Starting phenix.real_space_refine on Tue Aug 4 19:24:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dhx_46888/08_2026/9dhx_46888.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dhx_46888/08_2026/9dhx_46888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dhx_46888/08_2026/9dhx_46888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dhx_46888/08_2026/9dhx_46888.map" model { file = "/net/cci-nas-00/data/ceres_data/9dhx_46888/08_2026/9dhx_46888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dhx_46888/08_2026/9dhx_46888.cif" } resolution = 3.1 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= 0.036 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 P 40 5.49 5 Mg 1 5.21 5 S 34 5.16 5 C 3857 2.51 5 N 1134 2.21 5 O 1252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6318 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5464 Classifications: {'peptide': 684} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 640} Chain breaks: 4 Chain: "B" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 433 Classifications: {'RNA': 20} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 17} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 418 Classifications: {'DNA': 1, 'RNA': 20} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 11} Link IDs: {'rna2p': 2, 'rna3p': 18} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.66, per 1000 atoms: 0.26 Number of scatterers: 6318 At special positions: 0 Unit cell: (75.48, 81.4, 112.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 P 40 15.00 Mg 1 11.99 O 1252 8.00 N 1134 7.00 C 3857 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: 0.63 Conformation dependent library (CDL) restraints added in 394.7 milliseconds 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1288 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 5 sheets defined 36.0% alpha, 19.9% beta 18 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 155 through 168 removed outlier: 3.751A pdb=" N ILE A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 357 through 368 Processing helix chain 'A' and resid 371 through 387 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 391 through 397 Processing helix chain 'A' and resid 463 through 482 Processing helix chain 'A' and resid 500 through 512 Processing helix chain 'A' and resid 527 through 539 Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 556 through 571 removed outlier: 4.058A pdb=" N VAL A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 583 removed outlier: 3.915A pdb=" N ARG A 583 " --> pdb=" O PRO A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 583' Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.911A pdb=" N GLN A 589 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 658 Processing helix chain 'A' and resid 675 through 695 removed outlier: 3.635A pdb=" N LEU A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 787 removed outlier: 3.632A pdb=" N CYS A 787 " --> pdb=" O THR A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 817 removed outlier: 4.294A pdb=" N TYR A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 846 removed outlier: 3.739A pdb=" N LYS A 844 " --> pdb=" O GLN A 840 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 854 removed outlier: 4.275A pdb=" N ARG A 854 " --> pdb=" O GLN A 850 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 625 through 632 removed outlier: 5.172A pdb=" N PHE A 593 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE A 592 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TYR A 667 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU A 594 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ASP A 669 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA A 596 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE A 702 " --> pdb=" O ASP A 770 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP A 770 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE A 704 " --> pdb=" O LEU A 768 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A 734 " --> pdb=" O CYS A 751 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.903A pdb=" N PHE A 200 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N MET A 213 " --> pdb=" O MET A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 5.706A pdb=" N GLU A 58 " --> pdb=" O TRP A 134 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N TRP A 134 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASP A 60 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE A 132 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 427 through 428 Processing sheet with id=AA5, first strand: chain 'A' and resid 491 through 494 removed outlier: 3.925A pdb=" N PHE A 491 " --> pdb=" O TRP A 451 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA A 452 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE A 521 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA A 454 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 518 " --> pdb=" O GLN A 545 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL A 547 " --> pdb=" O VAL A 518 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL A 520 " --> pdb=" O VAL A 547 " (cutoff:3.500A) 244 hydrogen bonds defined for protein. 687 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 0.83 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: 1374 1.33 - 1.45: 1606 1.45 - 1.57: 3433 1.57 - 1.70: 78 1.70 - 1.82: 53 Bond restraints: 6544 Sorted by residual: bond pdb=" C4 C C 20 " pdb=" N4 C C 20 " ideal model delta sigma weight residual 1.335 1.295 0.040 9.00e-03 1.23e+04 2.02e+01 bond pdb=" C2 G B 2 " pdb=" N2 G B 2 " ideal model delta sigma weight residual 1.341 1.298 0.043 1.00e-02 1.00e+04 1.89e+01 bond pdb=" C2 G B 5 " pdb=" N2 G B 5 " ideal model delta sigma weight residual 1.341 1.299 0.042 1.00e-02 1.00e+04 1.78e+01 bond pdb=" C4 C C 13 " pdb=" N4 C C 13 " ideal model delta sigma weight residual 1.335 1.298 0.037 9.00e-03 1.23e+04 1.67e+01 bond pdb=" O3' A C 21 " pdb=" P A C 22 " ideal model delta sigma weight residual 1.607 1.558 0.049 1.20e-02 6.94e+03 1.66e+01 ... (remaining 6539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 6942 2.12 - 4.24: 1881 4.24 - 6.35: 214 6.35 - 8.47: 9 8.47 - 10.59: 5 Bond angle restraints: 9051 Sorted by residual: angle pdb=" N6 A C 21 " pdb=" C6 A C 21 " pdb=" N1 A C 21 " ideal model delta sigma weight residual 118.60 112.77 5.83 6.00e-01 2.78e+00 9.43e+01 angle pdb=" C3' A C 2 " pdb=" O3' A C 2 " pdb=" P A C 3 " ideal model delta sigma weight residual 119.70 109.11 10.59 1.20e+00 6.94e-01 7.79e+01 angle pdb=" N6 A C 8 " pdb=" C6 A C 8 " pdb=" N1 A C 8 " ideal model delta sigma weight residual 118.60 113.31 5.29 6.00e-01 2.78e+00 7.76e+01 angle pdb=" N6 A B 4 " pdb=" C6 A B 4 " pdb=" N1 A B 4 " ideal model delta sigma weight residual 118.60 113.54 5.06 6.00e-01 2.78e+00 7.11e+01 angle pdb=" N6 A C 16 " pdb=" C6 A C 16 " pdb=" N1 A C 16 " ideal model delta sigma weight residual 118.60 113.56 5.04 6.00e-01 2.78e+00 7.05e+01 ... (remaining 9046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 3638 17.56 - 35.11: 247 35.11 - 52.67: 55 52.67 - 70.23: 50 70.23 - 87.78: 11 Dihedral angle restraints: 4001 sinusoidal: 2012 harmonic: 1989 Sorted by residual: dihedral pdb=" CA LYS A 62 " pdb=" C LYS A 62 " pdb=" N PRO A 63 " pdb=" CA PRO A 63 " ideal model delta harmonic sigma weight residual 180.00 152.09 27.91 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA LYS A 212 " pdb=" C LYS A 212 " pdb=" N MET A 213 " pdb=" CA MET A 213 " ideal model delta harmonic sigma weight residual 180.00 153.11 26.89 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA ASP A 669 " pdb=" C ASP A 669 " pdb=" N GLY A 670 " pdb=" CA GLY A 670 " ideal model delta harmonic sigma weight residual 180.00 -155.73 -24.27 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 3998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 774 0.101 - 0.201: 226 0.201 - 0.302: 24 0.302 - 0.402: 9 0.402 - 0.503: 1 Chirality restraints: 1034 Sorted by residual: chirality pdb=" P U B 1 " pdb=" OP1 U B 1 " pdb=" OP2 U B 1 " pdb=" O5' U B 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.91 -0.50 2.00e-01 2.50e+01 6.32e+00 chirality pdb=" P G B 18 " pdb=" OP1 G B 18 " pdb=" OP2 G B 18 " pdb=" O5' G B 18 " both_signs ideal model delta sigma weight residual True 2.41 -2.79 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" P A C 3 " pdb=" OP1 A C 3 " pdb=" OP2 A C 3 " pdb=" O5' A C 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.78 -0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 1031 not shown) Planarity restraints: 1021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 5 " 0.176 2.00e-02 2.50e+03 7.81e-02 1.83e+02 pdb=" N9 G B 5 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G B 5 " -0.094 2.00e-02 2.50e+03 pdb=" N7 G B 5 " -0.081 2.00e-02 2.50e+03 pdb=" C5 G B 5 " -0.030 2.00e-02 2.50e+03 pdb=" C6 G B 5 " 0.036 2.00e-02 2.50e+03 pdb=" O6 G B 5 " 0.127 2.00e-02 2.50e+03 pdb=" N1 G B 5 " 0.008 2.00e-02 2.50e+03 pdb=" C2 G B 5 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G B 5 " -0.085 2.00e-02 2.50e+03 pdb=" N3 G B 5 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G B 5 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 13 " 0.155 2.00e-02 2.50e+03 6.38e-02 1.12e+02 pdb=" N9 A B 13 " -0.046 2.00e-02 2.50e+03 pdb=" C8 A B 13 " -0.072 2.00e-02 2.50e+03 pdb=" N7 A B 13 " -0.027 2.00e-02 2.50e+03 pdb=" C5 A B 13 " -0.008 2.00e-02 2.50e+03 pdb=" C6 A B 13 " 0.029 2.00e-02 2.50e+03 pdb=" N6 A B 13 " 0.085 2.00e-02 2.50e+03 pdb=" N1 A B 13 " -0.000 2.00e-02 2.50e+03 pdb=" C2 A B 13 " -0.034 2.00e-02 2.50e+03 pdb=" N3 A B 13 " -0.048 2.00e-02 2.50e+03 pdb=" C4 A B 13 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 9 " -0.119 2.00e-02 2.50e+03 6.04e-02 1.09e+02 pdb=" N9 G B 9 " 0.003 2.00e-02 2.50e+03 pdb=" C8 G B 9 " 0.093 2.00e-02 2.50e+03 pdb=" N7 G B 9 " 0.072 2.00e-02 2.50e+03 pdb=" C5 G B 9 " 0.011 2.00e-02 2.50e+03 pdb=" C6 G B 9 " -0.037 2.00e-02 2.50e+03 pdb=" O6 G B 9 " -0.095 2.00e-02 2.50e+03 pdb=" N1 G B 9 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G B 9 " 0.011 2.00e-02 2.50e+03 pdb=" N2 G B 9 " 0.071 2.00e-02 2.50e+03 pdb=" N3 G B 9 " -0.012 2.00e-02 2.50e+03 pdb=" C4 G B 9 " -0.001 2.00e-02 2.50e+03 ... (remaining 1018 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 3 2.49 - 3.09: 3890 3.09 - 3.69: 9217 3.69 - 4.30: 14508 4.30 - 4.90: 23569 Nonbonded interactions: 51187 Sorted by model distance: nonbonded pdb=" ND1 HIS A 807 " pdb="MG MG A 901 " model vdw 1.887 2.250 nonbonded pdb=" OD2 ASP A 597 " pdb="MG MG A 901 " model vdw 1.996 2.170 nonbonded pdb=" OP1 U C 12 " pdb="MG MG A 901 " model vdw 2.004 2.170 nonbonded pdb=" N GLU A 157 " pdb=" OE1 GLU A 157 " model vdw 2.523 3.120 nonbonded pdb=" N HIS A 711 " pdb=" O HIS A 711 " model vdw 2.554 2.496 ... (remaining 51182 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: 1.620 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.270 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 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 : 0.013 0.049 6544 Z= 0.885 Angle : 1.822 10.589 9051 Z= 1.409 Chirality : 0.095 0.503 1034 Planarity : 0.017 0.224 1021 Dihedral : 15.075 87.784 2713 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.17 % Allowed : 3.35 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.80 (0.29), residues: 674 helix: -1.03 (0.30), residues: 225 sheet: -0.93 (0.35), residues: 164 loop : -1.31 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 28 TYR 0.129 0.019 TYR A 57 PHE 0.063 0.009 PHE A 593 TRP 0.034 0.012 TRP A 769 HIS 0.012 0.003 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.01253 / 0.89 ( 6544) covalent geometry : angle 1.82182 / 1.41 ( 9051) hydrogen bonds : bond 0.18499 / 11.22 ( 289) hydrogen bonds : angle 7.59969 / 5.50 ( 777) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 210 LEU cc_start: 0.8236 (mt) cc_final: 0.7923 (mp) REVERT: A 395 ARG cc_start: 0.7732 (mtm-85) cc_final: 0.7348 (mmm160) REVERT: A 425 LYS cc_start: 0.8021 (mmtm) cc_final: 0.7723 (mmmt) REVERT: A 493 LYS cc_start: 0.8383 (tptt) cc_final: 0.8054 (tppt) REVERT: A 659 PHE cc_start: 0.8295 (m-80) cc_final: 0.7984 (m-80) REVERT: A 695 GLU cc_start: 0.8045 (tp30) cc_final: 0.7652 (tm-30) REVERT: A 697 ASP cc_start: 0.8077 (p0) cc_final: 0.7616 (p0) REVERT: A 726 LYS cc_start: 0.8322 (tttp) cc_final: 0.8031 (ttpp) outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.1187 time to fit residues: 16.6879 Evaluate side-chains 79 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 HIS A 548 GLN ** A 711 HIS ** 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 = 0.3753 r_free = 0.3753 target = 0.152188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119736 restraints weight = 6696.249| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.61 r_work: 0.3244 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6544 Z= 0.154 Angle : 0.629 5.702 9051 Z= 0.352 Chirality : 0.045 0.149 1034 Planarity : 0.005 0.047 1021 Dihedral : 14.907 73.985 1359 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.01 % Allowed : 7.87 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.60 (0.31), residues: 674 helix: 0.60 (0.34), residues: 224 sheet: -0.65 (0.36), residues: 163 loop : -0.95 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 723 TYR 0.016 0.001 TYR A 698 PHE 0.012 0.002 PHE A 746 TRP 0.016 0.002 TRP A 435 HIS 0.006 0.001 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 6544) covalent geometry : angle 0.62892 / 0.35 ( 9051) hydrogen bonds : bond 0.05981 / 3.88 ( 289) hydrogen bonds : angle 5.32515 / 3.91 ( 777) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.186 Fit side-chains REVERT: A 83 LYS cc_start: 0.7893 (mtmt) cc_final: 0.7605 (mtpp) REVERT: A 104 MET cc_start: 0.6957 (mmp) cc_final: 0.6594 (mmp) REVERT: A 395 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.7623 (mmm160) REVERT: A 493 LYS cc_start: 0.8561 (tptt) cc_final: 0.8234 (tppt) REVERT: A 726 LYS cc_start: 0.8507 (tttp) cc_final: 0.8176 (ttpp) outliers start: 6 outliers final: 5 residues processed: 84 average time/residue: 0.1289 time to fit residues: 13.2482 Evaluate side-chains 78 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 775 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 29 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.149659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.116791 restraints weight = 6634.267| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.63 r_work: 0.3169 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6544 Z= 0.169 Angle : 0.570 5.534 9051 Z= 0.310 Chirality : 0.044 0.143 1034 Planarity : 0.005 0.041 1021 Dihedral : 14.879 73.752 1359 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.34 % Allowed : 9.38 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 (0.31), residues: 674 helix: 0.94 (0.35), residues: 224 sheet: -0.75 (0.36), residues: 174 loop : -0.89 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 723 TYR 0.014 0.002 TYR A 790 PHE 0.012 0.002 PHE A 44 TRP 0.013 0.002 TRP A 435 HIS 0.006 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 6544) covalent geometry : angle 0.57026 / 0.31 ( 9051) hydrogen bonds : bond 0.05128 / 3.30 ( 289) hydrogen bonds : angle 4.81978 / 3.60 ( 777) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.229 Fit side-chains REVERT: A 104 MET cc_start: 0.6969 (mmp) cc_final: 0.6616 (mmp) REVERT: A 377 GLU cc_start: 0.7686 (tp30) cc_final: 0.7453 (mm-30) REVERT: A 395 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7579 (mmm160) REVERT: A 425 LYS cc_start: 0.8041 (mmtm) cc_final: 0.7690 (mmmt) REVERT: A 493 LYS cc_start: 0.8599 (tptt) cc_final: 0.8218 (tppt) REVERT: A 726 LYS cc_start: 0.8481 (tttp) cc_final: 0.8123 (ttpp) outliers start: 8 outliers final: 3 residues processed: 86 average time/residue: 0.1156 time to fit residues: 12.4205 Evaluate side-chains 79 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 355 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.150183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.118323 restraints weight = 6648.758| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.54 r_work: 0.3223 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6544 Z= 0.179 Angle : 0.557 5.365 9051 Z= 0.301 Chirality : 0.044 0.153 1034 Planarity : 0.005 0.040 1021 Dihedral : 14.904 73.807 1359 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.51 % Allowed : 10.72 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.48 (0.31), residues: 674 helix: 0.97 (0.35), residues: 224 sheet: -0.83 (0.35), residues: 174 loop : -0.94 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 72 TYR 0.012 0.001 TYR A 790 PHE 0.012 0.002 PHE A 491 TRP 0.011 0.002 TRP A 435 HIS 0.005 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 ( 6544) covalent geometry : angle 0.55734 / 0.30 ( 9051) hydrogen bonds : bond 0.04964 / 3.20 ( 289) hydrogen bonds : angle 4.70204 / 3.52 ( 777) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.233 Fit side-chains REVERT: A 104 MET cc_start: 0.6909 (mmp) cc_final: 0.6642 (mmp) REVERT: A 377 GLU cc_start: 0.7712 (tp30) cc_final: 0.7433 (mm-30) REVERT: A 395 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7545 (mmm160) REVERT: A 425 LYS cc_start: 0.8090 (mmtm) cc_final: 0.7725 (mmmt) REVERT: A 493 LYS cc_start: 0.8592 (tptt) cc_final: 0.8216 (tppt) REVERT: A 726 LYS cc_start: 0.8447 (tttp) cc_final: 0.8097 (ttpp) outliers start: 9 outliers final: 7 residues processed: 87 average time/residue: 0.1081 time to fit residues: 11.7428 Evaluate side-chains 79 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 679 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.154346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121840 restraints weight = 6731.129| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.60 r_work: 0.3248 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6544 Z= 0.117 Angle : 0.505 8.523 9051 Z= 0.271 Chirality : 0.041 0.144 1034 Planarity : 0.005 0.041 1021 Dihedral : 14.882 73.737 1359 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.17 % Allowed : 12.56 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.31 (0.31), residues: 674 helix: 1.15 (0.35), residues: 226 sheet: -0.72 (0.35), residues: 171 loop : -0.91 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 723 TYR 0.009 0.001 TYR A 749 PHE 0.010 0.001 PHE A 491 TRP 0.011 0.001 TRP A 435 HIS 0.004 0.001 HIS A 764 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 6544) covalent geometry : angle 0.50471 / 0.27 ( 9051) hydrogen bonds : bond 0.04294 / 2.80 ( 289) hydrogen bonds : angle 4.54817 / 3.42 ( 777) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.217 Fit side-chains REVERT: A 99 ASN cc_start: 0.8747 (m-40) cc_final: 0.8441 (m110) REVERT: A 104 MET cc_start: 0.7082 (mmp) cc_final: 0.6701 (mmp) REVERT: A 377 GLU cc_start: 0.7629 (tp30) cc_final: 0.7348 (mm-30) REVERT: A 395 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7536 (mmm160) REVERT: A 425 LYS cc_start: 0.8081 (mmtm) cc_final: 0.7715 (mmmt) REVERT: A 493 LYS cc_start: 0.8564 (tptt) cc_final: 0.8207 (tppt) REVERT: A 726 LYS cc_start: 0.8381 (tttp) cc_final: 0.8092 (ttpp) outliers start: 7 outliers final: 4 residues processed: 78 average time/residue: 0.0993 time to fit residues: 9.6910 Evaluate side-chains 74 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 569 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 30 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.148361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.116367 restraints weight = 6746.075| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.55 r_work: 0.3196 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6544 Z= 0.227 Angle : 0.594 7.249 9051 Z= 0.314 Chirality : 0.046 0.153 1034 Planarity : 0.005 0.038 1021 Dihedral : 14.897 73.895 1359 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.34 % Allowed : 12.73 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.59 (0.31), residues: 674 helix: 0.98 (0.35), residues: 224 sheet: -0.92 (0.35), residues: 171 loop : -1.08 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 534 TYR 0.014 0.002 TYR A 790 PHE 0.014 0.002 PHE A 44 TRP 0.009 0.002 TRP A 435 HIS 0.006 0.002 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 ( 6544) covalent geometry : angle 0.59363 / 0.31 ( 9051) hydrogen bonds : bond 0.05221 / 3.35 ( 289) hydrogen bonds : angle 4.67593 / 3.51 ( 777) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.132 Fit side-chains REVERT: A 99 ASN cc_start: 0.8796 (m-40) cc_final: 0.8510 (m110) REVERT: A 377 GLU cc_start: 0.7782 (tp30) cc_final: 0.7487 (mm-30) REVERT: A 395 ARG cc_start: 0.7923 (mtm-85) cc_final: 0.7565 (mmm160) REVERT: A 493 LYS cc_start: 0.8601 (tptt) cc_final: 0.8232 (tppt) outliers start: 8 outliers final: 7 residues processed: 77 average time/residue: 0.0992 time to fit residues: 9.4568 Evaluate side-chains 74 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 30 optimal weight: 0.0040 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 0.0010 chunk 63 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 overall best weight: 0.5800 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.156005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123285 restraints weight = 6720.054| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.63 r_work: 0.3228 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6544 Z= 0.107 Angle : 0.485 6.321 9051 Z= 0.262 Chirality : 0.040 0.137 1034 Planarity : 0.005 0.042 1021 Dihedral : 14.892 73.709 1359 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.17 % Allowed : 13.40 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.32 (0.32), residues: 674 helix: 1.25 (0.35), residues: 226 sheet: -0.76 (0.36), residues: 171 loop : -1.00 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.009 0.001 TYR A 749 PHE 0.010 0.001 PHE A 491 TRP 0.011 0.001 TRP A 435 HIS 0.005 0.001 HIS A 764 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 6544) covalent geometry : angle 0.48467 / 0.26 ( 9051) hydrogen bonds : bond 0.04054 / 2.65 ( 289) hydrogen bonds : angle 4.46045 / 3.37 ( 777) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.158 Fit side-chains REVERT: A 99 ASN cc_start: 0.8752 (m-40) cc_final: 0.8482 (m110) REVERT: A 377 GLU cc_start: 0.7674 (tp30) cc_final: 0.7341 (mm-30) REVERT: A 395 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7502 (mmm160) REVERT: A 493 LYS cc_start: 0.8577 (tptt) cc_final: 0.8202 (tppt) outliers start: 7 outliers final: 5 residues processed: 74 average time/residue: 0.1045 time to fit residues: 9.6053 Evaluate side-chains 76 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.154519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121723 restraints weight = 6749.788| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.63 r_work: 0.3203 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6544 Z= 0.137 Angle : 0.503 6.114 9051 Z= 0.268 Chirality : 0.041 0.141 1034 Planarity : 0.005 0.047 1021 Dihedral : 14.865 73.754 1359 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.17 % Allowed : 13.23 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.32 (0.32), residues: 674 helix: 1.23 (0.36), residues: 226 sheet: -0.71 (0.36), residues: 171 loop : -1.03 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 72 TYR 0.011 0.001 TYR A 749 PHE 0.011 0.001 PHE A 491 TRP 0.009 0.001 TRP A 435 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 6544) covalent geometry : angle 0.50278 / 0.27 ( 9051) hydrogen bonds : bond 0.04230 / 2.75 ( 289) hydrogen bonds : angle 4.43817 / 3.35 ( 777) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.213 Fit side-chains REVERT: A 99 ASN cc_start: 0.8734 (m-40) cc_final: 0.8486 (m110) REVERT: A 377 GLU cc_start: 0.7723 (tp30) cc_final: 0.7405 (mm-30) REVERT: A 395 ARG cc_start: 0.7909 (mtm-85) cc_final: 0.7519 (mmm160) REVERT: A 493 LYS cc_start: 0.8620 (tptt) cc_final: 0.8239 (tppt) outliers start: 7 outliers final: 6 residues processed: 79 average time/residue: 0.1183 time to fit residues: 11.5635 Evaluate side-chains 76 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 69 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 42 optimal weight: 0.0670 chunk 54 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.150610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117300 restraints weight = 6812.679| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.66 r_work: 0.3179 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6544 Z= 0.228 Angle : 0.591 6.327 9051 Z= 0.313 Chirality : 0.046 0.151 1034 Planarity : 0.005 0.050 1021 Dihedral : 14.901 73.899 1359 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.51 % Allowed : 13.23 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.59 (0.31), residues: 674 helix: 1.05 (0.35), residues: 223 sheet: -0.86 (0.35), residues: 171 loop : -1.19 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 534 TYR 0.012 0.002 TYR A 790 PHE 0.014 0.002 PHE A 491 TRP 0.008 0.002 TRP A 211 HIS 0.005 0.001 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.23 ( 6544) covalent geometry : angle 0.59054 / 0.31 ( 9051) hydrogen bonds : bond 0.05187 / 3.33 ( 289) hydrogen bonds : angle 4.62573 / 3.47 ( 777) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.274 Fit side-chains REVERT: A 99 ASN cc_start: 0.8796 (m-40) cc_final: 0.8553 (m110) REVERT: A 377 GLU cc_start: 0.7834 (tp30) cc_final: 0.7517 (mm-30) REVERT: A 395 ARG cc_start: 0.7947 (mtm-85) cc_final: 0.7602 (mmm160) REVERT: A 493 LYS cc_start: 0.8606 (tptt) cc_final: 0.8217 (tppt) outliers start: 9 outliers final: 6 residues processed: 77 average time/residue: 0.1142 time to fit residues: 10.9502 Evaluate side-chains 74 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 71 optimal weight: 10.9990 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.153063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120758 restraints weight = 6669.973| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.60 r_work: 0.3242 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6544 Z= 0.130 Angle : 0.507 5.865 9051 Z= 0.272 Chirality : 0.041 0.142 1034 Planarity : 0.005 0.054 1021 Dihedral : 14.893 73.761 1359 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.84 % Allowed : 13.90 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.39 (0.32), residues: 674 helix: 1.30 (0.36), residues: 223 sheet: -0.83 (0.35), residues: 171 loop : -1.09 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 710 TYR 0.009 0.001 TYR A 749 PHE 0.012 0.001 PHE A 491 TRP 0.012 0.001 TRP A 435 HIS 0.004 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 6544) covalent geometry : angle 0.50662 / 0.27 ( 9051) hydrogen bonds : bond 0.04247 / 2.75 ( 289) hydrogen bonds : angle 4.48512 / 3.38 ( 777) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.233 Fit side-chains REVERT: A 99 ASN cc_start: 0.8719 (m-40) cc_final: 0.8488 (m110) REVERT: A 377 GLU cc_start: 0.7698 (tp30) cc_final: 0.7371 (mm-30) REVERT: A 395 ARG cc_start: 0.7927 (mtm-85) cc_final: 0.7579 (mmm160) REVERT: A 493 LYS cc_start: 0.8588 (tptt) cc_final: 0.8219 (tppt) outliers start: 5 outliers final: 5 residues processed: 72 average time/residue: 0.1222 time to fit residues: 10.8705 Evaluate side-chains 74 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 0.0040 chunk 59 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.155540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122861 restraints weight = 6740.552| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.62 r_work: 0.3254 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6544 Z= 0.123 Angle : 0.489 5.582 9051 Z= 0.262 Chirality : 0.041 0.140 1034 Planarity : 0.005 0.054 1021 Dihedral : 14.876 73.740 1359 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.67 % Allowed : 14.24 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.33 (0.32), residues: 674 helix: 1.34 (0.36), residues: 225 sheet: -0.84 (0.35), residues: 172 loop : -1.04 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 384 TYR 0.010 0.001 TYR A 749 PHE 0.011 0.001 PHE A 491 TRP 0.010 0.001 TRP A 435 HIS 0.004 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 6544) covalent geometry : angle 0.48892 / 0.26 ( 9051) hydrogen bonds : bond 0.04022 / 2.62 ( 289) hydrogen bonds : angle 4.41135 / 3.32 ( 777) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1587.37 seconds wall clock time: 27 minutes 49.67 seconds (1669.67 seconds total)