Starting phenix.real_space_refine on Tue Jan 13 13:04:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tny_26023/01_2026/7tny_26023.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tny_26023/01_2026/7tny_26023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tny_26023/01_2026/7tny_26023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tny_26023/01_2026/7tny_26023.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tny_26023/01_2026/7tny_26023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tny_26023/01_2026/7tny_26023.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 25 5.49 5 S 33 5.16 5 C 3654 2.51 5 N 996 2.21 5 O 1156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5865 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5347 Classifications: {'peptide': 666} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 28, 'TRANS': 637} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 264 Unusual residues: {'GDP': 1} Classifications: {'RNA': 11, 'undetermined': 1} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna3p': 10, None: 1} Not linked: pdbres="GDP B 1 " pdbres=" G B 2 " Chain: "C" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 253 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 7} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4423 SG CYS A 810 69.001 56.638 22.800 1.00 29.85 S ATOM 4862 SG CYS A 864 68.607 55.061 18.956 1.00 41.61 S ATOM 4901 SG CYS A 869 70.871 53.767 21.505 1.00 42.96 S Time building chain proxies: 1.46, per 1000 atoms: 0.25 Number of scatterers: 5865 At special positions: 0 Unit cell: (100.392, 85.44, 80.1, 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) Zn 1 29.99 S 33 16.00 P 25 15.00 O 1156 8.00 N 996 7.00 C 3654 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 166.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1274 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 5 sheets defined 48.5% alpha, 9.3% beta 8 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 251 through 257 removed outlier: 3.522A pdb=" N GLY A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 284 removed outlier: 3.790A pdb=" N THR A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 333 through 339 Processing helix chain 'A' and resid 347 through 358 removed outlier: 4.237A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.868A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 381 through 396 removed outlier: 3.636A pdb=" N GLN A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 435 Processing helix chain 'A' and resid 445 through 452 removed outlier: 3.916A pdb=" N LEU A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 488 removed outlier: 3.769A pdb=" N ARG A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 521 removed outlier: 3.896A pdb=" N GLU A 510 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 511 " --> pdb=" O GLN A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 558 removed outlier: 3.750A pdb=" N LYS A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 removed outlier: 3.871A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 564 " --> pdb=" O MET A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 603 removed outlier: 3.796A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 607 removed outlier: 3.514A pdb=" N GLU A 607 " --> pdb=" O PRO A 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 604 through 607' Processing helix chain 'A' and resid 608 through 625 removed outlier: 3.656A pdb=" N GLU A 612 " --> pdb=" O ASN A 608 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU A 621 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 649 removed outlier: 4.003A pdb=" N ASP A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 684 removed outlier: 3.511A pdb=" N LEU A 682 " --> pdb=" O GLN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 769 removed outlier: 3.526A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET A 755 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR A 756 " --> pdb=" O GLN A 752 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A 759 " --> pdb=" O MET A 755 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 794 removed outlier: 4.306A pdb=" N HIS A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 892 Processing sheet with id=AA1, first strand: chain 'A' and resid 321 through 324 removed outlier: 6.417A pdb=" N VAL A 293 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU A 346 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE A 295 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 460 removed outlier: 7.036A pdb=" N GLN A 457 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU A 740 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE A 459 " --> pdb=" O LEU A 740 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 816 through 819 Processing sheet with id=AA4, first strand: chain 'A' and resid 831 through 833 removed outlier: 4.531A pdb=" N ILE A 916 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 842 through 846 removed outlier: 6.755A pdb=" N LYS A 858 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LYS A 878 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N CYS A 864 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASP A 872 " --> pdb=" O CYS A 864 " (cutoff:3.500A) 243 hydrogen bonds defined for protein. 711 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1703 1.33 - 1.46: 918 1.46 - 1.58: 3316 1.58 - 1.70: 47 1.70 - 1.82: 46 Bond restraints: 6030 Sorted by residual: bond pdb=" CA SER A 654 " pdb=" CB SER A 654 " ideal model delta sigma weight residual 1.536 1.491 0.045 1.42e-02 4.96e+03 1.00e+01 bond pdb=" N VAL A 453 " pdb=" CA VAL A 453 " ideal model delta sigma weight residual 1.460 1.487 -0.027 8.60e-03 1.35e+04 9.57e+00 bond pdb=" C GLY A 663 " pdb=" O GLY A 663 " ideal model delta sigma weight residual 1.229 1.254 -0.024 8.20e-03 1.49e+04 8.73e+00 bond pdb=" N ILE A 725 " pdb=" CA ILE A 725 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.19e-02 7.06e+03 8.68e+00 bond pdb=" N VAL A 414 " pdb=" CA VAL A 414 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.66e+00 ... (remaining 6025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 6346 1.39 - 2.79: 1790 2.79 - 4.18: 98 4.18 - 5.57: 10 5.57 - 6.97: 3 Bond angle restraints: 8247 Sorted by residual: angle pdb=" N VAL A 453 " pdb=" CA VAL A 453 " pdb=" C VAL A 453 " ideal model delta sigma weight residual 113.71 108.29 5.42 9.50e-01 1.11e+00 3.25e+01 angle pdb=" N ILE A 489 " pdb=" CA ILE A 489 " pdb=" C ILE A 489 " ideal model delta sigma weight residual 111.45 108.11 3.34 9.30e-01 1.16e+00 1.29e+01 angle pdb=" C THR A 347 " pdb=" N PRO A 348 " pdb=" CA PRO A 348 " ideal model delta sigma weight residual 119.24 122.84 -3.60 1.04e+00 9.25e-01 1.20e+01 angle pdb=" N ASP A 529 " pdb=" CA ASP A 529 " pdb=" C ASP A 529 " ideal model delta sigma weight residual 113.43 109.11 4.32 1.26e+00 6.30e-01 1.17e+01 angle pdb=" CA VAL A 414 " pdb=" C VAL A 414 " pdb=" O VAL A 414 " ideal model delta sigma weight residual 120.30 117.38 2.92 9.40e-01 1.13e+00 9.65e+00 ... (remaining 8242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 3299 17.71 - 35.42: 280 35.42 - 53.13: 81 53.13 - 70.84: 30 70.84 - 88.55: 19 Dihedral angle restraints: 3709 sinusoidal: 1752 harmonic: 1957 Sorted by residual: dihedral pdb=" CA PHE A 853 " pdb=" C PHE A 853 " pdb=" N SER A 854 " pdb=" CA SER A 854 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" O4' C C 13 " pdb=" C1' C C 13 " pdb=" N1 C C 13 " pdb=" C2 C C 13 " ideal model delta sinusoidal sigma weight residual -160.00 -115.80 -44.20 1 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CA GLY A 358 " pdb=" C GLY A 358 " pdb=" N THR A 359 " pdb=" CA THR A 359 " ideal model delta harmonic sigma weight residual -180.00 -162.99 -17.01 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 3706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 388 0.038 - 0.076: 278 0.076 - 0.114: 199 0.114 - 0.152: 65 0.152 - 0.190: 9 Chirality restraints: 939 Sorted by residual: chirality pdb=" P G B 2 " pdb=" OP1 G B 2 " pdb=" OP2 G B 2 " pdb=" O5' G B 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.22 0.19 2.00e-01 2.50e+01 9.02e-01 chirality pdb=" C2' G C 14 " pdb=" C3' G C 14 " pdb=" O2' G C 14 " pdb=" C1' G C 14 " both_signs ideal model delta sigma weight residual False -2.75 -2.57 -0.18 2.00e-01 2.50e+01 8.22e-01 chirality pdb=" C2' G B 12 " pdb=" C3' G B 12 " pdb=" O2' G B 12 " pdb=" C1' G B 12 " both_signs ideal model delta sigma weight residual False -2.75 -2.57 -0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 936 not shown) Planarity restraints: 965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A C 19 " 0.020 2.00e-02 2.50e+03 8.51e-03 1.99e+00 pdb=" N9 A C 19 " -0.009 2.00e-02 2.50e+03 pdb=" C8 A C 19 " -0.009 2.00e-02 2.50e+03 pdb=" N7 A C 19 " -0.005 2.00e-02 2.50e+03 pdb=" C5 A C 19 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A C 19 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A C 19 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A C 19 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A C 19 " -0.010 2.00e-02 2.50e+03 pdb=" N3 A C 19 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A C 19 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 697 " -0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C THR A 697 " 0.023 2.00e-02 2.50e+03 pdb=" O THR A 697 " -0.008 2.00e-02 2.50e+03 pdb=" N SER A 698 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 5 " -0.013 2.00e-02 2.50e+03 7.52e-03 1.70e+00 pdb=" N9 G B 5 " -0.002 2.00e-02 2.50e+03 pdb=" C8 G B 5 " 0.010 2.00e-02 2.50e+03 pdb=" N7 G B 5 " 0.013 2.00e-02 2.50e+03 pdb=" C5 G B 5 " -0.005 2.00e-02 2.50e+03 pdb=" C6 G B 5 " -0.007 2.00e-02 2.50e+03 pdb=" O6 G B 5 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G B 5 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G B 5 " 0.008 2.00e-02 2.50e+03 pdb=" N2 G B 5 " 0.005 2.00e-02 2.50e+03 pdb=" N3 G B 5 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G B 5 " -0.002 2.00e-02 2.50e+03 ... (remaining 962 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 1461 2.82 - 3.34: 5630 3.34 - 3.86: 9571 3.86 - 4.38: 11184 4.38 - 4.90: 18702 Nonbonded interactions: 46548 Sorted by model distance: nonbonded pdb=" O LYS A 379 " pdb=" OP1 G B 5 " model vdw 2.306 3.040 nonbonded pdb=" OG SER A 362 " pdb=" OG SER A 364 " model vdw 2.355 3.040 nonbonded pdb=" O GLU A 503 " pdb=" OG1 THR A 506 " model vdw 2.364 3.040 nonbonded pdb=" N ASP A 580 " pdb=" OD1 ASP A 580 " model vdw 2.365 3.120 nonbonded pdb=" OE2 GLU A 531 " pdb=" NZ LYS A 814 " model vdw 2.422 3.120 ... (remaining 46543 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.350 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 : 0.014 0.591 6034 Z= 0.875 Angle : 1.143 6.967 8247 Z= 0.833 Chirality : 0.067 0.190 939 Planarity : 0.004 0.021 965 Dihedral : 16.383 88.548 2435 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.84 % Allowed : 8.60 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.29), residues: 658 helix: -0.79 (0.29), residues: 281 sheet: -3.50 (0.47), residues: 81 loop : -3.01 (0.31), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 845 TYR 0.015 0.003 TYR A 548 PHE 0.016 0.003 PHE A 853 TRP 0.014 0.003 TRP A 873 HIS 0.013 0.002 HIS A 876 Details of bonding type rmsd covalent geometry : bond 0.01080 ( 6030) covalent geometry : angle 1.14286 ( 8247) hydrogen bonds : bond 0.14479 ( 263) hydrogen bonds : angle 5.65574 ( 751) metal coordination : bond 0.40865 ( 3) Misc. bond : bond 0.14639 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 0.231 Fit side-chains REVERT: A 446 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6489 (mm) REVERT: A 492 ASP cc_start: 0.8066 (p0) cc_final: 0.7727 (p0) REVERT: A 588 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7741 (tm-30) REVERT: A 724 MET cc_start: 0.6429 (OUTLIER) cc_final: 0.5834 (tmm) outliers start: 5 outliers final: 2 residues processed: 124 average time/residue: 0.1047 time to fit residues: 16.1559 Evaluate side-chains 80 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 305 GLN A 340 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 GLN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 HIS A 902 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111601 restraints weight = 7444.976| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.21 r_work: 0.3136 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6034 Z= 0.128 Angle : 0.528 6.776 8247 Z= 0.262 Chirality : 0.040 0.206 939 Planarity : 0.003 0.033 965 Dihedral : 14.199 73.647 1086 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 1.18 % Allowed : 14.84 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.32), residues: 658 helix: 0.85 (0.31), residues: 289 sheet: -3.02 (0.51), residues: 79 loop : -2.65 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 859 TYR 0.012 0.001 TYR A 566 PHE 0.028 0.001 PHE A 616 TRP 0.005 0.001 TRP A 512 HIS 0.003 0.001 HIS A 623 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6030) covalent geometry : angle 0.52778 ( 8247) hydrogen bonds : bond 0.03041 ( 263) hydrogen bonds : angle 3.89808 ( 751) metal coordination : bond 0.00488 ( 3) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.173 Fit side-chains REVERT: A 312 LYS cc_start: 0.8467 (mtmt) cc_final: 0.8242 (mttp) REVERT: A 336 GLN cc_start: 0.8324 (mm110) cc_final: 0.8040 (mm-40) REVERT: A 435 ASP cc_start: 0.8724 (t0) cc_final: 0.8471 (t0) REVERT: A 446 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6939 (mm) REVERT: A 523 PHE cc_start: 0.8548 (t80) cc_final: 0.8321 (t80) REVERT: A 602 ARG cc_start: 0.7728 (ttt180) cc_final: 0.7423 (ptt180) REVERT: A 620 GLU cc_start: 0.7761 (mt-10) cc_final: 0.6967 (mt-10) REVERT: A 673 MET cc_start: 0.6705 (ttt) cc_final: 0.6365 (mtp) outliers start: 7 outliers final: 5 residues processed: 93 average time/residue: 0.0744 time to fit residues: 9.3011 Evaluate side-chains 80 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 298 ASN A 691 HIS ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.134975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.104636 restraints weight = 7472.392| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.14 r_work: 0.3043 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6034 Z= 0.164 Angle : 0.548 7.580 8247 Z= 0.273 Chirality : 0.041 0.207 939 Planarity : 0.003 0.038 965 Dihedral : 14.128 73.672 1080 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.53 % Allowed : 15.68 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.33), residues: 658 helix: 1.25 (0.31), residues: 296 sheet: -2.70 (0.50), residues: 87 loop : -2.44 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 859 TYR 0.007 0.001 TYR A 303 PHE 0.029 0.001 PHE A 616 TRP 0.005 0.001 TRP A 512 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6030) covalent geometry : angle 0.54809 ( 8247) hydrogen bonds : bond 0.03422 ( 263) hydrogen bonds : angle 3.83886 ( 751) metal coordination : bond 0.00222 ( 3) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.215 Fit side-chains REVERT: A 336 GLN cc_start: 0.8420 (mm110) cc_final: 0.8067 (mm-40) REVERT: A 435 ASP cc_start: 0.8930 (t0) cc_final: 0.8550 (t0) REVERT: A 620 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7107 (mt-10) REVERT: A 859 ARG cc_start: 0.8660 (mtt-85) cc_final: 0.8452 (mtt-85) REVERT: A 882 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7704 (p90) REVERT: A 883 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7873 (mp0) outliers start: 15 outliers final: 10 residues processed: 86 average time/residue: 0.0663 time to fit residues: 7.9740 Evaluate side-chains 78 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 47 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 375 HIS ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.104864 restraints weight = 7541.162| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.13 r_work: 0.3061 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6034 Z= 0.145 Angle : 0.527 7.482 8247 Z= 0.264 Chirality : 0.040 0.195 939 Planarity : 0.003 0.039 965 Dihedral : 14.056 73.629 1080 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.70 % Allowed : 15.68 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.33), residues: 658 helix: 1.25 (0.31), residues: 305 sheet: -2.66 (0.50), residues: 87 loop : -2.39 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 859 TYR 0.010 0.001 TYR A 390 PHE 0.029 0.001 PHE A 616 TRP 0.005 0.001 TRP A 512 HIS 0.002 0.001 HIS A 623 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6030) covalent geometry : angle 0.52730 ( 8247) hydrogen bonds : bond 0.03246 ( 263) hydrogen bonds : angle 3.77675 ( 751) metal coordination : bond 0.00220 ( 3) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.242 Fit side-chains REVERT: A 336 GLN cc_start: 0.8398 (mm110) cc_final: 0.8063 (mm-40) REVERT: A 435 ASP cc_start: 0.8962 (t0) cc_final: 0.8573 (t0) REVERT: A 724 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6089 (tmm) REVERT: A 882 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7585 (p90) REVERT: A 883 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7882 (mp0) outliers start: 16 outliers final: 12 residues processed: 81 average time/residue: 0.0656 time to fit residues: 7.4785 Evaluate side-chains 77 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 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 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.137781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.109231 restraints weight = 7671.925| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.07 r_work: 0.3127 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6034 Z= 0.129 Angle : 0.519 7.723 8247 Z= 0.259 Chirality : 0.039 0.209 939 Planarity : 0.003 0.039 965 Dihedral : 13.923 73.630 1080 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.20 % Allowed : 16.86 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.33), residues: 658 helix: 1.38 (0.32), residues: 305 sheet: -2.61 (0.50), residues: 87 loop : -2.34 (0.33), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 859 TYR 0.010 0.001 TYR A 390 PHE 0.018 0.001 PHE A 616 TRP 0.004 0.001 TRP A 512 HIS 0.002 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6030) covalent geometry : angle 0.51942 ( 8247) hydrogen bonds : bond 0.03130 ( 263) hydrogen bonds : angle 3.73880 ( 751) metal coordination : bond 0.00193 ( 3) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 435 ASP cc_start: 0.9007 (t0) cc_final: 0.8623 (t0) REVERT: A 724 MET cc_start: 0.7039 (OUTLIER) cc_final: 0.6373 (tmm) REVERT: A 882 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7465 (p90) REVERT: A 883 GLU cc_start: 0.8240 (mt-10) cc_final: 0.8026 (mp0) outliers start: 19 outliers final: 15 residues processed: 86 average time/residue: 0.0688 time to fit residues: 8.1684 Evaluate side-chains 83 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 5 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 608 ASN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.136369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.107799 restraints weight = 7512.560| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.03 r_work: 0.3108 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6034 Z= 0.146 Angle : 0.529 7.874 8247 Z= 0.266 Chirality : 0.040 0.185 939 Planarity : 0.003 0.040 965 Dihedral : 13.867 73.628 1080 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.37 % Allowed : 17.37 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.34), residues: 658 helix: 1.43 (0.32), residues: 305 sheet: -2.69 (0.50), residues: 88 loop : -2.27 (0.34), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 859 TYR 0.011 0.001 TYR A 390 PHE 0.026 0.001 PHE A 616 TRP 0.005 0.001 TRP A 512 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6030) covalent geometry : angle 0.52912 ( 8247) hydrogen bonds : bond 0.03233 ( 263) hydrogen bonds : angle 3.77010 ( 751) metal coordination : bond 0.00238 ( 3) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 435 ASP cc_start: 0.9025 (t0) cc_final: 0.8632 (t0) REVERT: A 621 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7804 (mm-30) REVERT: A 724 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6580 (tmm) REVERT: A 882 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7475 (p90) outliers start: 20 outliers final: 15 residues processed: 85 average time/residue: 0.0662 time to fit residues: 8.0043 Evaluate side-chains 83 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 39 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.102268 restraints weight = 7571.067| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.14 r_work: 0.3027 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6034 Z= 0.166 Angle : 0.548 8.382 8247 Z= 0.276 Chirality : 0.040 0.207 939 Planarity : 0.004 0.040 965 Dihedral : 13.824 73.660 1080 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.71 % Allowed : 17.37 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.34), residues: 658 helix: 1.59 (0.32), residues: 299 sheet: -2.65 (0.51), residues: 88 loop : -2.17 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 859 TYR 0.010 0.001 TYR A 390 PHE 0.027 0.001 PHE A 616 TRP 0.005 0.001 TRP A 512 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 6030) covalent geometry : angle 0.54828 ( 8247) hydrogen bonds : bond 0.03350 ( 263) hydrogen bonds : angle 3.84119 ( 751) metal coordination : bond 0.00287 ( 3) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 435 ASP cc_start: 0.8989 (t0) cc_final: 0.8531 (t0) REVERT: A 528 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7946 (mptp) REVERT: A 621 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7679 (mm-30) REVERT: A 724 MET cc_start: 0.7123 (OUTLIER) cc_final: 0.6551 (tmm) REVERT: A 882 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7566 (p90) outliers start: 22 outliers final: 15 residues processed: 84 average time/residue: 0.0627 time to fit residues: 7.4285 Evaluate side-chains 81 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 0.0470 chunk 34 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.105073 restraints weight = 7467.833| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.12 r_work: 0.3068 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6034 Z= 0.118 Angle : 0.515 6.775 8247 Z= 0.261 Chirality : 0.039 0.151 939 Planarity : 0.003 0.038 965 Dihedral : 13.836 73.612 1080 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.20 % Allowed : 17.71 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.34), residues: 658 helix: 1.52 (0.31), residues: 305 sheet: -2.48 (0.52), residues: 87 loop : -2.17 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 859 TYR 0.012 0.001 TYR A 390 PHE 0.026 0.001 PHE A 616 TRP 0.004 0.001 TRP A 512 HIS 0.002 0.001 HIS A 782 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6030) covalent geometry : angle 0.51545 ( 8247) hydrogen bonds : bond 0.03058 ( 263) hydrogen bonds : angle 3.79153 ( 751) metal coordination : bond 0.00172 ( 3) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 435 ASP cc_start: 0.8964 (t0) cc_final: 0.8547 (t0) REVERT: A 528 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7721 (mptp) REVERT: A 673 MET cc_start: 0.6247 (ttt) cc_final: 0.5721 (mtp) REVERT: A 724 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6547 (tmm) REVERT: A 882 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7136 (p90) outliers start: 19 outliers final: 15 residues processed: 82 average time/residue: 0.0740 time to fit residues: 8.3395 Evaluate side-chains 81 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.103247 restraints weight = 7593.185| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.13 r_work: 0.3034 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6034 Z= 0.144 Angle : 0.544 7.238 8247 Z= 0.274 Chirality : 0.039 0.162 939 Planarity : 0.003 0.039 965 Dihedral : 13.828 73.635 1080 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 3.04 % Allowed : 18.55 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.34), residues: 658 helix: 1.54 (0.31), residues: 305 sheet: -2.50 (0.52), residues: 88 loop : -2.11 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 859 TYR 0.012 0.001 TYR A 390 PHE 0.015 0.001 PHE A 616 TRP 0.004 0.001 TRP A 512 HIS 0.002 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6030) covalent geometry : angle 0.54420 ( 8247) hydrogen bonds : bond 0.03206 ( 263) hydrogen bonds : angle 3.81781 ( 751) metal coordination : bond 0.00237 ( 3) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 435 ASP cc_start: 0.9000 (t0) cc_final: 0.8556 (t0) REVERT: A 528 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7662 (mptp) REVERT: A 673 MET cc_start: 0.6260 (ttt) cc_final: 0.5731 (mtp) REVERT: A 724 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.6586 (tmm) REVERT: A 759 LYS cc_start: 0.8242 (tppt) cc_final: 0.7787 (tppt) REVERT: A 882 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7260 (p90) outliers start: 18 outliers final: 15 residues processed: 78 average time/residue: 0.0623 time to fit residues: 6.8850 Evaluate side-chains 81 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.104037 restraints weight = 7605.763| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.13 r_work: 0.3036 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6034 Z= 0.134 Angle : 0.535 7.037 8247 Z= 0.271 Chirality : 0.039 0.159 939 Planarity : 0.003 0.039 965 Dihedral : 13.837 73.613 1080 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.20 % Allowed : 18.38 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.34), residues: 658 helix: 1.66 (0.31), residues: 302 sheet: -2.43 (0.52), residues: 87 loop : -2.03 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 859 TYR 0.012 0.001 TYR A 390 PHE 0.014 0.001 PHE A 616 TRP 0.004 0.001 TRP A 512 HIS 0.002 0.001 HIS A 782 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6030) covalent geometry : angle 0.53487 ( 8247) hydrogen bonds : bond 0.03117 ( 263) hydrogen bonds : angle 3.81602 ( 751) metal coordination : bond 0.00221 ( 3) Misc. bond : bond 0.00003 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 435 ASP cc_start: 0.8995 (t0) cc_final: 0.8561 (t0) REVERT: A 528 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7689 (mptp) REVERT: A 621 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7693 (mm-30) REVERT: A 673 MET cc_start: 0.6333 (ttt) cc_final: 0.5806 (mtp) REVERT: A 724 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6462 (tmm) REVERT: A 882 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7214 (p90) outliers start: 19 outliers final: 15 residues processed: 78 average time/residue: 0.0624 time to fit residues: 6.9068 Evaluate side-chains 80 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 0.0670 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.105839 restraints weight = 7471.559| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.13 r_work: 0.3069 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6034 Z= 0.125 Angle : 0.534 6.905 8247 Z= 0.270 Chirality : 0.039 0.159 939 Planarity : 0.003 0.039 965 Dihedral : 13.852 73.626 1080 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.04 % Allowed : 18.55 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.34), residues: 658 helix: 1.68 (0.31), residues: 303 sheet: -2.27 (0.55), residues: 81 loop : -1.98 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 859 TYR 0.012 0.001 TYR A 390 PHE 0.015 0.001 PHE A 616 TRP 0.004 0.001 TRP A 512 HIS 0.002 0.001 HIS A 782 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6030) covalent geometry : angle 0.53384 ( 8247) hydrogen bonds : bond 0.03072 ( 263) hydrogen bonds : angle 3.78959 ( 751) metal coordination : bond 0.00179 ( 3) Misc. bond : bond 0.00002 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1473.86 seconds wall clock time: 26 minutes 0.46 seconds (1560.46 seconds total)