Starting phenix.real_space_refine on Sun Apr 5 00:02:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dhx_46888/04_2026/9dhx_46888.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dhx_46888/04_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dhx_46888/04_2026/9dhx_46888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dhx_46888/04_2026/9dhx_46888.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dhx_46888/04_2026/9dhx_46888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dhx_46888/04_2026/9dhx_46888.map" } 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-2.1rc1-6017/lib/python3.9/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: 1.48, per 1000 atoms: 0.23 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: 0.64 Conformation dependent library (CDL) restraints added in 228.6 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: 0.75 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: 1.31 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 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=" CA PRO A 26 " pdb=" C PRO A 26 " ideal model delta sigma weight residual 1.517 1.544 -0.027 6.70e-03 2.23e+04 1.59e+01 bond pdb=" CE1 HIS A 849 " pdb=" NE2 HIS A 849 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.53e+01 bond pdb=" CE1 HIS A 203 " pdb=" NE2 HIS A 203 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.52e+01 bond pdb=" CE1 HIS A 144 " pdb=" NE2 HIS A 144 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.50e+01 bond pdb=" CE1 HIS A 712 " pdb=" NE2 HIS A 712 " ideal model delta sigma weight residual 1.321 1.358 -0.037 1.00e-02 1.00e+04 1.38e+01 ... (remaining 6539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 7110 2.22 - 4.44: 1763 4.44 - 6.65: 168 6.65 - 8.87: 4 8.87 - 11.09: 6 Bond angle restraints: 9051 Sorted by residual: angle pdb=" C3' A C 2 " pdb=" O3' A C 2 " pdb=" P A C 3 " ideal model delta sigma weight residual 120.20 109.11 11.09 1.50e+00 4.44e-01 5.46e+01 angle pdb=" C3' U B 19 " pdb=" O3' U B 19 " pdb=" P U B 20 " ideal model delta sigma weight residual 120.20 109.87 10.33 1.50e+00 4.44e-01 4.74e+01 angle pdb=" O3' A C 21 " pdb=" P A C 22 " pdb=" O5' A C 22 " ideal model delta sigma weight residual 104.00 94.18 9.82 1.50e+00 4.44e-01 4.29e+01 angle pdb=" C3' G B 18 " pdb=" O3' G B 18 " pdb=" P U B 19 " ideal model delta sigma weight residual 120.20 110.46 9.74 1.50e+00 4.44e-01 4.22e+01 angle pdb=" C3' U B 17 " pdb=" O3' U B 17 " pdb=" P G B 18 " ideal model delta sigma weight residual 120.20 110.90 9.30 1.50e+00 4.44e-01 3.85e+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: 770 0.101 - 0.201: 230 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: 1.140 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.030 Find NCS groups from input model: 0.020 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 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= 0.781 Angle : 1.822 11.089 9051 Z= 1.219 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 covalent geometry : bond 0.01252 ( 6544) covalent geometry : angle 1.82156 ( 9051) hydrogen bonds : bond 0.18499 ( 289) hydrogen bonds : angle 7.59969 ( 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 : 0.173 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: 0.7349 (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: 0.8030 (ttpp) outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.1295 time to fit residues: 18.0895 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 : 0.226 ------------------------------------------------------------------------------- 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: 2.9990 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... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 548 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.153774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121294 restraints weight = 6669.060| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.59 r_work: 0.3261 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2081 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= 0.135 Angle : 0.573 5.322 9051 Z= 0.311 Chirality : 0.043 0.162 1034 Planarity : 0.005 0.035 1021 Dihedral : 14.893 73.896 1359 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.50 % Allowed : 8.71 % Favored : 90.79 % 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 (0.31), residues: 674 helix: 0.77 (0.34), residues: 224 sheet: -0.42 (0.36), residues: 168 loop : -0.78 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 723 TYR 0.015 0.001 TYR A 698 PHE 0.010 0.001 PHE A 94 TRP 0.014 0.002 TRP A 435 HIS 0.005 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6544) covalent geometry : angle 0.57334 ( 9051) hydrogen bonds : bond 0.04694 ( 289) hydrogen bonds : angle 4.93316 ( 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 85 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.217 Fit side-chains REVERT: A 104 MET cc_start: 0.6941 (mmp) cc_final: 0.6608 (mmp) REVERT: A 395 ARG cc_start: 0.7861 (mtm-85) cc_final: 0.7611 (mmm160) REVERT: A 405 MET cc_start: 0.9223 (mtt) cc_final: 0.8980 (mtt) REVERT: A 425 LYS cc_start: 0.8028 (mmtm) cc_final: 0.7710 (mmmt) REVERT: A 493 LYS cc_start: 0.8533 (tptt) cc_final: 0.8179 (tppt) REVERT: A 726 LYS cc_start: 0.8387 (tttp) cc_final: 0.8058 (ttpp) outliers start: 3 outliers final: 2 residues processed: 84 average time/residue: 0.1264 time to fit residues: 12.9401 Evaluate side-chains 76 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 638 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 29 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.150598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118962 restraints weight = 6602.044| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.53 r_work: 0.3184 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6544 Z= 0.171 Angle : 0.559 6.694 9051 Z= 0.300 Chirality : 0.044 0.188 1034 Planarity : 0.005 0.035 1021 Dihedral : 14.909 73.767 1359 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.84 % Allowed : 9.88 % 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: -0.20 (0.31), residues: 674 helix: 1.15 (0.35), residues: 223 sheet: -0.66 (0.36), residues: 174 loop : -0.73 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 179 TYR 0.015 0.002 TYR A 790 PHE 0.011 0.001 PHE A 491 TRP 0.010 0.002 TRP A 435 HIS 0.006 0.001 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 6544) covalent geometry : angle 0.55918 ( 9051) hydrogen bonds : bond 0.04684 ( 289) hydrogen bonds : angle 4.65105 ( 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 89 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.157 Fit side-chains REVERT: A 104 MET cc_start: 0.6901 (mmp) cc_final: 0.6646 (mmp) REVERT: A 377 GLU cc_start: 0.7733 (tp30) cc_final: 0.7455 (mm-30) REVERT: A 395 ARG cc_start: 0.7926 (mtm-85) cc_final: 0.7537 (mmm160) REVERT: A 493 LYS cc_start: 0.8596 (tptt) cc_final: 0.8195 (tppt) REVERT: A 726 LYS cc_start: 0.8378 (tttp) cc_final: 0.8094 (ttpp) outliers start: 5 outliers final: 2 residues processed: 88 average time/residue: 0.1194 time to fit residues: 12.9306 Evaluate side-chains 76 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 183 THR 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: 1.9990 chunk 67 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 63 optimal weight: 0.0270 chunk 31 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.147488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115788 restraints weight = 6704.392| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.54 r_work: 0.3118 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 6544 Z= 0.241 Angle : 0.609 6.721 9051 Z= 0.324 Chirality : 0.046 0.218 1034 Planarity : 0.005 0.035 1021 Dihedral : 14.952 73.859 1359 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.84 % Allowed : 10.72 % Favored : 87.44 % 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: 223 sheet: -0.79 (0.35), residues: 171 loop : -0.97 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 179 TYR 0.013 0.002 TYR A 790 PHE 0.013 0.002 PHE A 491 TRP 0.011 0.002 TRP A 211 HIS 0.007 0.001 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00577 ( 6544) covalent geometry : angle 0.60943 ( 9051) hydrogen bonds : bond 0.05178 ( 289) hydrogen bonds : angle 4.74878 ( 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 85 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.207 Fit side-chains REVERT: A 357 THR cc_start: 0.6095 (OUTLIER) cc_final: 0.5801 (p) REVERT: A 377 GLU cc_start: 0.7805 (tp30) cc_final: 0.7511 (mm-30) REVERT: A 395 ARG cc_start: 0.7937 (mtm-85) cc_final: 0.7572 (mmm160) REVERT: A 493 LYS cc_start: 0.8584 (tptt) cc_final: 0.8152 (tppt) REVERT: A 726 LYS cc_start: 0.8403 (tttp) cc_final: 0.8109 (ttpp) outliers start: 11 outliers final: 6 residues processed: 83 average time/residue: 0.1019 time to fit residues: 10.6253 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 : 0.240 ------------------------------------------------------------------------------- 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 357 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.150494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118791 restraints weight = 6751.474| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.55 r_work: 0.3201 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2767 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= 0.143 Angle : 0.524 7.443 9051 Z= 0.277 Chirality : 0.042 0.174 1034 Planarity : 0.005 0.041 1021 Dihedral : 14.898 73.734 1359 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.51 % Allowed : 12.23 % 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: 1.24 (0.35), residues: 223 sheet: -0.76 (0.35), residues: 171 loop : -0.94 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.010 0.001 TYR A 749 PHE 0.012 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 covalent geometry : bond 0.00330 ( 6544) covalent geometry : angle 0.52369 ( 9051) hydrogen bonds : bond 0.04189 ( 289) hydrogen bonds : angle 4.53478 ( 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 89 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.163 Fit side-chains REVERT: A 99 ASN cc_start: 0.8723 (m-40) cc_final: 0.8395 (m110) REVERT: A 357 THR cc_start: 0.6096 (OUTLIER) cc_final: 0.5826 (p) REVERT: A 377 GLU cc_start: 0.7716 (tp30) cc_final: 0.7419 (mm-30) REVERT: A 395 ARG cc_start: 0.7943 (mtm-85) cc_final: 0.7592 (mmm160) REVERT: A 493 LYS cc_start: 0.8567 (tptt) cc_final: 0.8156 (tppt) outliers start: 9 outliers final: 8 residues processed: 86 average time/residue: 0.1092 time to fit residues: 11.7301 Evaluate side-chains 82 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 357 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 30 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 0.0870 chunk 60 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.117592 restraints weight = 6753.139| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.53 r_work: 0.3186 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6544 Z= 0.179 Angle : 0.540 6.281 9051 Z= 0.285 Chirality : 0.043 0.187 1034 Planarity : 0.005 0.046 1021 Dihedral : 14.901 73.778 1359 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.68 % Allowed : 12.23 % Favored : 86.10 % 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: -0.38 (0.31), residues: 674 helix: 1.21 (0.35), residues: 223 sheet: -0.82 (0.35), residues: 171 loop : -0.99 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 179 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 0.005 0.001 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 6544) covalent geometry : angle 0.53960 ( 9051) hydrogen bonds : bond 0.04472 ( 289) hydrogen bonds : angle 4.54578 ( 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 86 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.202 Fit side-chains REVERT: A 81 HIS cc_start: 0.7025 (OUTLIER) cc_final: 0.6391 (t-90) REVERT: A 99 ASN cc_start: 0.8718 (m-40) cc_final: 0.8437 (m110) REVERT: A 357 THR cc_start: 0.6151 (OUTLIER) cc_final: 0.5871 (p) REVERT: A 377 GLU cc_start: 0.7755 (tp30) cc_final: 0.7456 (mm-30) REVERT: A 395 ARG cc_start: 0.7946 (mtm-85) cc_final: 0.7567 (mmm160) REVERT: A 493 LYS cc_start: 0.8601 (tptt) cc_final: 0.8192 (tppt) outliers start: 10 outliers final: 8 residues processed: 83 average time/residue: 0.1074 time to fit residues: 11.2265 Evaluate side-chains 80 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 81 HIS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 357 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: 0.6980 chunk 19 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 63 optimal weight: 0.0770 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.151992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120459 restraints weight = 6696.575| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.53 r_work: 0.3254 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2954 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= 0.126 Angle : 0.496 5.508 9051 Z= 0.262 Chirality : 0.042 0.155 1034 Planarity : 0.005 0.051 1021 Dihedral : 14.871 73.703 1359 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.84 % Allowed : 13.90 % Favored : 84.25 % 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: -0.25 (0.32), residues: 674 helix: 1.30 (0.35), residues: 226 sheet: -0.76 (0.35), residues: 171 loop : -0.92 (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 494 PHE 0.010 0.001 PHE A 491 TRP 0.010 0.001 TRP A 435 HIS 0.004 0.001 HIS A 764 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6544) covalent geometry : angle 0.49627 ( 9051) hydrogen bonds : bond 0.03852 ( 289) hydrogen bonds : angle 4.40144 ( 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 82 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.192 Fit side-chains REVERT: A 81 HIS cc_start: 0.7035 (OUTLIER) cc_final: 0.6379 (t-90) REVERT: A 99 ASN cc_start: 0.8635 (m-40) cc_final: 0.8402 (m110) REVERT: A 357 THR cc_start: 0.6273 (OUTLIER) cc_final: 0.6024 (p) REVERT: A 377 GLU cc_start: 0.7666 (tp30) cc_final: 0.7361 (mm-30) REVERT: A 395 ARG cc_start: 0.7910 (mtm-85) cc_final: 0.7570 (mmm160) REVERT: A 480 ASP cc_start: 0.7966 (m-30) cc_final: 0.7612 (m-30) REVERT: A 493 LYS cc_start: 0.8582 (tptt) cc_final: 0.8205 (tppt) outliers start: 11 outliers final: 7 residues processed: 79 average time/residue: 0.1103 time to fit residues: 10.9436 Evaluate side-chains 77 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 81 HIS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 679 VAL 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: 3.9990 chunk 10 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.153538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120479 restraints weight = 6772.444| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.65 r_work: 0.3226 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2986 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= 0.141 Angle : 0.500 5.137 9051 Z= 0.263 Chirality : 0.042 0.161 1034 Planarity : 0.005 0.053 1021 Dihedral : 14.851 73.714 1359 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.84 % Allowed : 14.41 % Favored : 83.75 % 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: -0.25 (0.32), residues: 674 helix: 1.28 (0.35), residues: 226 sheet: -0.73 (0.35), residues: 171 loop : -0.91 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.010 0.001 TYR A 749 PHE 0.010 0.001 PHE A 491 TRP 0.009 0.001 TRP A 435 HIS 0.005 0.001 HIS A 764 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6544) covalent geometry : angle 0.50018 ( 9051) hydrogen bonds : bond 0.03994 ( 289) hydrogen bonds : angle 4.40012 ( 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 82 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.137 Fit side-chains REVERT: A 23 PHE cc_start: 0.8700 (m-80) cc_final: 0.8483 (m-80) REVERT: A 81 HIS cc_start: 0.7028 (OUTLIER) cc_final: 0.6385 (t-90) REVERT: A 355 LYS cc_start: 0.6639 (OUTLIER) cc_final: 0.6207 (mttt) REVERT: A 357 THR cc_start: 0.6330 (OUTLIER) cc_final: 0.6073 (p) REVERT: A 377 GLU cc_start: 0.7711 (tp30) cc_final: 0.7414 (mm-30) REVERT: A 395 ARG cc_start: 0.7922 (mtm-85) cc_final: 0.7576 (mmm160) REVERT: A 480 ASP cc_start: 0.7936 (m-30) cc_final: 0.7580 (m-30) REVERT: A 493 LYS cc_start: 0.8594 (tptt) cc_final: 0.8221 (tppt) outliers start: 11 outliers final: 7 residues processed: 79 average time/residue: 0.1153 time to fit residues: 11.3517 Evaluate side-chains 77 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 81 HIS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 357 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 69 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 42 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.154491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.121425 restraints weight = 6808.795| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.65 r_work: 0.3237 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3042 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= 0.132 Angle : 0.496 4.888 9051 Z= 0.261 Chirality : 0.041 0.153 1034 Planarity : 0.005 0.054 1021 Dihedral : 14.833 73.700 1359 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.68 % Allowed : 14.74 % Favored : 83.58 % 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: -0.17 (0.32), residues: 674 helix: 1.32 (0.35), residues: 226 sheet: -0.66 (0.36), residues: 171 loop : -0.86 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 179 TYR 0.010 0.001 TYR A 749 PHE 0.010 0.001 PHE A 491 TRP 0.009 0.001 TRP A 435 HIS 0.004 0.001 HIS A 764 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6544) covalent geometry : angle 0.49557 ( 9051) hydrogen bonds : bond 0.03885 ( 289) hydrogen bonds : angle 4.35509 ( 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 80 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.238 Fit side-chains REVERT: A 81 HIS cc_start: 0.7063 (OUTLIER) cc_final: 0.6412 (t-90) REVERT: A 355 LYS cc_start: 0.6705 (OUTLIER) cc_final: 0.6266 (mttt) REVERT: A 357 THR cc_start: 0.6330 (OUTLIER) cc_final: 0.6083 (p) REVERT: A 377 GLU cc_start: 0.7695 (tp30) cc_final: 0.7401 (mm-30) REVERT: A 395 ARG cc_start: 0.7935 (mtm-85) cc_final: 0.7595 (mmm160) REVERT: A 480 ASP cc_start: 0.7961 (m-30) cc_final: 0.7612 (m-30) REVERT: A 493 LYS cc_start: 0.8596 (tptt) cc_final: 0.8231 (tppt) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.1118 time to fit residues: 10.6763 Evaluate side-chains 78 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 81 HIS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 357 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 41 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.156667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124139 restraints weight = 6683.618| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.61 r_work: 0.3245 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3127 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= 0.111 Angle : 0.479 4.759 9051 Z= 0.252 Chirality : 0.041 0.137 1034 Planarity : 0.005 0.052 1021 Dihedral : 14.818 73.660 1359 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.51 % Allowed : 15.08 % Favored : 83.42 % 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: -0.03 (0.32), residues: 674 helix: 1.40 (0.35), residues: 227 sheet: -0.51 (0.37), residues: 166 loop : -0.82 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.008 0.001 TYR A 749 PHE 0.010 0.001 PHE A 491 TRP 0.009 0.001 TRP A 435 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6544) covalent geometry : angle 0.47940 ( 9051) hydrogen bonds : bond 0.03576 ( 289) hydrogen bonds : angle 4.25151 ( 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 84 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.167 Fit side-chains REVERT: A 81 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.6404 (t-90) REVERT: A 355 LYS cc_start: 0.6627 (tptt) cc_final: 0.6248 (mttt) REVERT: A 357 THR cc_start: 0.6385 (OUTLIER) cc_final: 0.6164 (p) REVERT: A 377 GLU cc_start: 0.7657 (tp30) cc_final: 0.7369 (mm-30) REVERT: A 395 ARG cc_start: 0.7989 (mtm-85) cc_final: 0.7596 (mmm160) REVERT: A 480 ASP cc_start: 0.7972 (m-30) cc_final: 0.7624 (m-30) REVERT: A 493 LYS cc_start: 0.8586 (tptt) cc_final: 0.8220 (tppt) outliers start: 9 outliers final: 7 residues processed: 82 average time/residue: 0.1222 time to fit residues: 12.2835 Evaluate side-chains 79 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 81 HIS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 357 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 8 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS ** A 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.158683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.126197 restraints weight = 6726.880| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.60 r_work: 0.3271 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6544 Z= 0.097 Angle : 0.463 4.758 9051 Z= 0.243 Chirality : 0.040 0.135 1034 Planarity : 0.005 0.052 1021 Dihedral : 14.807 73.602 1359 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.68 % Allowed : 15.41 % Favored : 82.91 % 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: 0.10 (0.32), residues: 674 helix: 1.57 (0.35), residues: 226 sheet: -0.46 (0.37), residues: 167 loop : -0.77 (0.37), residues: 281 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 0.009 0.001 PHE A 491 TRP 0.009 0.001 TRP A 435 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 6544) covalent geometry : angle 0.46335 ( 9051) hydrogen bonds : bond 0.03338 ( 289) hydrogen bonds : angle 4.17206 ( 777) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1673.17 seconds wall clock time: 29 minutes 15.90 seconds (1755.90 seconds total)