Starting phenix.real_space_refine on Fri May 16 12:51:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pjb_17703/05_2025/8pjb_17703.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pjb_17703/05_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_17703/05_2025/8pjb_17703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pjb_17703/05_2025/8pjb_17703.map" model { file = "/net/cci-nas-00/data/ceres_data/8pjb_17703/05_2025/8pjb_17703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pjb_17703/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 8.05, per 1000 atoms: 1.03 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: 1.90 Conformation dependent library (CDL) restraints added in 1.7 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: 1.26 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: 3.01 Time building geometry restraints manager: 2.22 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.890 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:3.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.840 ------------------------------------------------------------------------------- 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 : 0.943 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: 0.2071 time to fit residues: 53.8232 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 : 0.876 ------------------------------------------------------------------------------- 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 = 0.072877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.056712 restraints weight = 57134.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.059663 restraints weight = 23477.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.061760 restraints weight = 13745.489| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 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 = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 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 77.712 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 0.03864 ( 357) hydrogen bonds : angle 4.46106 ( 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 : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8548 (p) REVERT: A 253 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8517 (mmmt) REVERT: A 525 ASP cc_start: 0.8860 (OUTLIER) cc_final: 0.8610 (t0) REVERT: A 670 MET cc_start: 0.8946 (ttm) cc_final: 0.8433 (tmm) REVERT: A 697 ASP cc_start: 0.9033 (m-30) cc_final: 0.8709 (t0) REVERT: A 718 ASN cc_start: 0.8426 (OUTLIER) cc_final: 0.8191 (p0) REVERT: A 740 MET cc_start: 0.8684 (ptm) cc_final: 0.8482 (ptp) REVERT: A 884 MET cc_start: 0.8981 (tpp) cc_final: 0.8394 (mmm) REVERT: A 954 MET cc_start: 0.8575 (ttm) cc_final: 0.8293 (tpp) REVERT: A 969 ASP cc_start: 0.9456 (t0) cc_final: 0.9039 (m-30) REVERT: A 1005 CYS cc_start: 0.8589 (m) cc_final: 0.8384 (m) REVERT: A 1030 LEU cc_start: 0.9284 (mt) cc_final: 0.9068 (tp) REVERT: A 1054 GLU cc_start: 0.8718 (tt0) cc_final: 0.8368 (tt0) REVERT: A 1131 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8481 (ptp-110) outliers start: 28 outliers final: 16 residues processed: 144 average time/residue: 0.1779 time to fit residues: 36.0325 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 : 0.842 ------------------------------------------------------------------------------- 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: 0.9990 chunk 70 optimal weight: 0.9980 chunk 95 optimal weight: 0.0270 chunk 52 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 5 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.073659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.058051 restraints weight = 48167.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.060823 restraints weight = 21533.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.062803 restraints weight = 13031.790| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 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 = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8006 Z= 0.133 Angle : 0.727 10.113 10881 Z= 0.350 Chirality : 0.044 0.220 1251 Planarity : 0.006 0.115 1371 Dihedral : 9.717 75.495 1213 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.60 % Favored : 95.08 % Rotamer: Outliers : 3.54 % Allowed : 25.86 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 454 sheet: -0.36 (0.44), residues: 159 loop : -0.75 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 949 HIS 0.004 0.001 HIS A 910 PHE 0.024 0.001 PHE A 155 TYR 0.039 0.002 TYR A 420 ARG 0.007 0.001 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 357) hydrogen bonds : angle 4.22043 ( 1017) covalent geometry : bond 0.00300 ( 8006) covalent geometry : angle 0.72670 (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 149 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 TRP cc_start: 0.8173 (t60) cc_final: 0.7752 (t60) REVERT: A 440 GLN cc_start: 0.8455 (mm110) cc_final: 0.7768 (mt0) REVERT: A 663 TRP cc_start: 0.9005 (t-100) cc_final: 0.8689 (t-100) REVERT: A 670 MET cc_start: 0.8922 (ttm) cc_final: 0.8401 (tmm) REVERT: A 694 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.8975 (tt) REVERT: A 697 ASP cc_start: 0.8981 (OUTLIER) cc_final: 0.8629 (p0) REVERT: A 884 MET cc_start: 0.8884 (tpp) cc_final: 0.8499 (mmm) REVERT: A 954 MET cc_start: 0.8579 (ttm) cc_final: 0.8347 (tpp) REVERT: A 998 ASP cc_start: 0.8639 (m-30) cc_final: 0.8378 (m-30) REVERT: A 1054 GLU cc_start: 0.8763 (tt0) cc_final: 0.8420 (tt0) REVERT: A 1064 LYS cc_start: 0.9313 (tptp) cc_final: 0.9070 (tppp) REVERT: A 1131 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8710 (ptp90) outliers start: 29 outliers final: 17 residues processed: 140 average time/residue: 0.1620 time to fit residues: 33.0241 Evaluate side-chains 122 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 345 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 17 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3275 r_free = 0.3275 target = 0.070757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.054239 restraints weight = 73538.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.057143 restraints weight = 27369.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.059225 restraints weight = 15746.903| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8006 Z= 0.173 Angle : 0.718 9.496 10881 Z= 0.348 Chirality : 0.044 0.218 1251 Planarity : 0.006 0.106 1371 Dihedral : 9.367 76.391 1207 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.13 % Favored : 94.56 % Rotamer: Outliers : 3.42 % Allowed : 25.97 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.28), residues: 958 helix: 1.20 (0.24), residues: 455 sheet: -0.48 (0.42), residues: 169 loop : -0.66 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 949 HIS 0.005 0.001 HIS A 503 PHE 0.018 0.001 PHE A1045 TYR 0.015 0.002 TYR A 420 ARG 0.008 0.001 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 357) hydrogen bonds : angle 4.26615 ( 1017) covalent geometry : bond 0.00395 ( 8006) covalent geometry : angle 0.71790 (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 133 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9175 (mmmt) cc_final: 0.8915 (mmmt) REVERT: A 328 TRP cc_start: 0.7935 (t60) cc_final: 0.7734 (t60) REVERT: A 440 GLN cc_start: 0.8561 (mm110) cc_final: 0.7757 (mt0) REVERT: A 627 MET cc_start: 0.9212 (tmm) cc_final: 0.8188 (tpp) REVERT: A 663 TRP cc_start: 0.9164 (t-100) cc_final: 0.8797 (t-100) REVERT: A 694 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8891 (tt) REVERT: A 697 ASP cc_start: 0.9029 (OUTLIER) cc_final: 0.8694 (p0) REVERT: A 884 MET cc_start: 0.8913 (tpp) cc_final: 0.8560 (mmm) REVERT: A 898 PHE cc_start: 0.9116 (m-80) cc_final: 0.8866 (m-80) REVERT: A 905 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7841 (pmt-80) REVERT: A 954 MET cc_start: 0.8513 (ttm) cc_final: 0.8290 (tpp) REVERT: A 998 ASP cc_start: 0.8573 (m-30) cc_final: 0.8337 (m-30) REVERT: A 1054 GLU cc_start: 0.8913 (tt0) cc_final: 0.8554 (tt0) REVERT: A 1131 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8778 (ptp90) outliers start: 28 outliers final: 20 residues processed: 123 average time/residue: 0.1727 time to fit residues: 30.1939 Evaluate side-chains 125 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 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: 6.9990 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3276 r_free = 0.3276 target = 0.070144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.055683 restraints weight = 37542.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.058086 restraints weight = 18956.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.059805 restraints weight = 12172.417| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 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 = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3214 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= 0.139 Angle : 0.703 9.141 10881 Z= 0.337 Chirality : 0.043 0.203 1251 Planarity : 0.005 0.101 1371 Dihedral : 9.151 74.841 1204 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.92 % Favored : 94.87 % Rotamer: Outliers : 3.54 % Allowed : 26.09 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.37 (0.28), residues: 958 helix: 1.31 (0.24), residues: 454 sheet: -0.54 (0.41), residues: 171 loop : -0.70 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 328 HIS 0.004 0.001 HIS A 503 PHE 0.017 0.001 PHE A1045 TYR 0.016 0.001 TYR A 187 ARG 0.005 0.000 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 357) hydrogen bonds : angle 4.17485 ( 1017) covalent geometry : bond 0.00321 ( 8006) covalent geometry : angle 0.70302 (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 139 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9144 (mmmt) cc_final: 0.8868 (mmmt) REVERT: A 328 TRP cc_start: 0.7990 (t60) cc_final: 0.7628 (t60) REVERT: A 440 GLN cc_start: 0.8512 (mm110) cc_final: 0.7740 (mt0) REVERT: A 538 MET cc_start: 0.7455 (tmm) cc_final: 0.6356 (tmm) REVERT: A 541 THR cc_start: 0.9442 (OUTLIER) cc_final: 0.9231 (p) REVERT: A 627 MET cc_start: 0.9214 (tmm) cc_final: 0.8172 (tpp) REVERT: A 641 GLU cc_start: 0.9317 (tt0) cc_final: 0.9063 (pp20) REVERT: A 663 TRP cc_start: 0.9134 (t-100) cc_final: 0.8806 (t-100) REVERT: A 694 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8912 (tt) REVERT: A 697 ASP cc_start: 0.9033 (m-30) cc_final: 0.8719 (p0) REVERT: A 740 MET cc_start: 0.8450 (ptm) cc_final: 0.8229 (ptm) REVERT: A 884 MET cc_start: 0.8899 (tpp) cc_final: 0.8522 (mmm) REVERT: A 905 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7860 (pmt-80) REVERT: A 942 MET cc_start: 0.9237 (mmp) cc_final: 0.8397 (tpt) REVERT: A 1131 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8772 (ptp90) outliers start: 29 outliers final: 19 residues processed: 130 average time/residue: 0.1858 time to fit residues: 33.8490 Evaluate side-chains 125 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 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 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 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 1072 LEU Chi-restraints excluded: chain A residue 1094 ASN Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 42 optimal weight: 0.3980 chunk 77 optimal weight: 4.9990 chunk 17 optimal weight: 0.0770 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 = 0.3306 r_free = 0.3306 target = 0.071903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.057119 restraints weight = 42597.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.059675 restraints weight = 20021.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.061493 restraints weight = 12398.196| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 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 = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3486 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= 0.125 Angle : 0.700 9.248 10881 Z= 0.336 Chirality : 0.043 0.201 1251 Planarity : 0.005 0.098 1371 Dihedral : 9.076 74.171 1204 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.02 % Favored : 94.77 % Rotamer: Outliers : 3.78 % Allowed : 25.38 % 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: 0.35 (0.28), residues: 958 helix: 1.34 (0.24), residues: 453 sheet: -0.53 (0.42), residues: 163 loop : -0.80 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 949 HIS 0.006 0.001 HIS A 910 PHE 0.032 0.001 PHE A 155 TYR 0.015 0.001 TYR A 187 ARG 0.004 0.000 ARG A 524 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 357) hydrogen bonds : angle 4.11278 ( 1017) covalent geometry : bond 0.00289 ( 8006) covalent geometry : angle 0.69955 (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 137 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9137 (mmmt) cc_final: 0.8847 (mmmt) REVERT: A 328 TRP cc_start: 0.7980 (t60) cc_final: 0.7605 (t60) REVERT: A 440 GLN cc_start: 0.8517 (mm110) cc_final: 0.7780 (mt0) REVERT: A 472 GLU cc_start: 0.6979 (mp0) cc_final: 0.6677 (mp0) REVERT: A 627 MET cc_start: 0.9228 (tmm) cc_final: 0.8803 (tpp) REVERT: A 641 GLU cc_start: 0.9329 (tt0) cc_final: 0.9056 (pp20) REVERT: A 663 TRP cc_start: 0.9085 (t-100) cc_final: 0.8825 (t-100) REVERT: A 697 ASP cc_start: 0.9065 (m-30) cc_final: 0.8744 (p0) REVERT: A 884 MET cc_start: 0.8869 (tpp) cc_final: 0.8518 (mmm) REVERT: A 905 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7914 (pmt-80) REVERT: A 954 MET cc_start: 0.7983 (tpp) cc_final: 0.7711 (tpp) REVERT: A 1004 LEU cc_start: 0.9618 (tp) cc_final: 0.9353 (tt) REVERT: A 1064 LYS cc_start: 0.9055 (tptm) cc_final: 0.8726 (tppt) REVERT: A 1131 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8789 (ptp90) outliers start: 31 outliers final: 20 residues processed: 128 average time/residue: 0.1668 time to fit residues: 30.8252 Evaluate side-chains 127 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 79 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3265 r_free = 0.3265 target = 0.070031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.054476 restraints weight = 56300.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.057179 restraints weight = 23565.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.059092 restraints weight = 13998.553| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- 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: 0.8456 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8006 Z= 0.180 Angle : 0.725 9.380 10881 Z= 0.353 Chirality : 0.044 0.199 1251 Planarity : 0.005 0.097 1371 Dihedral : 9.108 74.380 1204 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.23 % Favored : 94.56 % Rotamer: Outliers : 3.19 % Allowed : 26.68 % 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: 0.43 (0.28), residues: 958 helix: 1.42 (0.24), residues: 452 sheet: -0.51 (0.40), residues: 168 loop : -0.75 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 932 HIS 0.008 0.002 HIS A 910 PHE 0.029 0.001 PHE A 155 TYR 0.012 0.001 TYR A 550 ARG 0.004 0.000 ARG A 524 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 357) hydrogen bonds : angle 4.29028 ( 1017) covalent geometry : bond 0.00412 ( 8006) covalent geometry : angle 0.72493 (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 132 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9145 (mmmt) cc_final: 0.8901 (mmmt) REVERT: A 328 TRP cc_start: 0.8102 (t60) cc_final: 0.7671 (t60) REVERT: A 440 GLN cc_start: 0.8565 (mm110) cc_final: 0.7737 (mt0) REVERT: A 472 GLU cc_start: 0.7033 (mp0) cc_final: 0.6784 (mp0) REVERT: A 508 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8063 (mm-30) REVERT: A 538 MET cc_start: 0.7672 (tmm) cc_final: 0.6576 (tmm) REVERT: A 541 THR cc_start: 0.9496 (OUTLIER) cc_final: 0.9287 (p) REVERT: A 641 GLU cc_start: 0.9318 (tt0) cc_final: 0.9115 (tt0) REVERT: A 663 TRP cc_start: 0.9158 (t-100) cc_final: 0.8884 (t-100) REVERT: A 697 ASP cc_start: 0.9096 (m-30) cc_final: 0.8757 (p0) REVERT: A 884 MET cc_start: 0.9032 (tpp) cc_final: 0.8463 (mmm) REVERT: A 905 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7945 (pmt-80) REVERT: A 954 MET cc_start: 0.7976 (tpp) cc_final: 0.7696 (tpp) REVERT: A 1054 GLU cc_start: 0.8741 (tt0) cc_final: 0.8382 (tm-30) REVERT: A 1064 LYS cc_start: 0.9167 (tptm) cc_final: 0.8518 (tppt) REVERT: A 1131 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8794 (ptp90) outliers start: 26 outliers final: 21 residues processed: 124 average time/residue: 0.1920 time to fit residues: 33.1754 Evaluate side-chains 126 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 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: 3.9990 chunk 17 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 56 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3306 r_free = 0.3306 target = 0.071547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.055640 restraints weight = 63024.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.058499 restraints weight = 24729.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.060535 restraints weight = 14324.438| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3839 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= 0.123 Angle : 0.727 10.935 10881 Z= 0.349 Chirality : 0.043 0.202 1251 Planarity : 0.005 0.096 1371 Dihedral : 9.000 73.517 1204 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.71 % Favored : 95.08 % Rotamer: Outliers : 3.19 % Allowed : 27.15 % 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 (0.25), residues: 452 sheet: -0.36 (0.41), residues: 168 loop : -0.74 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 932 HIS 0.007 0.001 HIS A 910 PHE 0.029 0.001 PHE A 155 TYR 0.016 0.001 TYR A1009 ARG 0.005 0.000 ARG A1080 Details of bonding type rmsd hydrogen bonds : bond 0.03176 ( 357) hydrogen bonds : angle 4.22396 ( 1017) covalent geometry : bond 0.00284 ( 8006) covalent geometry : angle 0.72667 (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 133 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.974 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: 0.8870 (mmmt) REVERT: A 328 TRP cc_start: 0.8037 (t60) cc_final: 0.7626 (t60) REVERT: A 440 GLN cc_start: 0.8516 (mm110) cc_final: 0.7775 (mt0) REVERT: A 472 GLU cc_start: 0.7057 (mp0) cc_final: 0.6837 (mp0) REVERT: A 508 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8015 (mm-30) REVERT: A 538 MET cc_start: 0.7753 (tmm) cc_final: 0.6640 (tmm) REVERT: A 629 MET cc_start: 0.9315 (pmm) cc_final: 0.9035 (pmm) REVERT: A 641 GLU cc_start: 0.9301 (tt0) cc_final: 0.9098 (tt0) REVERT: A 645 MET cc_start: 0.8828 (tmm) cc_final: 0.8538 (tmm) REVERT: A 697 ASP cc_start: 0.9079 (m-30) cc_final: 0.8741 (p0) REVERT: A 798 PHE cc_start: 0.9476 (m-80) cc_final: 0.9254 (m-80) REVERT: A 884 MET cc_start: 0.9027 (tpp) cc_final: 0.8401 (mmm) REVERT: A 905 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7948 (pmt-80) REVERT: A 954 MET cc_start: 0.7918 (tpp) cc_final: 0.7621 (tpp) REVERT: A 1131 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8797 (ptp90) outliers start: 26 outliers final: 20 residues processed: 127 average time/residue: 0.1956 time to fit residues: 35.1233 Evaluate side-chains 123 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 905 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 0.0670 chunk 28 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 HIS A 910 HIS 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 = 0.071558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.056344 restraints weight = 48156.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.058957 restraints weight = 21680.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.060822 restraints weight = 13278.645| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 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 = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3948 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= 0.139 Angle : 0.737 12.082 10881 Z= 0.356 Chirality : 0.044 0.198 1251 Planarity : 0.005 0.095 1371 Dihedral : 8.878 73.493 1200 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.34 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: 0.59 (0.28), residues: 958 helix: 1.57 (0.25), residues: 446 sheet: -0.36 (0.41), residues: 169 loop : -0.73 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP A 663 HIS 0.009 0.001 HIS A 910 PHE 0.017 0.001 PHE A 155 TYR 0.011 0.001 TYR A 420 ARG 0.006 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 357) hydrogen bonds : angle 4.24597 ( 1017) covalent geometry : bond 0.00328 ( 8006) covalent geometry : angle 0.73726 (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 125 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.982 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: 0.9121 (mmmt) cc_final: 0.8884 (mmmt) REVERT: A 328 TRP cc_start: 0.8045 (t60) cc_final: 0.7632 (t60) REVERT: A 440 GLN cc_start: 0.8523 (mm110) cc_final: 0.7745 (mt0) REVERT: A 472 GLU cc_start: 0.7015 (mp0) cc_final: 0.6801 (mp0) REVERT: A 508 GLU cc_start: 0.8611 (mm-30) cc_final: 0.7995 (mm-30) REVERT: A 538 MET cc_start: 0.7753 (tmm) cc_final: 0.6661 (tmm) REVERT: A 641 GLU cc_start: 0.9295 (tt0) cc_final: 0.9094 (tt0) REVERT: A 645 MET cc_start: 0.8817 (tmm) cc_final: 0.8525 (tmm) REVERT: A 697 ASP cc_start: 0.9078 (m-30) cc_final: 0.8737 (p0) REVERT: A 798 PHE cc_start: 0.9494 (m-80) cc_final: 0.9287 (m-80) REVERT: A 884 MET cc_start: 0.9062 (tpp) cc_final: 0.8592 (mmm) REVERT: A 905 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7924 (pmt-80) REVERT: A 954 MET cc_start: 0.7917 (tpp) cc_final: 0.7447 (tpp) REVERT: A 1131 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8799 (ptp90) outliers start: 25 outliers final: 19 residues processed: 119 average time/residue: 0.1825 time to fit residues: 30.8828 Evaluate side-chains 122 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1131 ARG Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 0.0670 chunk 63 optimal weight: 0.7980 chunk 75 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- 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 = 0.3281 r_free = 0.3281 target = 0.070152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.054488 restraints weight = 58396.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.057237 restraints weight = 23958.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.059217 restraints weight = 14137.659| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 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 = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8006 Z= 0.161 Angle : 0.733 13.263 10881 Z= 0.355 Chirality : 0.044 0.199 1251 Planarity : 0.005 0.095 1371 Dihedral : 8.888 73.475 1200 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.81 % Favored : 94.98 % 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: 0.55 (0.28), residues: 958 helix: 1.55 (0.25), residues: 447 sheet: -0.45 (0.41), residues: 171 loop : -0.72 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 663 HIS 0.008 0.001 HIS A 910 PHE 0.013 0.001 PHE A 155 TYR 0.012 0.001 TYR A 420 ARG 0.006 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 357) hydrogen bonds : angle 4.30906 ( 1017) covalent geometry : bond 0.00372 ( 8006) covalent geometry : angle 0.73326 (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 123 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.952 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: 0.9131 (mmmt) cc_final: 0.8896 (mmmt) REVERT: A 328 TRP cc_start: 0.8079 (t60) cc_final: 0.7631 (t60) REVERT: A 440 GLN cc_start: 0.8593 (mm110) cc_final: 0.7769 (mt0) REVERT: A 508 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8000 (mm-30) REVERT: A 538 MET cc_start: 0.7858 (tmm) cc_final: 0.6532 (tmm) REVERT: A 645 MET cc_start: 0.8826 (tmm) cc_final: 0.8531 (tmm) REVERT: A 697 ASP cc_start: 0.9086 (m-30) cc_final: 0.8759 (p0) REVERT: A 798 PHE cc_start: 0.9520 (m-80) cc_final: 0.9294 (m-80) REVERT: A 884 MET cc_start: 0.9098 (tpp) cc_final: 0.8631 (mmm) REVERT: A 887 MET cc_start: 0.9383 (mtp) cc_final: 0.9152 (mtp) REVERT: A 905 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7931 (pmt-80) REVERT: A 954 MET cc_start: 0.7910 (tpp) cc_final: 0.7450 (tpp) REVERT: A 1054 GLU cc_start: 0.8620 (tt0) cc_final: 0.8209 (tm-30) REVERT: A 1131 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8832 (ptp90) outliers start: 24 outliers final: 21 residues processed: 116 average time/residue: 0.1834 time to fit residues: 30.2395 Evaluate side-chains 117 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1056 ILE Chi-restraints excluded: chain A residue 1131 ARG Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 68 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 89 optimal weight: 0.0470 chunk 17 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 = 0.3317 r_free = 0.3317 target = 0.071764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.056173 restraints weight = 51402.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.058932 restraints weight = 22509.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.060866 restraints weight = 13556.709| |-----------------------------------------------------------------------------| 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) = 0.062 | | 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) = 0.062 | | 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: 0.8411 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8006 Z= 0.127 Angle : 0.739 12.263 10881 Z= 0.356 Chirality : 0.044 0.201 1251 Planarity : 0.005 0.093 1371 Dihedral : 8.855 73.524 1200 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.71 % Favored : 95.08 % Rotamer: Outliers : 3.19 % Allowed : 27.27 % 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: 0.48 (0.28), residues: 958 helix: 1.46 (0.25), residues: 448 sheet: -0.44 (0.41), residues: 171 loop : -0.73 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 663 HIS 0.007 0.001 HIS A 910 PHE 0.012 0.001 PHE A 155 TYR 0.012 0.001 TYR A 420 ARG 0.007 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 357) hydrogen bonds : angle 4.31262 ( 1017) covalent geometry : bond 0.00296 ( 8006) covalent geometry : angle 0.73935 (10881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2997.94 seconds wall clock time: 53 minutes 0.10 seconds (3180.10 seconds total)