers : 3.07 % Allowed : 27.27 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.28), residues: 958 helix: 1.49 (0.24), residues: 454 sheet: -0.27 (0.42), residues: 169 loop : -0.81 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 932 HIS 0.005 0.001 HIS A 910 PHE 0.030 0.001 PHE A 155 TYR 0.010 0.001 TYR A 420 ARG 0.005 0.000 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.03208 ( 357) hydrogen bonds : angle 4.17265 ( 1017) covalent geometry : bond 0.00285 ( 8006) covalent geometry : angle 0.71890 (10881) *********************** 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 132 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9097 (mmmt) cc_final: 0.8857 (mmmt) REVERT: A 440 GLN cc_start: 0.8564 (mm110) cc_final: 0.7796 (mt0) REVERT: A 538 MET cc_start: 0.7915 (tmm) cc_final: 0.6726 (tmm) REVERT: A 577 MET cc_start: 0.8942 (tmm) cc_final: 0.8706 (tmm) REVERT: A 627 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.8349 (tpp) REVERT: A 645 MET cc_start: 0.8850 (tmm) cc_final: 0.8509 (tmm) REVERT: A 663 TRP cc_start: 0.9182 (t-100) cc_final: 0.8896 (t-100) REVERT: A 697 ASP cc_start: 0.9086 (m-30) cc_final: 0.8744 (p0) REVERT: A 789 LEU cc_start: 0.9503 (mt) cc_final: 0.9175 (mt) REVERT: A 884 MET cc_start: 0.8921 (tpp) cc_final: 0.8479 (mmm) REVERT: A 905 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7967 (pmt-80) REVERT: A 954 MET cc_start: 0.7970 (tpp) cc_final: 0.7649 (tpp) REVERT: A 1034 THR cc_start: 0.9302 (m) cc_final: 0.9096 (p) REVERT: A 1064 LYS cc_start: 0.9271 (tptp) cc_final: 0.9058 (tptm) REVERT: A 1131 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8797 (ptp90) outliers start: 25 outliers final: 20 residues processed: 127 average time/residue: 0.1883 time to fit residues: 34.0444 Evaluate side-chains 121 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 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 627 MET 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 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 78 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 93 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 0.0570 chunk 16 optimal weight: 0.0470 chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.072761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.057529 restraints weight = 47959.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.060200 restraints weight = 21476.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.062029 restraints weight = 13110.639| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 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 = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3999 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= 0.121 Angle : 0.732 13.056 10881 Z= 0.346 Chirality : 0.043 0.200 1251 Planarity : 0.005 0.095 1371 Dihedral : 9.015 73.940 1204 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.81 % Favored : 94.98 % Rotamer: Outliers : 2.72 % Allowed : 27.74 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.28), residues: 958 helix: 1.64 (0.25), residues: 447 sheet: -0.27 (0.42), residues: 167 loop : -0.75 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 932 HIS 0.009 0.001 HIS A 910 PHE 0.020 0.001 PHE A 155 TYR 0.015 0.001 TYR A1009 ARG 0.005 0.000 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.03136 ( 357) hydrogen bonds : angle 4.12820 ( 1017) covalent geometry : bond 0.00283 ( 8006) covalent geometry : angle 0.73154 (10881) *********************** 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 126 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9110 (mmmt) cc_final: 0.8859 (mmmt) REVERT: A 440 GLN cc_start: 0.8538 (mm110) cc_final: 0.7805 (mt0) REVERT: A 538 MET cc_start: 0.7925 (tmm) cc_final: 0.6650 (tmm) REVERT: A 577 MET cc_start: 0.8922 (tmm) cc_final: 0.8655 (tmm) REVERT: A 627 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8297 (tpp) REVERT: A 645 MET cc_start: 0.8828 (tmm) cc_final: 0.8481 (tmm) REVERT: A 697 ASP cc_start: 0.9065 (m-30) cc_final: 0.8729 (p0) REVERT: A 789 LEU cc_start: 0.9472 (mt) cc_final: 0.9149 (mt) REVERT: A 884 MET cc_start: 0.8953 (tpp) cc_final: 0.8533 (mmm) REVERT: A 905 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7953 (pmt-80) REVERT: A 954 MET cc_start: 0.7942 (tpp) cc_final: 0.7428 (tpp) REVERT: A 1064 LYS cc_start: 0.9319 (tptp) cc_final: 0.9019 (tppp) REVERT: A 1131 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8800 (ptp90) outliers start: 22 outliers final: 17 residues processed: 121 average time/residue: 0.1779 time to fit residues: 30.3786 Evaluate side-chains 120 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 326 ILE Chi-restraints excluded: chain A residue 356 LEU 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 627 MET 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 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 9 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 910 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.071015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.055159 restraints weight = 58603.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.057957 restraints weight = 24133.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.059941 restraints weight = 14328.438| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4067 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= 0.142 Angle : 0.748 12.976 10881 Z= 0.354 Chirality : 0.044 0.199 1251 Planarity : 0.006 0.109 1371 Dihedral : 8.906 73.743 1200 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.67 % Rotamer: Outliers : 2.95 % Allowed : 27.39 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.28), residues: 958 helix: 1.66 (0.24), residues: 448 sheet: -0.34 (0.42), residues: 170 loop : -0.70 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP A 663 HIS 0.008 0.001 HIS A 910 PHE 0.022 0.001 PHE A 155 TYR 0.009 0.001 TYR A 420 ARG 0.013 0.001 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 357) hydrogen bonds : angle 4.26315 ( 1017) covalent geometry : bond 0.00334 ( 8006) covalent geometry : angle 0.74848 (10881) ********************** 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 124 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9122 (mmmt) cc_final: 0.8871 (mmmt) REVERT: A 440 GLN cc_start: 0.8564 (mm110) cc_final: 0.7743 (mt0) REVERT: A 538 MET cc_start: 0.7942 (tmm) cc_final: 0.6685 (tmm) REVERT: A 577 MET cc_start: 0.8924 (tmm) cc_final: 0.8654 (tmm) REVERT: A 627 MET cc_start: 0.9243 (tmm) cc_final: 0.8581 (tmm) REVERT: A 645 MET cc_start: 0.8807 (tmm) cc_final: 0.8461 (tmm) REVERT: A 697 ASP cc_start: 0.9072 (m-30) cc_final: 0.8728 (p0) REVERT: A 789 LEU cc_start: 0.9484 (mt) cc_final: 0.9157 (mt) REVERT: A 884 MET cc_start: 0.9094 (tpp) cc_final: 0.8424 (mmm) REVERT: A 905 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7931 (pmt-80) REVERT: A 914 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8357 (tp) REVERT: A 954 MET cc_start: 0.7915 (tpp) cc_final: 0.7418 (tpp) REVERT: A 1054 GLU cc_start: 0.8527 (tt0) cc_final: 0.8173 (tm-30) REVERT: A 1131 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8822 (ptp90) outliers start: 24 outliers final: 18 residues processed: 116 average time/residue: 0.1770 time to fit residues: 30.1460 Evaluate side-chains 119 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 326 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 635 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 724 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 68 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 910 HIS A1037 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.071510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.055928 restraints weight = 51185.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.058641 restraints weight = 22144.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.060546 restraints weight = 13311.234| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4160 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= 0.141 Angle : 0.747 12.570 10881 Z= 0.352 Chirality : 0.044 0.199 1251 Planarity : 0.005 0.094 1371 Dihedral : 8.860 73.810 1200 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.67 % Rotamer: Outliers : 2.48 % Allowed : 28.34 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.28), residues: 958 helix: 1.68 (0.24), residues: 448 sheet: -0.21 (0.42), residues: 168 loop : -0.78 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP A 663 HIS 0.006 0.001 HIS A 910 PHE 0.022 0.001 PHE A 155 TYR 0.008 0.001 TYR A1009 ARG 0.008 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 357) hydrogen bonds : angle 4.28353 ( 1017) covalent geometry : bond 0.00333 ( 8006) covalent geometry : angle 0.74725 (10881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3207.11 seconds wall clock time: 56 minutes 1.47 seconds (3361.47 seconds total)