Starting phenix.real_space_refine on Fri Oct 23 20:49:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tq4_56124/10_2026/9tq4_56124.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tq4_56124/10_2026/9tq4_56124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tq4_56124/10_2026/9tq4_56124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tq4_56124/10_2026/9tq4_56124.map" model { file = "/net/cci-nas-00/data/ceres_data/9tq4_56124/10_2026/9tq4_56124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tq4_56124/10_2026/9tq4_56124.cif" } resolution = 2.51 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= 1.000 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: 5 Type Number sf(0) Gaussians P 209 5.49 5 S 23 5.16 5 C 6148 2.51 5 N 2007 2.21 5 O 2581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10968 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 824, 6622 Classifications: {'peptide': 824} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 48, 'TRANS': 775} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3144 Classifications: {'RNA': 149} Modifications used: {'rna2p_pur': 16, 'rna2p_pyr': 7, 'rna3p_pur': 63, 'rna3p_pyr': 63} Link IDs: {'rna2p': 22, 'rna3p': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {' G%rna2p_pur:plan': 2, ' G%rna2p_pur:plan2': 2, ' C%rna2p_pyr:plan': 1, ' C%rna2p_pyr:plan2': 1, ' A%rna2p_pur:plan': 1, ' A%rna2p_pur:plan2': 1} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 503 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DG:plan': 1, ' DG:plan2': 1, ' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 699 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Time building chain proxies: 2.70, per 1000 atoms: 0.25 Number of scatterers: 10968 At special positions: 0 Unit cell: (93.5, 118.8, 126.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 209 15.00 O 2581 8.00 N 2007 7.00 C 6148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 415.5 milliseconds 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1548 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 9 sheets defined 46.0% alpha, 14.7% beta 81 base pairs and 131 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 13 through 43 removed outlier: 3.501A pdb=" N HIS A 43 " --> pdb=" O HIS A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 47 removed outlier: 3.828A pdb=" N LYS A 47 " --> pdb=" O PRO A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 47' Processing helix chain 'A' and resid 49 through 59 Processing helix chain 'A' and resid 59 through 72 removed outlier: 3.596A pdb=" N GLU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A 72 " --> pdb=" O TYR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 175 through 188 Processing helix chain 'A' and resid 190 through 203 Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.671A pdb=" N GLU A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.702A pdb=" N PHE A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 226 " --> pdb=" O GLN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 237 Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 244 through 271 removed outlier: 3.593A pdb=" N ARG A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.600A pdb=" N GLY A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 330 removed outlier: 3.695A pdb=" N ASP A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 470 through 473 Processing helix chain 'A' and resid 556 through 580 Processing helix chain 'A' and resid 583 through 603 removed outlier: 4.070A pdb=" N ALA A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 625 Processing helix chain 'A' and resid 637 through 641 removed outlier: 3.598A pdb=" N MET A 641 " --> pdb=" O MET A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 647 Processing helix chain 'A' and resid 651 through 666 Processing helix chain 'A' and resid 699 through 710 Processing helix chain 'A' and resid 715 through 719 removed outlier: 3.569A pdb=" N LYS A 718 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 719 " --> pdb=" O GLY A 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 715 through 719' Processing helix chain 'A' and resid 802 through 817 Proline residue: A 814 - end of helix Processing helix chain 'A' and resid 825 through 837 removed outlier: 3.594A pdb=" N ILE A 835 " --> pdb=" O ARG A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 840 No H-bonds generated for 'chain 'A' and resid 838 through 840' Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126 removed outlier: 6.797A pdb=" N ALA A 125 " --> pdb=" O GLN A 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 147 removed outlier: 4.125A pdb=" N THR A 479 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LYS A 501 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N HIS A 477 " --> pdb=" O LYS A 501 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 147 removed outlier: 4.390A pdb=" N LEU A 494 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU A 153 " --> pdb=" O LYS A 449 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU A 401 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 680 through 683 removed outlier: 8.213A pdb=" N ARG A 681 " --> pdb=" O TYR A 629 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE A 631 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N GLU A 683 " --> pdb=" O PHE A 631 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU A 633 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU A 634 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ARG A 529 " --> pdb=" O GLU A 634 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 535 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA A 549 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASP A 541 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL A 547 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 670 through 671 Processing sheet with id=AA6, first strand: chain 'A' and resid 737 through 739 removed outlier: 6.632A pdb=" N TRP A 859 " --> pdb=" O GLU A 854 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLU A 854 " --> pdb=" O TRP A 859 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 742 through 743 Processing sheet with id=AA8, first strand: chain 'A' and resid 780 through 783 Processing sheet with id=AA9, first strand: chain 'A' and resid 788 through 789 315 hydrogen bonds defined for protein. 900 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 207 hydrogen bonds 382 hydrogen bond angles 0 basepair planarities 81 basepair parallelities 131 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 1.18 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: 2198 1.33 - 1.45: 3567 1.45 - 1.57: 5411 1.57 - 1.69: 414 1.69 - 1.81: 37 Bond restraints: 11627 Sorted by residual: bond pdb=" C3' DC C 11 " pdb=" C2' DC C 11 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.31e+01 bond pdb=" C3' DA C 5 " pdb=" C2' DA C 5 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DG C 6 " pdb=" C2' DG C 6 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.85e+00 bond pdb=" C1' DC C 11 " pdb=" N1 DC C 11 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 7.99e+00 bond pdb=" C3' DG C 2 " pdb=" C2' DG C 2 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.78e+00 ... (remaining 11622 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 15694 1.41 - 2.82: 884 2.82 - 4.23: 88 4.23 - 5.63: 7 5.63 - 7.04: 4 Bond angle restraints: 16677 Sorted by residual: angle pdb=" O4' DC D -15 " pdb=" C4' DC D -15 " pdb=" C3' DC D -15 " ideal model delta sigma weight residual 106.00 102.63 3.37 6.00e-01 2.78e+00 3.16e+01 angle pdb=" O4' DG D -3 " pdb=" C4' DG D -3 " pdb=" C3' DG D -3 " ideal model delta sigma weight residual 106.00 103.00 3.00 6.00e-01 2.78e+00 2.49e+01 angle pdb=" C3' C B -91 " pdb=" O3' C B -91 " pdb=" P G B -90 " ideal model delta sigma weight residual 119.70 125.47 -5.77 1.20e+00 6.94e-01 2.31e+01 angle pdb=" O4' DG D -23 " pdb=" C4' DG D -23 " pdb=" C3' DG D -23 " ideal model delta sigma weight residual 106.00 103.31 2.69 6.00e-01 2.78e+00 2.00e+01 angle pdb=" C1' U B-142 " pdb=" N1 U B-142 " pdb=" C2 U B-142 " ideal model delta sigma weight residual 117.70 122.84 -5.14 1.20e+00 6.94e-01 1.84e+01 ... (remaining 16672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 6463 35.64 - 71.28: 570 71.28 - 106.92: 49 106.92 - 142.56: 2 142.56 - 178.20: 4 Dihedral angle restraints: 7088 sinusoidal: 4698 harmonic: 2390 Sorted by residual: dihedral pdb=" O4' U B-142 " pdb=" C1' U B-142 " pdb=" N1 U B-142 " pdb=" C2 U B-142 " ideal model delta sinusoidal sigma weight residual 232.00 68.77 163.23 1 1.70e+01 3.46e-03 6.50e+01 dihedral pdb=" O4' C B -60 " pdb=" C1' C B -60 " pdb=" N1 C B -60 " pdb=" C2 C B -60 " ideal model delta sinusoidal sigma weight residual 200.00 85.00 115.00 1 1.50e+01 4.44e-03 6.07e+01 dihedral pdb=" C4' DG C 6 " pdb=" C3' DG C 6 " pdb=" O3' DG C 6 " pdb=" P DT C 7 " ideal model delta sinusoidal sigma weight residual 220.00 41.80 178.20 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 7085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1724 0.094 - 0.187: 221 0.187 - 0.281: 2 0.281 - 0.375: 0 0.375 - 0.468: 1 Chirality restraints: 1948 Sorted by residual: chirality pdb=" P C B -60 " pdb=" OP1 C B -60 " pdb=" OP2 C B -60 " pdb=" O5' C B -60 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.48e+00 chirality pdb=" C3' C B -91 " pdb=" C4' C B -91 " pdb=" O3' C B -91 " pdb=" C2' C B -91 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA PRO A 306 " pdb=" N PRO A 306 " pdb=" C PRO A 306 " pdb=" CB PRO A 306 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1945 not shown) Planarity restraints: 1400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 305 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO A 306 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 306 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 306 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G B 1 " -0.029 2.00e-02 2.50e+03 1.27e-02 4.82e+00 pdb=" N9 G B 1 " 0.031 2.00e-02 2.50e+03 pdb=" C8 G B 1 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G B 1 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G B 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 1 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G B 1 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G B 1 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G B 1 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G B 1 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G B 1 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G B 1 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B -52 " 0.019 2.00e-02 2.50e+03 9.76e-03 2.15e+00 pdb=" N1 U B -52 " -0.019 2.00e-02 2.50e+03 pdb=" C2 U B -52 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U B -52 " -0.004 2.00e-02 2.50e+03 pdb=" N3 U B -52 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U B -52 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U B -52 " 0.006 2.00e-02 2.50e+03 pdb=" C5 U B -52 " -0.004 2.00e-02 2.50e+03 pdb=" C6 U B -52 " -0.003 2.00e-02 2.50e+03 ... (remaining 1397 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2120 2.77 - 3.31: 9585 3.31 - 3.84: 21643 3.84 - 4.37: 26081 4.37 - 4.90: 37742 Nonbonded interactions: 97171 Sorted by model distance: nonbonded pdb=" O4 U B-129 " pdb=" O2' G B -62 " model vdw 2.242 3.040 nonbonded pdb=" O VAL A 509 " pdb=" OG1 THR A 512 " model vdw 2.244 3.040 nonbonded pdb=" O2 U B-122 " pdb=" O6 G B -67 " model vdw 2.251 2.432 nonbonded pdb=" O HIS A 58 " pdb=" O2' U B 16 " model vdw 2.253 3.040 nonbonded pdb=" OG1 THR A 147 " pdb=" N2 G B 1 " model vdw 2.262 3.120 ... (remaining 97166 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: 0.770 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.740 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:9.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 : 0.005 0.043 11627 Z= 0.371 Angle : 0.685 7.042 16677 Z= 0.542 Chirality : 0.055 0.468 1948 Planarity : 0.004 0.058 1400 Dihedral : 21.053 178.198 5540 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.87 % Allowed : 2.89 % Favored : 96.25 % 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: 1.08 (0.30), residues: 814 helix: 1.59 (0.28), residues: 336 sheet: 0.13 (0.53), residues: 110 loop : 0.20 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 497 TYR 0.011 0.001 TYR A 723 PHE 0.011 0.001 PHE A 607 TRP 0.009 0.001 TRP A 516 HIS 0.006 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.37 (11627) covalent geometry : angle 0.68528 / 0.54 (16677) hydrogen bonds : bond 0.11629 / 8.00 ( 518) hydrogen bonds : angle 5.28372 / 4.07 ( 1282) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.294 Fit side-chains REVERT: A 34 GLU cc_start: 0.7698 (tp30) cc_final: 0.7325 (tm-30) REVERT: A 68 TYR cc_start: 0.8035 (t80) cc_final: 0.7817 (t80) REVERT: A 79 LYS cc_start: 0.8597 (mmtt) cc_final: 0.8230 (mmtm) REVERT: A 118 VAL cc_start: 0.8523 (t) cc_final: 0.8071 (m) REVERT: A 121 LYS cc_start: 0.8841 (mttm) cc_final: 0.8560 (mtpp) REVERT: A 244 ASP cc_start: 0.8197 (m-30) cc_final: 0.7931 (m-30) REVERT: A 257 ARG cc_start: 0.7415 (mmm-85) cc_final: 0.7011 (mmt180) REVERT: A 322 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7555 (tp40) REVERT: A 330 ASP cc_start: 0.8130 (m-30) cc_final: 0.7920 (m-30) REVERT: A 343 ASP cc_start: 0.7481 (t70) cc_final: 0.7254 (t0) REVERT: A 355 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7292 (mm-30) REVERT: A 366 GLU cc_start: 0.7792 (mt-10) cc_final: 0.6857 (mm-30) REVERT: A 396 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7753 (mttp) REVERT: A 638 MET cc_start: 0.8261 (mmm) cc_final: 0.7976 (mmp) REVERT: A 657 GLU cc_start: 0.7744 (tt0) cc_final: 0.7328 (tt0) REVERT: A 742 TYR cc_start: 0.7483 (p90) cc_final: 0.7113 (p90) REVERT: A 760 SER cc_start: 0.8865 (t) cc_final: 0.8511 (p) REVERT: A 827 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7758 (mt-10) REVERT: A 859 TRP cc_start: 0.8660 (m-90) cc_final: 0.8310 (m-90) outliers start: 6 outliers final: 4 residues processed: 113 average time/residue: 0.7840 time to fit residues: 93.5237 Evaluate side-chains 90 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 538 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 38, 61] chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.148506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.095291 restraints weight = 12274.403| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.77 r_work: 0.2903 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 11627 Z= 0.292 Angle : 0.615 6.700 16677 Z= 0.351 Chirality : 0.046 0.445 1948 Planarity : 0.005 0.066 1400 Dihedral : 23.529 177.841 3857 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.89 % Allowed : 6.78 % Favored : 90.33 % 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: 0.84 (0.29), residues: 814 helix: 1.35 (0.28), residues: 342 sheet: -0.16 (0.51), residues: 112 loop : 0.16 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 246 TYR 0.014 0.002 TYR A 668 PHE 0.017 0.002 PHE A 607 TRP 0.013 0.002 TRP A 686 HIS 0.007 0.002 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.29 (11627) covalent geometry : angle 0.61450 / 0.35 (16677) hydrogen bonds : bond 0.06071 / 4.39 ( 518) hydrogen bonds : angle 4.32006 / 3.32 ( 1282) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.334 Fit side-chains REVERT: A 33 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8192 (tt0) REVERT: A 34 GLU cc_start: 0.7816 (tp30) cc_final: 0.7527 (tm-30) REVERT: A 68 TYR cc_start: 0.7942 (t80) cc_final: 0.7705 (t80) REVERT: A 79 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8141 (mmtm) REVERT: A 118 VAL cc_start: 0.8440 (t) cc_final: 0.7990 (m) REVERT: A 121 LYS cc_start: 0.9002 (mttm) cc_final: 0.8670 (mtpp) REVERT: A 196 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7167 (mm-30) REVERT: A 244 ASP cc_start: 0.8263 (m-30) cc_final: 0.8009 (m-30) REVERT: A 322 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7610 (tp40) REVERT: A 343 ASP cc_start: 0.7307 (t70) cc_final: 0.7076 (t0) REVERT: A 355 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7263 (mm-30) REVERT: A 366 GLU cc_start: 0.7558 (mt-10) cc_final: 0.6633 (mm-30) REVERT: A 396 LYS cc_start: 0.7851 (mtpt) cc_final: 0.7599 (mttp) REVERT: A 486 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8531 (m-30) REVERT: A 638 MET cc_start: 0.8244 (mmm) cc_final: 0.7939 (mmp) REVERT: A 657 GLU cc_start: 0.7834 (tt0) cc_final: 0.7461 (tt0) REVERT: A 742 TYR cc_start: 0.7587 (p90) cc_final: 0.7272 (p90) REVERT: A 760 SER cc_start: 0.8890 (t) cc_final: 0.8436 (p) REVERT: A 827 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7956 (mt-10) REVERT: A 859 TRP cc_start: 0.8700 (m-90) cc_final: 0.8412 (m-90) outliers start: 20 outliers final: 11 residues processed: 92 average time/residue: 0.7568 time to fit residues: 73.7241 Evaluate side-chains 91 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 761 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [79, 7, 90, 4, 28, 56, 52, 63, 93, 35, 36] chunk 79 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 93 optimal weight: 50.0000 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.151302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098712 restraints weight = 12484.753| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.74 r_work: 0.2978 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11627 Z= 0.148 Angle : 0.508 6.384 16677 Z= 0.301 Chirality : 0.039 0.408 1948 Planarity : 0.004 0.060 1400 Dihedral : 23.503 179.497 3854 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.31 % Allowed : 7.94 % Favored : 89.75 % 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 (0.30), residues: 814 helix: 1.66 (0.28), residues: 343 sheet: -0.27 (0.50), residues: 111 loop : 0.21 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 212 TYR 0.009 0.001 TYR A 151 PHE 0.010 0.001 PHE A 607 TRP 0.014 0.001 TRP A 686 HIS 0.004 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (11627) covalent geometry : angle 0.50765 / 0.30 (16677) hydrogen bonds : bond 0.05125 / 3.87 ( 518) hydrogen bonds : angle 4.00662 / 3.05 ( 1282) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.306 Fit side-chains REVERT: A 42 GLN cc_start: 0.8303 (mp-120) cc_final: 0.8037 (mp10) REVERT: A 68 TYR cc_start: 0.8005 (t80) cc_final: 0.7796 (t80) REVERT: A 79 LYS cc_start: 0.8481 (mmtt) cc_final: 0.8072 (mmtm) REVERT: A 118 VAL cc_start: 0.8446 (t) cc_final: 0.7996 (m) REVERT: A 121 LYS cc_start: 0.9013 (mttm) cc_final: 0.8716 (mtpp) REVERT: A 231 GLN cc_start: 0.8100 (mp10) cc_final: 0.7248 (mp10) REVERT: A 244 ASP cc_start: 0.8202 (m-30) cc_final: 0.7946 (m-30) REVERT: A 322 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7684 (tp40) REVERT: A 334 GLN cc_start: 0.8641 (mt0) cc_final: 0.8375 (mt0) REVERT: A 343 ASP cc_start: 0.7385 (t70) cc_final: 0.7122 (t0) REVERT: A 355 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7247 (mm-30) REVERT: A 366 GLU cc_start: 0.7591 (mt-10) cc_final: 0.6625 (mm-30) REVERT: A 367 LEU cc_start: 0.9037 (mp) cc_final: 0.8828 (mm) REVERT: A 504 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8384 (m-30) REVERT: A 556 ARG cc_start: 0.6854 (mtm180) cc_final: 0.6577 (mpp-170) REVERT: A 638 MET cc_start: 0.8246 (mmm) cc_final: 0.7915 (mmp) REVERT: A 657 GLU cc_start: 0.7813 (tt0) cc_final: 0.7438 (tt0) REVERT: A 742 TYR cc_start: 0.7622 (p90) cc_final: 0.7305 (p90) REVERT: A 760 SER cc_start: 0.8840 (t) cc_final: 0.8404 (p) REVERT: A 793 GLU cc_start: 0.8358 (tt0) cc_final: 0.8065 (tm-30) REVERT: A 827 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7917 (mt-10) REVERT: A 859 TRP cc_start: 0.8694 (m-90) cc_final: 0.8471 (m-90) outliers start: 16 outliers final: 9 residues processed: 96 average time/residue: 0.7179 time to fit residues: 73.3004 Evaluate side-chains 93 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 761 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [56, 55, 50, 74, 41, 90, 35, 20, 37, 66, 27] chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 27 optimal weight: 0.0270 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.150038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097204 restraints weight = 12415.261| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.76 r_work: 0.2953 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11627 Z= 0.175 Angle : 0.516 6.319 16677 Z= 0.303 Chirality : 0.040 0.422 1948 Planarity : 0.005 0.061 1400 Dihedral : 23.449 178.942 3854 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.31 % Allowed : 9.24 % Favored : 88.46 % 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 (0.30), residues: 814 helix: 1.67 (0.28), residues: 343 sheet: -0.33 (0.50), residues: 112 loop : 0.22 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 212 TYR 0.011 0.001 TYR A 668 PHE 0.012 0.001 PHE A 607 TRP 0.011 0.001 TRP A 686 HIS 0.005 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (11627) covalent geometry : angle 0.51647 / 0.30 (16677) hydrogen bonds : bond 0.05078 / 3.82 ( 518) hydrogen bonds : angle 3.93978 / 3.00 ( 1282) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.292 Fit side-chains REVERT: A 68 TYR cc_start: 0.7849 (t80) cc_final: 0.7619 (t80) REVERT: A 79 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8083 (mmtm) REVERT: A 118 VAL cc_start: 0.8436 (t) cc_final: 0.7987 (m) REVERT: A 121 LYS cc_start: 0.9012 (mttm) cc_final: 0.8690 (mtpp) REVERT: A 196 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7132 (mm-30) REVERT: A 231 GLN cc_start: 0.8081 (mp10) cc_final: 0.7269 (mp10) REVERT: A 244 ASP cc_start: 0.8191 (m-30) cc_final: 0.7933 (m-30) REVERT: A 299 LYS cc_start: 0.8863 (mttm) cc_final: 0.8607 (mtmt) REVERT: A 322 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7667 (tp40) REVERT: A 334 GLN cc_start: 0.8630 (mt0) cc_final: 0.8421 (mt0) REVERT: A 343 ASP cc_start: 0.7382 (t70) cc_final: 0.7137 (t0) REVERT: A 355 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7202 (mm-30) REVERT: A 366 GLU cc_start: 0.7586 (mt-10) cc_final: 0.6629 (mm-30) REVERT: A 367 LEU cc_start: 0.9024 (mp) cc_final: 0.8808 (mm) REVERT: A 486 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8592 (m-30) REVERT: A 504 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8461 (m-30) REVERT: A 638 MET cc_start: 0.8204 (mmm) cc_final: 0.7869 (mmp) REVERT: A 657 GLU cc_start: 0.7777 (tt0) cc_final: 0.7394 (tt0) REVERT: A 742 TYR cc_start: 0.7611 (p90) cc_final: 0.7291 (p90) REVERT: A 760 SER cc_start: 0.8833 (t) cc_final: 0.8367 (p) REVERT: A 793 GLU cc_start: 0.8334 (tt0) cc_final: 0.7998 (tm-30) REVERT: A 827 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7900 (mt-10) REVERT: A 835 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8420 (mt) REVERT: A 859 TRP cc_start: 0.8695 (m-90) cc_final: 0.8430 (m-90) outliers start: 16 outliers final: 9 residues processed: 94 average time/residue: 0.7455 time to fit residues: 74.3574 Evaluate side-chains 90 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 443 CYS Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 835 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [8, 15, 5, 0, 94, 85, 84, 64, 7, 92, 21] chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 92 optimal weight: 40.0000 chunk 21 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.146519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.093356 restraints weight = 12354.175| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.78 r_work: 0.2878 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.104 11627 Z= 0.406 Angle : 0.690 8.131 16677 Z= 0.380 Chirality : 0.052 0.486 1948 Planarity : 0.006 0.069 1400 Dihedral : 23.481 178.186 3854 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.45 % Allowed : 10.25 % Favored : 87.30 % 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: 0.63 (0.29), residues: 814 helix: 1.21 (0.28), residues: 341 sheet: -0.35 (0.49), residues: 113 loop : 0.05 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 681 TYR 0.018 0.003 TYR A 668 PHE 0.018 0.003 PHE A 607 TRP 0.012 0.002 TRP A 722 HIS 0.010 0.002 HIS A 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00884 / 0.41 (11627) covalent geometry : angle 0.69027 / 0.38 (16677) hydrogen bonds : bond 0.06250 / 4.51 ( 518) hydrogen bonds : angle 4.18575 / 3.20 ( 1282) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.359 Fit side-chains REVERT: A 23 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7850 (mm-30) REVERT: A 68 TYR cc_start: 0.7870 (t80) cc_final: 0.7624 (t80) REVERT: A 79 LYS cc_start: 0.8556 (mmtt) cc_final: 0.8138 (mmtm) REVERT: A 118 VAL cc_start: 0.8485 (t) cc_final: 0.8032 (m) REVERT: A 121 LYS cc_start: 0.9023 (mttm) cc_final: 0.8689 (mtpp) REVERT: A 196 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7204 (mm-30) REVERT: A 231 GLN cc_start: 0.8107 (mp10) cc_final: 0.7371 (mp10) REVERT: A 299 LYS cc_start: 0.8932 (mttm) cc_final: 0.8661 (mtmt) REVERT: A 322 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7692 (tp40) REVERT: A 334 GLN cc_start: 0.8601 (mt0) cc_final: 0.8395 (mt0) REVERT: A 355 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7282 (mm-30) REVERT: A 366 GLU cc_start: 0.7579 (mt-10) cc_final: 0.6659 (mm-30) REVERT: A 638 MET cc_start: 0.8289 (mmm) cc_final: 0.7996 (mmp) REVERT: A 657 GLU cc_start: 0.7892 (tt0) cc_final: 0.7497 (tt0) REVERT: A 742 TYR cc_start: 0.7683 (p90) cc_final: 0.7373 (p90) REVERT: A 760 SER cc_start: 0.8959 (t) cc_final: 0.8456 (p) REVERT: A 793 GLU cc_start: 0.8333 (tt0) cc_final: 0.8109 (tm-30) REVERT: A 827 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7945 (mt-10) REVERT: A 859 TRP cc_start: 0.8774 (m-90) cc_final: 0.8502 (m-90) outliers start: 17 outliers final: 12 residues processed: 92 average time/residue: 0.8066 time to fit residues: 78.6742 Evaluate side-chains 89 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 443 CYS Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 761 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [44, 62, 89, 11, 61, 33, 7, 40, 4, 57, 14] chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.151437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.099251 restraints weight = 12412.810| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.73 r_work: 0.2968 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11627 Z= 0.142 Angle : 0.512 6.353 16677 Z= 0.302 Chirality : 0.039 0.412 1948 Planarity : 0.005 0.061 1400 Dihedral : 23.489 179.892 3854 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.45 % Allowed : 10.39 % Favored : 87.16 % 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: 0.96 (0.30), residues: 814 helix: 1.61 (0.28), residues: 343 sheet: -0.44 (0.49), residues: 111 loop : 0.17 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 246 TYR 0.009 0.001 TYR A 151 PHE 0.010 0.001 PHE A 607 TRP 0.017 0.001 TRP A 686 HIS 0.003 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (11627) covalent geometry : angle 0.51169 / 0.30 (16677) hydrogen bonds : bond 0.05032 / 3.77 ( 518) hydrogen bonds : angle 3.93730 / 2.99 ( 1282) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.240 Fit side-chains REVERT: A 33 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: A 68 TYR cc_start: 0.7883 (t80) cc_final: 0.7665 (t80) REVERT: A 79 LYS cc_start: 0.8423 (mmtt) cc_final: 0.8011 (mmtm) REVERT: A 118 VAL cc_start: 0.8471 (t) cc_final: 0.8020 (m) REVERT: A 121 LYS cc_start: 0.9033 (mttm) cc_final: 0.8704 (mtpp) REVERT: A 196 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7198 (mm-30) REVERT: A 231 GLN cc_start: 0.8137 (mp10) cc_final: 0.7396 (mp10) REVERT: A 258 HIS cc_start: 0.8063 (m-70) cc_final: 0.7479 (m-70) REVERT: A 299 LYS cc_start: 0.8964 (mttm) cc_final: 0.8691 (mtmt) REVERT: A 301 THR cc_start: 0.7809 (OUTLIER) cc_final: 0.7596 (p) REVERT: A 322 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7744 (tp40) REVERT: A 334 GLN cc_start: 0.8634 (mt0) cc_final: 0.8417 (mt0) REVERT: A 355 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7235 (mm-30) REVERT: A 366 GLU cc_start: 0.7546 (mt-10) cc_final: 0.6654 (mm-30) REVERT: A 504 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8432 (m-30) REVERT: A 638 MET cc_start: 0.8280 (mmm) cc_final: 0.7956 (mmp) REVERT: A 657 GLU cc_start: 0.7833 (tt0) cc_final: 0.7437 (tt0) REVERT: A 742 TYR cc_start: 0.7692 (p90) cc_final: 0.7386 (p90) REVERT: A 760 SER cc_start: 0.8924 (t) cc_final: 0.8495 (p) REVERT: A 793 GLU cc_start: 0.8324 (tt0) cc_final: 0.8102 (tm-30) REVERT: A 827 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7902 (mt-10) REVERT: A 859 TRP cc_start: 0.8700 (m-90) cc_final: 0.8495 (m-90) outliers start: 17 outliers final: 10 residues processed: 91 average time/residue: 0.7708 time to fit residues: 74.6959 Evaluate side-chains 90 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 761 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [54, 36, 9, 64, 45, 56, 90, 11, 95, 99, 21] chunk 54 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 11 optimal weight: 0.0870 chunk 95 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 21 optimal weight: 0.0070 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.153363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100925 restraints weight = 12383.604| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.77 r_work: 0.3011 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11627 Z= 0.125 Angle : 0.487 6.258 16677 Z= 0.289 Chirality : 0.037 0.402 1948 Planarity : 0.005 0.060 1400 Dihedral : 23.388 179.851 3853 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.88 % Allowed : 10.97 % Favored : 87.16 % 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: 1.19 (0.30), residues: 814 helix: 1.87 (0.28), residues: 343 sheet: -0.29 (0.49), residues: 111 loop : 0.20 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 212 TYR 0.009 0.001 TYR A 668 PHE 0.008 0.001 PHE A 454 TRP 0.017 0.001 TRP A 686 HIS 0.003 0.001 HIS A 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (11627) covalent geometry : angle 0.48655 / 0.29 (16677) hydrogen bonds : bond 0.04581 / 3.53 ( 518) hydrogen bonds : angle 3.78067 / 2.87 ( 1282) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.332 Fit side-chains REVERT: A 68 TYR cc_start: 0.7822 (t80) cc_final: 0.7596 (t80) REVERT: A 79 LYS cc_start: 0.8339 (mmtt) cc_final: 0.7928 (mmtm) REVERT: A 118 VAL cc_start: 0.8412 (t) cc_final: 0.7971 (m) REVERT: A 121 LYS cc_start: 0.9038 (mttm) cc_final: 0.8693 (mtpp) REVERT: A 299 LYS cc_start: 0.8925 (mttm) cc_final: 0.8654 (mtmt) REVERT: A 322 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7691 (tp40) REVERT: A 334 GLN cc_start: 0.8605 (mt0) cc_final: 0.8396 (mt0) REVERT: A 355 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7144 (mm-30) REVERT: A 366 GLU cc_start: 0.7570 (mt-10) cc_final: 0.6653 (mm-30) REVERT: A 504 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8328 (m-30) REVERT: A 546 LYS cc_start: 0.8457 (mttt) cc_final: 0.8148 (mttt) REVERT: A 638 MET cc_start: 0.8203 (mmm) cc_final: 0.7895 (mmp) REVERT: A 657 GLU cc_start: 0.7813 (tt0) cc_final: 0.7384 (tt0) REVERT: A 742 TYR cc_start: 0.7621 (p90) cc_final: 0.7304 (p90) REVERT: A 760 SER cc_start: 0.8847 (t) cc_final: 0.8384 (p) REVERT: A 793 GLU cc_start: 0.8386 (tt0) cc_final: 0.8100 (tm-30) REVERT: A 827 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7884 (mt-10) REVERT: A 859 TRP cc_start: 0.8594 (m-90) cc_final: 0.8380 (m-90) outliers start: 13 outliers final: 7 residues processed: 89 average time/residue: 0.7968 time to fit residues: 75.1395 Evaluate side-chains 84 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 761 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [66, 68, 14, 87, 35, 59, 38, 6, 25, 0, 70] chunk 66 optimal weight: 0.1980 chunk 68 optimal weight: 0.0870 chunk 14 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.153303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100939 restraints weight = 12401.391| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.77 r_work: 0.3007 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11627 Z= 0.124 Angle : 0.480 6.246 16677 Z= 0.284 Chirality : 0.037 0.408 1948 Planarity : 0.004 0.058 1400 Dihedral : 23.370 179.571 3853 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.73 % Allowed : 11.83 % Favored : 86.44 % 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: 1.30 (0.30), residues: 814 helix: 2.01 (0.28), residues: 343 sheet: -0.33 (0.49), residues: 112 loop : 0.23 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 246 TYR 0.009 0.001 TYR A 151 PHE 0.009 0.001 PHE A 607 TRP 0.012 0.001 TRP A 686 HIS 0.003 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 (11627) covalent geometry : angle 0.48024 / 0.28 (16677) hydrogen bonds : bond 0.04521 / 3.49 ( 518) hydrogen bonds : angle 3.72521 / 2.83 ( 1282) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.228 Fit side-chains REVERT: A 68 TYR cc_start: 0.7885 (t80) cc_final: 0.7653 (t80) REVERT: A 79 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7940 (mmtm) REVERT: A 118 VAL cc_start: 0.8441 (t) cc_final: 0.8000 (m) REVERT: A 121 LYS cc_start: 0.9060 (mttm) cc_final: 0.8724 (mtpp) REVERT: A 196 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7154 (mm-30) REVERT: A 257 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.7119 (mmt180) REVERT: A 299 LYS cc_start: 0.8961 (mttm) cc_final: 0.8692 (mtmt) REVERT: A 322 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7709 (tp40) REVERT: A 334 GLN cc_start: 0.8630 (mt0) cc_final: 0.8425 (mt0) REVERT: A 355 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7189 (mm-30) REVERT: A 366 GLU cc_start: 0.7573 (mt-10) cc_final: 0.6640 (mm-30) REVERT: A 476 LEU cc_start: 0.8519 (mp) cc_final: 0.8290 (pp) REVERT: A 504 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8388 (m-30) REVERT: A 546 LYS cc_start: 0.8533 (mttt) cc_final: 0.8239 (mttt) REVERT: A 638 MET cc_start: 0.8261 (mmm) cc_final: 0.7943 (mmp) REVERT: A 657 GLU cc_start: 0.7849 (tt0) cc_final: 0.7425 (tt0) REVERT: A 704 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8129 (mm-30) REVERT: A 742 TYR cc_start: 0.7662 (p90) cc_final: 0.7331 (p90) REVERT: A 760 SER cc_start: 0.8818 (t) cc_final: 0.8339 (p) REVERT: A 793 GLU cc_start: 0.8412 (tt0) cc_final: 0.8122 (tm-30) REVERT: A 827 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7907 (mt-10) REVERT: A 859 TRP cc_start: 0.8693 (m-90) cc_final: 0.8486 (m-90) outliers start: 12 outliers final: 7 residues processed: 84 average time/residue: 0.8133 time to fit residues: 72.3481 Evaluate side-chains 83 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 761 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [90, 6, 84, 0, 80, 58, 17, 34, 2, 72, 82] chunk 90 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 0 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.0040 chunk 2 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.153366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.101184 restraints weight = 12316.998| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.74 r_work: 0.3015 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11627 Z= 0.127 Angle : 0.483 6.230 16677 Z= 0.285 Chirality : 0.037 0.408 1948 Planarity : 0.004 0.058 1400 Dihedral : 23.352 179.688 3853 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.59 % Allowed : 12.55 % Favored : 85.86 % 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: 1.34 (0.30), residues: 814 helix: 2.08 (0.28), residues: 343 sheet: -0.32 (0.48), residues: 112 loop : 0.23 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 246 TYR 0.009 0.001 TYR A 151 PHE 0.011 0.001 PHE A 824 TRP 0.012 0.001 TRP A 686 HIS 0.004 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (11627) covalent geometry : angle 0.48348 / 0.29 (16677) hydrogen bonds : bond 0.04506 / 3.49 ( 518) hydrogen bonds : angle 3.68681 / 2.81 ( 1282) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.361 Fit side-chains REVERT: A 68 TYR cc_start: 0.7960 (t80) cc_final: 0.7738 (t80) REVERT: A 79 LYS cc_start: 0.8407 (mmtt) cc_final: 0.7979 (mmtm) REVERT: A 118 VAL cc_start: 0.8526 (t) cc_final: 0.8090 (m) REVERT: A 121 LYS cc_start: 0.9075 (mttm) cc_final: 0.8760 (mtpp) REVERT: A 257 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.7213 (mmt180) REVERT: A 299 LYS cc_start: 0.9053 (mttm) cc_final: 0.8777 (mtmt) REVERT: A 322 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7748 (tp40) REVERT: A 355 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7265 (mm-30) REVERT: A 366 GLU cc_start: 0.7578 (mt-10) cc_final: 0.6716 (mm-30) REVERT: A 504 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8386 (m-30) REVERT: A 546 LYS cc_start: 0.8604 (mttt) cc_final: 0.8284 (mttt) REVERT: A 638 MET cc_start: 0.8361 (mmm) cc_final: 0.8039 (mmp) REVERT: A 657 GLU cc_start: 0.7911 (tt0) cc_final: 0.7505 (tt0) REVERT: A 742 TYR cc_start: 0.7720 (p90) cc_final: 0.7379 (p90) REVERT: A 760 SER cc_start: 0.8935 (t) cc_final: 0.8502 (p) REVERT: A 793 GLU cc_start: 0.8376 (tt0) cc_final: 0.8077 (tm-30) REVERT: A 827 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7933 (mt-10) REVERT: A 859 TRP cc_start: 0.8764 (m-90) cc_final: 0.8562 (m-90) outliers start: 11 outliers final: 6 residues processed: 83 average time/residue: 0.8043 time to fit residues: 70.6352 Evaluate side-chains 83 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 761 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [38, 59, 0, 94, 31, 99, 41, 93, 26, 100, 15] chunk 38 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 93 optimal weight: 50.0000 chunk 26 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.149345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.096546 restraints weight = 12356.910| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.73 r_work: 0.2926 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 11627 Z= 0.268 Angle : 0.589 6.914 16677 Z= 0.332 Chirality : 0.045 0.461 1948 Planarity : 0.005 0.063 1400 Dihedral : 23.379 179.580 3853 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.16 % Allowed : 12.12 % Favored : 85.71 % 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: 1.00 (0.29), residues: 814 helix: 1.69 (0.28), residues: 343 sheet: -0.44 (0.48), residues: 112 loop : 0.13 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 246 TYR 0.014 0.002 TYR A 668 PHE 0.019 0.002 PHE A 607 TRP 0.008 0.002 TRP A 392 HIS 0.007 0.002 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.27 (11627) covalent geometry : angle 0.58900 / 0.33 (16677) hydrogen bonds : bond 0.05337 / 3.93 ( 518) hydrogen bonds : angle 3.87471 / 2.97 ( 1282) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.327 Fit side-chains REVERT: A 34 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7373 (tp30) REVERT: A 79 LYS cc_start: 0.8491 (mmtt) cc_final: 0.8066 (mmtm) REVERT: A 118 VAL cc_start: 0.8481 (t) cc_final: 0.8027 (m) REVERT: A 121 LYS cc_start: 0.9054 (mttm) cc_final: 0.8714 (mtpp) REVERT: A 299 LYS cc_start: 0.8970 (mttm) cc_final: 0.8703 (mtmt) REVERT: A 322 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7769 (tp40) REVERT: A 355 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7241 (mm-30) REVERT: A 366 GLU cc_start: 0.7531 (mt-10) cc_final: 0.6645 (mm-30) REVERT: A 546 LYS cc_start: 0.8535 (mttt) cc_final: 0.8218 (mttt) REVERT: A 638 MET cc_start: 0.8318 (mmm) cc_final: 0.7998 (mmp) REVERT: A 657 GLU cc_start: 0.7927 (tt0) cc_final: 0.7518 (tt0) REVERT: A 742 TYR cc_start: 0.7751 (p90) cc_final: 0.7416 (p90) REVERT: A 760 SER cc_start: 0.8976 (t) cc_final: 0.8471 (p) REVERT: A 793 GLU cc_start: 0.8350 (tt0) cc_final: 0.8092 (tm-30) REVERT: A 827 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7925 (mt-10) outliers start: 15 outliers final: 8 residues processed: 87 average time/residue: 0.8143 time to fit residues: 74.9685 Evaluate side-chains 84 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 761 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [63, 38, 82, 80, 73, 98, 3, 49, 60, 52, 10] chunk 63 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 80 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.151262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.098810 restraints weight = 12419.621| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.75 r_work: 0.2975 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11627 Z= 0.131 Angle : 0.513 6.392 16677 Z= 0.299 Chirality : 0.039 0.419 1948 Planarity : 0.005 0.065 1400 Dihedral : 23.424 179.911 3853 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.59 % Allowed : 12.99 % Favored : 85.43 % 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: 1.18 (0.30), residues: 814 helix: 1.98 (0.28), residues: 337 sheet: -0.43 (0.49), residues: 112 loop : 0.15 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 246 TYR 0.011 0.001 TYR A 668 PHE 0.009 0.001 PHE A 607 TRP 0.016 0.001 TRP A 859 HIS 0.003 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 (11627) covalent geometry : angle 0.51301 / 0.30 (16677) hydrogen bonds : bond 0.04801 / 3.61 ( 518) hydrogen bonds : angle 3.81075 / 2.91 ( 1282) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4694.65 seconds wall clock time: 80 minutes 33.59 seconds (4833.59 seconds total)