Starting phenix.real_space_refine on Sun Jul 27 22:14:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywh_39633/07_2025/8ywh_39633.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywh_39633/07_2025/8ywh_39633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ywh_39633/07_2025/8ywh_39633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywh_39633/07_2025/8ywh_39633.map" model { file = "/net/cci-nas-00/data/ceres_data/8ywh_39633/07_2025/8ywh_39633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywh_39633/07_2025/8ywh_39633.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 141 5.49 5 S 9 5.16 5 C 5801 2.51 5 N 1750 2.21 5 O 2256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9957 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6993 Classifications: {'peptide': 845} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 824} Chain breaks: 1 Chain: "B" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2085 Classifications: {'RNA': 98} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 8, 'rna3p_pur': 43, 'rna3p_pyr': 39} Link IDs: {'rna2p': 16, 'rna3p': 81} Chain: "C" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 630 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "D" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 249 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Time building chain proxies: 6.95, per 1000 atoms: 0.70 Number of scatterers: 9957 At special positions: 0 Unit cell: (86.775, 105.3, 139.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 P 141 15.00 O 2256 8.00 N 1750 7.00 C 5801 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: 2.60 Conformation dependent library (CDL) restraints added in 1.1 seconds 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1610 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 49.0% alpha, 12.5% beta 37 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 4.29 Creating SS restraints... Processing helix chain 'A' and resid 40 through 74 removed outlier: 3.909A pdb=" N ASN A 44 " --> pdb=" O ASN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.649A pdb=" N GLU A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 124 " --> pdb=" O ASN A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 119 through 124' Processing helix chain 'A' and resid 133 through 144 removed outlier: 3.809A pdb=" N SER A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 166 through 170 removed outlier: 3.936A pdb=" N ARG A 170 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 191 removed outlier: 4.301A pdb=" N ALA A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 207 removed outlier: 3.577A pdb=" N ILE A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 Processing helix chain 'A' and resid 250 through 265 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 326 through 336 removed outlier: 3.531A pdb=" N ILE A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.790A pdb=" N ILE A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 358 Processing helix chain 'A' and resid 360 through 372 removed outlier: 3.723A pdb=" N ASN A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 386 Processing helix chain 'A' and resid 396 through 408 Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 438 through 444 removed outlier: 3.844A pdb=" N ASP A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 468 Processing helix chain 'A' and resid 481 through 500 removed outlier: 3.668A pdb=" N ALA A 485 " --> pdb=" O GLY A 481 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR A 486 " --> pdb=" O GLY A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 520 Processing helix chain 'A' and resid 531 through 549 Processing helix chain 'A' and resid 647 through 656 removed outlier: 3.663A pdb=" N LYS A 651 " --> pdb=" O ASP A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 660 through 665 removed outlier: 3.762A pdb=" N HIS A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 681 removed outlier: 4.270A pdb=" N TYR A 670 " --> pdb=" O ASP A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 695 removed outlier: 3.609A pdb=" N LYS A 689 " --> pdb=" O ASN A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 730 Processing helix chain 'A' and resid 776 through 788 removed outlier: 3.503A pdb=" N LYS A 787 " --> pdb=" O ALA A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing sheet with id=AA1, first strand: chain 'A' and resid 505 through 507 removed outlier: 3.616A pdb=" N ASP A 473 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 11 " --> pdb=" O GLU A 477 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL A 16 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL A 33 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR A 18 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ALA A 31 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE A 20 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 246 through 247 removed outlier: 3.707A pdb=" N SER A 246 " --> pdb=" O HIS A 393 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 713 through 719 removed outlier: 4.118A pdb=" N ILE A 634 " --> pdb=" O GLY A 717 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS A 719 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR A 632 " --> pdb=" O LYS A 719 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER A 623 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ASN A 637 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 11.922A pdb=" N LEU A 621 " --> pdb=" O ASN A 637 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 755 through 762 removed outlier: 3.675A pdb=" N ALA A 797 " --> pdb=" O VAL A 749 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 751 " --> pdb=" O PHE A 795 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N PHE A 795 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 766 through 769 Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 852 removed outlier: 4.587A pdb=" N ILE A 849 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG A 824 " --> pdb=" O ASN A 818 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASN A 828 " --> pdb=" O VAL A 814 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL A 814 " --> pdb=" O ASN A 828 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 804 " --> pdb=" O TYR A 863 " (cutoff:3.500A) 326 hydrogen bonds defined for protein. 951 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 91 hydrogen bonds 182 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 4.77 Time building geometry restraints manager: 3.05 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: 2211 1.33 - 1.45: 2813 1.45 - 1.57: 5110 1.57 - 1.69: 279 1.69 - 1.81: 16 Bond restraints: 10429 Sorted by residual: bond pdb=" O5' G B 67 " pdb=" C5' G B 67 " ideal model delta sigma weight residual 1.420 1.444 -0.024 1.50e-02 4.44e+03 2.50e+00 bond pdb=" CG1 ILE A 475 " pdb=" CD1 ILE A 475 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.27e+00 bond pdb=" CG1 ILE A 789 " pdb=" CD1 ILE A 789 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.88e+00 bond pdb=" O5' C B 69 " pdb=" C5' C B 69 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.61e+00 bond pdb=" O5' A B 64 " pdb=" C5' A B 64 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.60e+00 ... (remaining 10424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 14244 1.89 - 3.77: 408 3.77 - 5.66: 38 5.66 - 7.54: 11 7.54 - 9.43: 4 Bond angle restraints: 14705 Sorted by residual: angle pdb=" C LEU A 421 " pdb=" N LYS A 422 " pdb=" CA LYS A 422 " ideal model delta sigma weight residual 123.05 128.22 -5.17 1.57e+00 4.06e-01 1.09e+01 angle pdb=" C TRP A 521 " pdb=" CA TRP A 521 " pdb=" CB TRP A 521 " ideal model delta sigma weight residual 116.34 111.95 4.39 1.40e+00 5.10e-01 9.82e+00 angle pdb=" N ASN A 613 " pdb=" CA ASN A 613 " pdb=" C ASN A 613 " ideal model delta sigma weight residual 111.02 114.84 -3.82 1.25e+00 6.40e-01 9.33e+00 angle pdb=" C LEU A 430 " pdb=" N SER A 431 " pdb=" CA SER A 431 " ideal model delta sigma weight residual 121.54 127.22 -5.68 1.91e+00 2.74e-01 8.86e+00 angle pdb=" C3' G B 89 " pdb=" O3' G B 89 " pdb=" P U B 90 " ideal model delta sigma weight residual 120.20 124.55 -4.35 1.50e+00 4.44e-01 8.40e+00 ... (remaining 14700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 5675 35.86 - 71.73: 629 71.73 - 107.59: 48 107.59 - 143.45: 0 143.45 - 179.31: 3 Dihedral angle restraints: 6355 sinusoidal: 3849 harmonic: 2506 Sorted by residual: dihedral pdb=" O4' U B 4 " pdb=" C1' U B 4 " pdb=" N1 U B 4 " pdb=" C2 U B 4 " ideal model delta sinusoidal sigma weight residual -160.00 17.90 -177.90 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' A B 65 " pdb=" C1' A B 65 " pdb=" N9 A B 65 " pdb=" C4 A B 65 " ideal model delta sinusoidal sigma weight residual -106.00 -173.14 67.14 1 1.70e+01 3.46e-03 2.03e+01 dihedral pdb=" CA GLU A 794 " pdb=" C GLU A 794 " pdb=" N PHE A 795 " pdb=" CA PHE A 795 " ideal model delta harmonic sigma weight residual -180.00 -158.11 -21.89 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 6352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1336 0.044 - 0.088: 269 0.088 - 0.132: 83 0.132 - 0.177: 14 0.177 - 0.221: 4 Chirality restraints: 1706 Sorted by residual: chirality pdb=" C3' A B 64 " pdb=" C4' A B 64 " pdb=" O3' A B 64 " pdb=" C2' A B 64 " both_signs ideal model delta sigma weight residual False -2.48 -2.70 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB ILE A 475 " pdb=" CA ILE A 475 " pdb=" CG1 ILE A 475 " pdb=" CG2 ILE A 475 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C2' A B 64 " pdb=" C3' A B 64 " pdb=" O2' A B 64 " pdb=" C1' A B 64 " both_signs ideal model delta sigma weight residual False -2.75 -2.56 -0.19 2.00e-01 2.50e+01 9.17e-01 ... (remaining 1703 not shown) Planarity restraints: 1364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 53 " -0.034 2.00e-02 2.50e+03 1.54e-02 6.55e+00 pdb=" N9 A B 53 " 0.033 2.00e-02 2.50e+03 pdb=" C8 A B 53 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A B 53 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A B 53 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 53 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A B 53 " -0.011 2.00e-02 2.50e+03 pdb=" N1 A B 53 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A B 53 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B 53 " 0.001 2.00e-02 2.50e+03 pdb=" C4 A B 53 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 54 " -0.029 2.00e-02 2.50e+03 1.36e-02 5.08e+00 pdb=" N9 A B 54 " 0.032 2.00e-02 2.50e+03 pdb=" C8 A B 54 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B 54 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A B 54 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A B 54 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A B 54 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A B 54 " -0.007 2.00e-02 2.50e+03 pdb=" C2 A B 54 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A B 54 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A B 54 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 52 " 0.029 2.00e-02 2.50e+03 1.28e-02 4.53e+00 pdb=" N9 A B 52 " -0.028 2.00e-02 2.50e+03 pdb=" C8 A B 52 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A B 52 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A B 52 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 52 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A B 52 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A B 52 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A B 52 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A B 52 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A B 52 " -0.002 2.00e-02 2.50e+03 ... (remaining 1361 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1297 2.74 - 3.28: 9288 3.28 - 3.82: 18384 3.82 - 4.36: 22406 4.36 - 4.90: 34436 Nonbonded interactions: 85811 Sorted by model distance: nonbonded pdb=" OE2 GLU A 322 " pdb=" O2' A B 8 " model vdw 2.205 3.040 nonbonded pdb=" NZ LYS A 700 " pdb=" O2 C B 32 " model vdw 2.225 3.120 nonbonded pdb=" NH2 ARG A 48 " pdb=" OP2 U B 15 " model vdw 2.227 3.120 nonbonded pdb=" NE2 GLN A 433 " pdb=" OE1 GLU A 435 " model vdw 2.227 3.120 nonbonded pdb=" OD2 ASP A 261 " pdb=" NH1 ARG A 314 " model vdw 2.247 3.120 ... (remaining 85806 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: 1.700 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.190 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10429 Z= 0.218 Angle : 0.746 9.426 14705 Z= 0.430 Chirality : 0.042 0.221 1706 Planarity : 0.004 0.038 1364 Dihedral : 24.041 179.313 4745 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 6.22 % Allowed : 38.60 % Favored : 55.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.28), residues: 841 helix: 0.60 (0.26), residues: 365 sheet: -0.46 (0.66), residues: 59 loop : -0.24 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 408 HIS 0.005 0.001 HIS A 879 PHE 0.029 0.002 PHE A 758 TYR 0.028 0.002 TYR A 670 ARG 0.008 0.001 ARG A 734 Details of bonding type rmsd hydrogen bonds : bond 0.19705 ( 417) hydrogen bonds : angle 6.94984 ( 1133) covalent geometry : bond 0.00454 (10429) covalent geometry : angle 0.74637 (14705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 85 time to evaluate : 0.935 Fit side-chains REVERT: A 199 ASP cc_start: 0.7694 (m-30) cc_final: 0.7487 (m-30) REVERT: A 366 GLU cc_start: 0.7066 (tp30) cc_final: 0.6736 (tp30) REVERT: A 380 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7810 (mp) REVERT: A 505 LYS cc_start: 0.7647 (mppt) cc_final: 0.7067 (mmmt) REVERT: A 549 LYS cc_start: 0.2904 (OUTLIER) cc_final: 0.1659 (mppt) REVERT: A 611 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8644 (tmtt) REVERT: A 615 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8600 (tt0) REVERT: A 619 ASP cc_start: 0.7987 (t0) cc_final: 0.7606 (m-30) REVERT: A 629 LYS cc_start: 0.6949 (mttt) cc_final: 0.6697 (mmtp) REVERT: A 645 ASP cc_start: 0.6542 (OUTLIER) cc_final: 0.6035 (m-30) REVERT: A 648 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7522 (mtmm) REVERT: A 729 ASP cc_start: 0.8391 (m-30) cc_final: 0.8043 (m-30) REVERT: A 782 GLU cc_start: 0.7891 (tp30) cc_final: 0.7517 (tt0) REVERT: A 785 LYS cc_start: 0.7479 (mttp) cc_final: 0.7247 (mmtp) outliers start: 48 outliers final: 23 residues processed: 120 average time/residue: 1.2296 time to fit residues: 159.0006 Evaluate side-chains 99 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 549 LYS Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 812 TYR Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 883 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.0270 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN A 370 ASN A 419 ASN A 842 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.188752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.153628 restraints weight = 10127.044| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.67 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10429 Z= 0.209 Angle : 0.672 9.247 14705 Z= 0.349 Chirality : 0.042 0.193 1706 Planarity : 0.005 0.055 1364 Dihedral : 23.814 178.007 2974 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 9.72 % Allowed : 31.61 % Favored : 58.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.28), residues: 841 helix: 1.06 (0.26), residues: 376 sheet: -0.42 (0.58), residues: 69 loop : -0.25 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.004 0.001 HIS A 330 PHE 0.021 0.002 PHE A 795 TYR 0.017 0.002 TYR A 730 ARG 0.007 0.001 ARG A 494 Details of bonding type rmsd hydrogen bonds : bond 0.04869 ( 417) hydrogen bonds : angle 4.50952 ( 1133) covalent geometry : bond 0.00460 (10429) covalent geometry : angle 0.67190 (14705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 90 time to evaluate : 0.851 Fit side-chains REVERT: A 65 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8209 (mm-40) REVERT: A 240 PHE cc_start: 0.7646 (m-10) cc_final: 0.7377 (m-80) REVERT: A 292 LYS cc_start: 0.6668 (mmtp) cc_final: 0.6060 (mptt) REVERT: A 370 ASN cc_start: 0.7436 (m-40) cc_final: 0.7228 (m110) REVERT: A 524 LYS cc_start: 0.6188 (OUTLIER) cc_final: 0.5971 (mtmt) REVERT: A 619 ASP cc_start: 0.7168 (OUTLIER) cc_final: 0.6822 (m-30) REVERT: A 645 ASP cc_start: 0.6012 (OUTLIER) cc_final: 0.5714 (m-30) REVERT: A 658 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7091 (tp30) REVERT: A 729 ASP cc_start: 0.8119 (m-30) cc_final: 0.7787 (m-30) REVERT: A 848 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7312 (ttp80) outliers start: 75 outliers final: 34 residues processed: 152 average time/residue: 1.0441 time to fit residues: 172.0960 Evaluate side-chains 116 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 76 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 879 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 6 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 74 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN A 282 GLN A 365 GLN A 413 ASN A 419 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.192410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.158657 restraints weight = 10208.082| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.55 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10429 Z= 0.138 Angle : 0.578 9.440 14705 Z= 0.302 Chirality : 0.038 0.176 1706 Planarity : 0.004 0.031 1364 Dihedral : 23.397 177.215 2935 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 8.68 % Allowed : 33.03 % Favored : 58.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.28), residues: 841 helix: 1.45 (0.26), residues: 376 sheet: -0.28 (0.60), residues: 69 loop : -0.17 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 229 HIS 0.002 0.001 HIS A 723 PHE 0.014 0.001 PHE A 747 TYR 0.016 0.001 TYR A 358 ARG 0.008 0.001 ARG A 734 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 417) hydrogen bonds : angle 4.17178 ( 1133) covalent geometry : bond 0.00293 (10429) covalent geometry : angle 0.57804 (14705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 86 time to evaluate : 0.848 Fit side-chains REVERT: A 292 LYS cc_start: 0.6697 (mmtp) cc_final: 0.6256 (mptt) REVERT: A 505 LYS cc_start: 0.7424 (mptt) cc_final: 0.7005 (mmtp) REVERT: A 619 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6940 (m-30) REVERT: A 729 ASP cc_start: 0.8051 (m-30) cc_final: 0.7754 (m-30) REVERT: A 768 LYS cc_start: 0.8064 (ttmm) cc_final: 0.7772 (ttpp) outliers start: 67 outliers final: 29 residues processed: 140 average time/residue: 1.2807 time to fit residues: 194.5501 Evaluate side-chains 104 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 879 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 GLN A 370 ASN A 419 ASN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.186853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.151059 restraints weight = 10018.105| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.63 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10429 Z= 0.224 Angle : 0.665 14.878 14705 Z= 0.344 Chirality : 0.041 0.157 1706 Planarity : 0.005 0.053 1364 Dihedral : 23.450 175.562 2924 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 8.55 % Allowed : 33.16 % Favored : 58.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.28), residues: 841 helix: 1.30 (0.26), residues: 376 sheet: -0.33 (0.58), residues: 70 loop : -0.26 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 229 HIS 0.007 0.001 HIS A 533 PHE 0.020 0.002 PHE A 758 TYR 0.018 0.002 TYR A 730 ARG 0.009 0.001 ARG A 734 Details of bonding type rmsd hydrogen bonds : bond 0.04708 ( 417) hydrogen bonds : angle 4.27781 ( 1133) covalent geometry : bond 0.00494 (10429) covalent geometry : angle 0.66512 (14705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 79 time to evaluate : 0.928 Fit side-chains REVERT: A 65 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8282 (mm-40) REVERT: A 199 ASP cc_start: 0.7267 (m-30) cc_final: 0.6995 (m-30) REVERT: A 346 GLU cc_start: 0.7187 (tp30) cc_final: 0.6946 (tp30) REVERT: A 524 LYS cc_start: 0.5897 (OUTLIER) cc_final: 0.5660 (mtmt) REVERT: A 619 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6959 (m-30) REVERT: A 699 THR cc_start: 0.8309 (p) cc_final: 0.8097 (p) REVERT: A 729 ASP cc_start: 0.8088 (m-30) cc_final: 0.7795 (m-30) outliers start: 66 outliers final: 32 residues processed: 134 average time/residue: 0.9217 time to fit residues: 136.4324 Evaluate side-chains 110 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 879 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 0.2980 chunk 92 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 GLN A 359 GLN A 370 ASN A 543 ASN A 606 HIS A 637 ASN A 668 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.186877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.160081 restraints weight = 10049.898| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.24 r_work: 0.3169 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10429 Z= 0.205 Angle : 0.635 12.323 14705 Z= 0.331 Chirality : 0.041 0.165 1706 Planarity : 0.004 0.047 1364 Dihedral : 23.343 175.696 2922 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 8.03 % Allowed : 33.94 % Favored : 58.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.28), residues: 841 helix: 1.30 (0.26), residues: 376 sheet: -0.24 (0.58), residues: 70 loop : -0.34 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.007 0.001 HIS A 533 PHE 0.019 0.002 PHE A 747 TYR 0.016 0.002 TYR A 358 ARG 0.008 0.001 ARG A 734 Details of bonding type rmsd hydrogen bonds : bond 0.04392 ( 417) hydrogen bonds : angle 4.20639 ( 1133) covalent geometry : bond 0.00449 (10429) covalent geometry : angle 0.63521 (14705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 77 time to evaluate : 0.922 Fit side-chains REVERT: A 65 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8553 (mm-40) REVERT: A 161 ASP cc_start: 0.7812 (t0) cc_final: 0.7590 (t0) REVERT: A 163 GLU cc_start: 0.8548 (pt0) cc_final: 0.8270 (pt0) REVERT: A 199 ASP cc_start: 0.7840 (m-30) cc_final: 0.7603 (m-30) REVERT: A 346 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7362 (tp30) REVERT: A 417 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.7102 (mm) REVERT: A 505 LYS cc_start: 0.8024 (mptt) cc_final: 0.7322 (mmtp) REVERT: A 619 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7321 (m-30) REVERT: A 699 THR cc_start: 0.8687 (p) cc_final: 0.8478 (p) REVERT: A 729 ASP cc_start: 0.8459 (m-30) cc_final: 0.8089 (m-30) REVERT: A 875 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8140 (mmmm) outliers start: 62 outliers final: 33 residues processed: 125 average time/residue: 0.9547 time to fit residues: 130.6669 Evaluate side-chains 111 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 73 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain A residue 879 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 0.0020 chunk 43 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 264 ASN A 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.186338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.158473 restraints weight = 10030.666| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.27 r_work: 0.3173 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10429 Z= 0.162 Angle : 0.589 11.530 14705 Z= 0.307 Chirality : 0.038 0.157 1706 Planarity : 0.004 0.036 1364 Dihedral : 23.146 175.669 2922 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 7.77 % Allowed : 34.20 % Favored : 58.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.28), residues: 841 helix: 1.47 (0.27), residues: 376 sheet: -0.07 (0.59), residues: 70 loop : -0.32 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 229 HIS 0.007 0.001 HIS A 533 PHE 0.017 0.001 PHE A 747 TYR 0.016 0.001 TYR A 358 ARG 0.007 0.001 ARG A 734 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 417) hydrogen bonds : angle 4.04737 ( 1133) covalent geometry : bond 0.00354 (10429) covalent geometry : angle 0.58878 (14705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 83 time to evaluate : 0.946 Fit side-chains REVERT: A 137 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7674 (tp40) REVERT: A 161 ASP cc_start: 0.7838 (t0) cc_final: 0.7609 (t0) REVERT: A 163 GLU cc_start: 0.8544 (pt0) cc_final: 0.8294 (pt0) REVERT: A 199 ASP cc_start: 0.7815 (m-30) cc_final: 0.7581 (m-30) REVERT: A 346 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7282 (tp30) REVERT: A 477 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: A 619 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7307 (m-30) REVERT: A 699 THR cc_start: 0.8694 (p) cc_final: 0.8476 (p) REVERT: A 729 ASP cc_start: 0.8353 (m-30) cc_final: 0.7982 (m-30) REVERT: A 875 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8199 (mmmm) outliers start: 60 outliers final: 37 residues processed: 130 average time/residue: 0.9002 time to fit residues: 128.8769 Evaluate side-chains 122 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 80 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain A residue 879 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 69 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN A 282 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.183856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.151167 restraints weight = 10185.170| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.48 r_work: 0.3104 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 10429 Z= 0.287 Angle : 0.716 10.638 14705 Z= 0.370 Chirality : 0.045 0.184 1706 Planarity : 0.005 0.065 1364 Dihedral : 23.345 175.554 2922 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 8.29 % Allowed : 33.81 % Favored : 57.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.28), residues: 841 helix: 1.01 (0.26), residues: 381 sheet: -0.18 (0.58), residues: 70 loop : -0.52 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 229 HIS 0.005 0.001 HIS A 533 PHE 0.021 0.002 PHE A 758 TYR 0.024 0.002 TYR A 23 ARG 0.008 0.001 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.05049 ( 417) hydrogen bonds : angle 4.36357 ( 1133) covalent geometry : bond 0.00637 (10429) covalent geometry : angle 0.71625 (14705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 78 time to evaluate : 0.940 Fit side-chains REVERT: A 65 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8578 (mm-40) REVERT: A 160 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8049 (ttpt) REVERT: A 161 ASP cc_start: 0.7846 (t0) cc_final: 0.7641 (t0) REVERT: A 163 GLU cc_start: 0.8606 (pt0) cc_final: 0.8369 (pt0) REVERT: A 170 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8122 (mtp85) REVERT: A 199 ASP cc_start: 0.7910 (m-30) cc_final: 0.7625 (m-30) REVERT: A 346 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7330 (tp30) REVERT: A 366 GLU cc_start: 0.7402 (tp30) cc_final: 0.7080 (tp30) REVERT: A 406 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6952 (tp30) REVERT: A 619 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7532 (m-30) REVERT: A 729 ASP cc_start: 0.8539 (m-30) cc_final: 0.8160 (m-30) outliers start: 64 outliers final: 34 residues processed: 128 average time/residue: 1.0004 time to fit residues: 139.7756 Evaluate side-chains 108 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 68 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 879 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 38 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 57 optimal weight: 0.0770 chunk 67 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 636 ASN A 819 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.187603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.153644 restraints weight = 10147.770| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.49 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10429 Z= 0.132 Angle : 0.586 10.104 14705 Z= 0.303 Chirality : 0.038 0.160 1706 Planarity : 0.003 0.032 1364 Dihedral : 23.095 175.379 2922 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.70 % Allowed : 36.01 % Favored : 58.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.28), residues: 841 helix: 1.48 (0.27), residues: 374 sheet: -0.03 (0.60), residues: 70 loop : -0.35 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 229 HIS 0.007 0.001 HIS A 533 PHE 0.013 0.001 PHE A 747 TYR 0.020 0.001 TYR A 358 ARG 0.009 0.000 ARG A 734 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 417) hydrogen bonds : angle 4.07950 ( 1133) covalent geometry : bond 0.00283 (10429) covalent geometry : angle 0.58607 (14705) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 80 time to evaluate : 0.847 Fit side-chains REVERT: A 163 GLU cc_start: 0.7848 (pt0) cc_final: 0.7477 (pt0) REVERT: A 199 ASP cc_start: 0.7251 (m-30) cc_final: 0.6998 (m-30) REVERT: A 346 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6863 (tp30) REVERT: A 490 MET cc_start: 0.7120 (mmm) cc_final: 0.6870 (mtt) REVERT: A 505 LYS cc_start: 0.7462 (mptt) cc_final: 0.7164 (mmmt) REVERT: A 619 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6837 (m-30) REVERT: A 729 ASP cc_start: 0.7968 (m-30) cc_final: 0.7699 (m-30) outliers start: 44 outliers final: 29 residues processed: 116 average time/residue: 0.9670 time to fit residues: 122.8851 Evaluate side-chains 105 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 879 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 57 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 282 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.185370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.148794 restraints weight = 10154.569| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.68 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10429 Z= 0.235 Angle : 0.680 9.752 14705 Z= 0.352 Chirality : 0.042 0.172 1706 Planarity : 0.005 0.050 1364 Dihedral : 23.182 174.881 2922 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 5.70 % Allowed : 36.79 % Favored : 57.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.28), residues: 841 helix: 1.21 (0.27), residues: 379 sheet: 0.03 (0.59), residues: 70 loop : -0.51 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 229 HIS 0.006 0.001 HIS A 723 PHE 0.024 0.002 PHE A 758 TYR 0.022 0.002 TYR A 358 ARG 0.008 0.001 ARG A 734 Details of bonding type rmsd hydrogen bonds : bond 0.04604 ( 417) hydrogen bonds : angle 4.25682 ( 1133) covalent geometry : bond 0.00523 (10429) covalent geometry : angle 0.68032 (14705) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 78 time to evaluate : 1.327 Fit side-chains REVERT: A 163 GLU cc_start: 0.7888 (pt0) cc_final: 0.7578 (pt0) REVERT: A 199 ASP cc_start: 0.7277 (m-30) cc_final: 0.7068 (m-30) REVERT: A 346 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6920 (tp30) REVERT: A 406 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6305 (tp30) REVERT: A 619 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.6915 (m-30) REVERT: A 729 ASP cc_start: 0.8079 (m-30) cc_final: 0.7792 (m-30) outliers start: 44 outliers final: 29 residues processed: 115 average time/residue: 1.3882 time to fit residues: 175.2464 Evaluate side-chains 100 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 879 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 26 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 71 optimal weight: 0.0060 chunk 75 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 264 ASN A 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.190458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.164701 restraints weight = 10134.522| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.16 r_work: 0.3240 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10429 Z= 0.142 Angle : 0.601 9.451 14705 Z= 0.311 Chirality : 0.038 0.156 1706 Planarity : 0.004 0.032 1364 Dihedral : 22.888 174.874 2922 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.79 % Allowed : 37.44 % Favored : 57.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.28), residues: 841 helix: 1.43 (0.26), residues: 378 sheet: 0.25 (0.61), residues: 70 loop : -0.41 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 229 HIS 0.007 0.001 HIS A 533 PHE 0.015 0.001 PHE A 758 TYR 0.024 0.001 TYR A 358 ARG 0.009 0.000 ARG A 734 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 417) hydrogen bonds : angle 4.05279 ( 1133) covalent geometry : bond 0.00309 (10429) covalent geometry : angle 0.60104 (14705) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 70 time to evaluate : 1.497 Fit side-chains REVERT: A 163 GLU cc_start: 0.8439 (pt0) cc_final: 0.8191 (pt0) REVERT: A 199 ASP cc_start: 0.7820 (m-30) cc_final: 0.7583 (m-30) REVERT: A 346 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7210 (tp30) REVERT: A 366 GLU cc_start: 0.7301 (tp30) cc_final: 0.7064 (tp30) REVERT: A 406 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6801 (tp30) REVERT: A 490 MET cc_start: 0.7734 (mmm) cc_final: 0.7454 (mtt) REVERT: A 505 LYS cc_start: 0.7777 (mptt) cc_final: 0.7075 (mmmt) REVERT: A 619 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7114 (m-30) REVERT: A 729 ASP cc_start: 0.8258 (m-30) cc_final: 0.7936 (m-30) outliers start: 37 outliers final: 27 residues processed: 101 average time/residue: 1.0696 time to fit residues: 119.4989 Evaluate side-chains 98 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 879 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 65 optimal weight: 0.2980 chunk 55 optimal weight: 0.0070 chunk 87 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS A 264 ASN A 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.193020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.167008 restraints weight = 10147.988| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.18 r_work: 0.3264 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10429 Z= 0.126 Angle : 0.573 9.337 14705 Z= 0.297 Chirality : 0.037 0.155 1706 Planarity : 0.003 0.029 1364 Dihedral : 22.701 174.046 2920 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.27 % Allowed : 37.82 % Favored : 57.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.29), residues: 841 helix: 1.63 (0.27), residues: 372 sheet: 0.43 (0.64), residues: 70 loop : -0.16 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 229 HIS 0.008 0.001 HIS A 533 PHE 0.012 0.001 PHE A 747 TYR 0.020 0.001 TYR A 358 ARG 0.009 0.000 ARG A 734 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 417) hydrogen bonds : angle 3.90079 ( 1133) covalent geometry : bond 0.00272 (10429) covalent geometry : angle 0.57290 (14705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5475.74 seconds wall clock time: 97 minutes 58.17 seconds (5878.17 seconds total)