Starting phenix.real_space_refine on Sat Aug 23 04:39:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywh_39633/08_2025/8ywh_39633.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywh_39633/08_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_39633/08_2025/8ywh_39633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywh_39633/08_2025/8ywh_39633.map" model { file = "/net/cci-nas-00/data/ceres_data/8ywh_39633/08_2025/8ywh_39633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywh_39633/08_2025/8ywh_39633.cif" } resolution = 2.97 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= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.59, per 1000 atoms: 0.26 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: 1.03 Conformation dependent library (CDL) restraints added in 283.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.41 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: 2.29 Time building geometry restraints manager: 1.33 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: 1.240 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.350 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.440 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG A 734 TYR 0.028 0.002 TYR A 670 PHE 0.029 0.002 PHE A 758 TRP 0.011 0.002 TRP A 408 HIS 0.005 0.001 HIS A 879 Details of bonding type rmsd covalent geometry : bond 0.00454 (10429) covalent geometry : angle 0.74637 (14705) hydrogen bonds : bond 0.19705 ( 417) hydrogen bonds : angle 6.94984 ( 1133) *********************** 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 : 0.322 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: 0.6744 (tp30) REVERT: A 380 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7813 (mp) REVERT: A 505 LYS cc_start: 0.7647 (mppt) cc_final: 0.7066 (mmmt) REVERT: A 549 LYS cc_start: 0.2904 (OUTLIER) cc_final: 0.1658 (mppt) REVERT: A 611 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8645 (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: 0.7603 (m-30) REVERT: A 629 LYS cc_start: 0.6949 (mttt) cc_final: 0.6701 (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: 0.7521 (mtmm) REVERT: A 729 ASP cc_start: 0.8391 (m-30) cc_final: 0.8040 (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: 0.7248 (mmtp) outliers start: 48 outliers final: 23 residues processed: 120 average time/residue: 0.5909 time to fit residues: 76.0879 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 : 0.341 ------------------------------------------------------------------------------- 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 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4124 r_free = 0.4124 target = 0.192734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.157069 restraints weight = 10242.500| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.65 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1319 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= 0.155 Angle : 0.622 9.153 14705 Z= 0.323 Chirality : 0.039 0.193 1706 Planarity : 0.004 0.032 1364 Dihedral : 23.757 178.559 2974 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 8.68 % Allowed : 33.94 % Favored : 57.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.28), residues: 841 helix: 1.20 (0.26), residues: 376 sheet: -0.37 (0.59), residues: 69 loop : -0.15 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 494 TYR 0.017 0.001 TYR A 358 PHE 0.015 0.002 PHE A 758 TRP 0.006 0.001 TRP A 229 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00334 (10429) covalent geometry : angle 0.62168 (14705) hydrogen bonds : bond 0.04851 ( 417) hydrogen bonds : angle 4.50475 ( 1133) *********************** 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 161 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 94 time to evaluate : 0.195 Fit side-chains REVERT: A 524 LYS cc_start: 0.6259 (OUTLIER) cc_final: 0.6017 (mtmt) REVERT: A 533 HIS cc_start: 0.6482 (OUTLIER) cc_final: 0.6261 (t70) REVERT: A 619 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6867 (m-30) REVERT: A 629 LYS cc_start: 0.6972 (mttt) cc_final: 0.6768 (mmtp) REVERT: A 645 ASP cc_start: 0.6029 (OUTLIER) cc_final: 0.5765 (m-30) REVERT: A 658 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7172 (tp30) REVERT: A 729 ASP cc_start: 0.8056 (m-30) cc_final: 0.7732 (m-30) REVERT: A 768 LYS cc_start: 0.7928 (ttmm) cc_final: 0.7651 (ttpp) REVERT: A 848 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7130 (ttp80) outliers start: 67 outliers final: 28 residues processed: 147 average time/residue: 0.4702 time to fit residues: 74.8401 Evaluate side-chains 107 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 73 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER 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 284 ILE 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 509 ILE 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 658 GLU Chi-restraints excluded: chain A residue 673 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 796 ILE Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 850 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 69 optimal weight: 0.0970 chunk 60 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 43 optimal weight: 0.0470 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- 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 370 ASN 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 = 0.4113 r_free = 0.4113 target = 0.191745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.163358 restraints weight = 10205.498| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.37 r_work: 0.3237 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1897 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= 0.152 Angle : 0.591 9.281 14705 Z= 0.308 Chirality : 0.038 0.179 1706 Planarity : 0.004 0.029 1364 Dihedral : 23.454 178.190 2934 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 8.81 % Allowed : 33.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.28), residues: 841 helix: 1.48 (0.26), residues: 376 sheet: -0.28 (0.60), residues: 69 loop : -0.19 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 734 TYR 0.016 0.002 TYR A 812 PHE 0.016 0.002 PHE A 747 TRP 0.008 0.001 TRP A 229 HIS 0.003 0.001 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00326 (10429) covalent geometry : angle 0.59081 (14705) hydrogen bonds : bond 0.04216 ( 417) hydrogen bonds : angle 4.19894 ( 1133) *********************** 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 148 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 80 time to evaluate : 0.301 Fit side-chains REVERT: A 292 LYS cc_start: 0.7189 (mmtp) cc_final: 0.6408 (mptt) REVERT: A 301 LYS cc_start: 0.7287 (mtmt) cc_final: 0.6917 (mmmt) REVERT: A 304 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6711 (tt) REVERT: A 502 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7476 (pp) REVERT: A 505 LYS cc_start: 0.7833 (mptt) cc_final: 0.7102 (mmtp) REVERT: A 619 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: A 629 LYS cc_start: 0.6917 (mttt) cc_final: 0.6645 (mmtp) REVERT: A 658 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.6933 (tp30) REVERT: A 729 ASP cc_start: 0.8428 (m-30) cc_final: 0.8018 (m-30) REVERT: A 768 LYS cc_start: 0.8416 (ttmm) cc_final: 0.8045 (ttpp) REVERT: A 875 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8293 (mmtp) outliers start: 68 outliers final: 30 residues processed: 135 average time/residue: 0.4952 time to fit residues: 72.2223 Evaluate side-chains 107 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 194 ASP Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 326 LEU 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 449 VAL Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 502 LEU 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 658 GLU 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 796 ILE 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 875 LYS 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 93 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 370 ASN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN A 668 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.189389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.159016 restraints weight = 10209.532| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.45 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10429 Z= 0.182 Angle : 0.605 9.169 14705 Z= 0.317 Chirality : 0.040 0.160 1706 Planarity : 0.004 0.035 1364 Dihedral : 23.359 176.173 2925 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 8.68 % Allowed : 33.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.28), residues: 841 helix: 1.51 (0.26), residues: 376 sheet: -0.27 (0.59), residues: 69 loop : -0.24 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 734 TYR 0.015 0.002 TYR A 358 PHE 0.018 0.002 PHE A 758 TRP 0.009 0.001 TRP A 229 HIS 0.007 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00399 (10429) covalent geometry : angle 0.60542 (14705) hydrogen bonds : bond 0.04278 ( 417) hydrogen bonds : angle 4.15091 ( 1133) *********************** 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 144 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 77 time to evaluate : 0.238 Fit side-chains REVERT: A 65 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8206 (mm110) REVERT: A 619 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.6989 (m-30) REVERT: A 729 ASP cc_start: 0.8049 (m-30) cc_final: 0.7758 (m-30) outliers start: 67 outliers final: 33 residues processed: 133 average time/residue: 0.3882 time to fit residues: 57.0101 Evaluate side-chains 111 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 33 VAL 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 194 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 326 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 438 THR Chi-restraints excluded: chain A residue 439 THR 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 509 ILE Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 619 ASP 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 796 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 57 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 A 359 GLN A 370 ASN A 419 ASN A 462 ASN A 543 ASN A 606 HIS A 637 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.185910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.158184 restraints weight = 10118.598| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.31 r_work: 0.3151 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10429 Z= 0.234 Angle : 0.674 15.727 14705 Z= 0.348 Chirality : 0.042 0.162 1706 Planarity : 0.005 0.052 1364 Dihedral : 23.435 176.258 2923 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 8.42 % Allowed : 33.03 % Favored : 58.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.28), residues: 841 helix: 1.26 (0.26), residues: 375 sheet: -0.36 (0.58), residues: 70 loop : -0.37 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 734 TYR 0.016 0.002 TYR A 201 PHE 0.020 0.002 PHE A 758 TRP 0.010 0.001 TRP A 229 HIS 0.007 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00517 (10429) covalent geometry : angle 0.67377 (14705) hydrogen bonds : bond 0.04740 ( 417) hydrogen bonds : angle 4.29966 ( 1133) *********************** 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 140 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 75 time to evaluate : 0.317 Fit side-chains REVERT: A 65 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8570 (mm-40) REVERT: A 346 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7305 (tp30) REVERT: A 406 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6963 (tp30) REVERT: A 505 LYS cc_start: 0.8056 (mptt) cc_final: 0.7290 (mmtp) REVERT: A 619 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7394 (m-30) REVERT: A 658 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7209 (tp30) REVERT: A 729 ASP cc_start: 0.8447 (m-30) cc_final: 0.8058 (m-30) outliers start: 65 outliers final: 33 residues processed: 126 average time/residue: 0.4575 time to fit residues: 62.9450 Evaluate side-chains 102 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 64 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 242 GLU 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 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 477 GLU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 658 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 75 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4071 r_free = 0.4071 target = 0.187756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.159888 restraints weight = 10075.973| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.27 r_work: 0.3183 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2870 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= 0.154 Angle : 0.592 13.554 14705 Z= 0.307 Chirality : 0.038 0.156 1706 Planarity : 0.004 0.033 1364 Dihedral : 23.222 176.293 2921 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 6.22 % Allowed : 36.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.28), residues: 841 helix: 1.50 (0.27), residues: 376 sheet: -0.24 (0.59), residues: 70 loop : -0.32 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 734 TYR 0.016 0.001 TYR A 358 PHE 0.021 0.001 PHE A 758 TRP 0.007 0.001 TRP A 229 HIS 0.007 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00335 (10429) covalent geometry : angle 0.59203 (14705) hydrogen bonds : bond 0.04014 ( 417) hydrogen bonds : angle 4.08763 ( 1133) *********************** 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 128 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 80 time to evaluate : 0.311 Fit side-chains REVERT: A 346 GLU cc_start: 0.7577 (tp30) cc_final: 0.7193 (tp30) REVERT: A 366 GLU cc_start: 0.7311 (tp30) cc_final: 0.7101 (tp30) REVERT: A 619 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7352 (m-30) REVERT: A 655 LYS cc_start: 0.7795 (mmtm) cc_final: 0.7526 (mttt) REVERT: A 729 ASP cc_start: 0.8410 (m-30) cc_final: 0.8038 (m-30) outliers start: 48 outliers final: 32 residues processed: 117 average time/residue: 0.4560 time to fit residues: 58.4332 Evaluate side-chains 109 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 76 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 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 284 ILE Chi-restraints excluded: chain A residue 376 THR 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 438 THR Chi-restraints excluded: chain A residue 439 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 653 ILE 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 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 849 ILE 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 2 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 1 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.188682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.155120 restraints weight = 10063.140| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.52 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3076 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= 0.148 Angle : 0.583 12.045 14705 Z= 0.301 Chirality : 0.038 0.154 1706 Planarity : 0.004 0.029 1364 Dihedral : 23.071 176.030 2921 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 6.74 % Allowed : 35.62 % Favored : 57.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.28), residues: 841 helix: 1.59 (0.26), residues: 374 sheet: -0.11 (0.59), residues: 70 loop : -0.29 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 734 TYR 0.018 0.001 TYR A 358 PHE 0.018 0.001 PHE A 758 TRP 0.006 0.001 TRP A 229 HIS 0.007 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00318 (10429) covalent geometry : angle 0.58254 (14705) hydrogen bonds : bond 0.03910 ( 417) hydrogen bonds : angle 4.00064 ( 1133) *********************** 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 134 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 82 time to evaluate : 0.324 Fit side-chains REVERT: A 346 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6891 (tp30) REVERT: A 406 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6422 (tp30) REVERT: A 505 LYS cc_start: 0.7413 (mptt) cc_final: 0.7113 (mmmt) REVERT: A 607 ARG cc_start: 0.8323 (ttt-90) cc_final: 0.8077 (ttt-90) REVERT: A 619 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.6890 (m-30) REVERT: A 729 ASP cc_start: 0.7960 (m-30) cc_final: 0.7679 (m-30) REVERT: A 824 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8371 (ptp90) outliers start: 52 outliers final: 35 residues processed: 121 average time/residue: 0.4089 time to fit residues: 54.2849 Evaluate side-chains 114 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 75 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU 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 194 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 277 TYR 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 406 GLU Chi-restraints excluded: chain A residue 423 LEU 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 509 ILE Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 653 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4079 r_free = 0.4079 target = 0.188581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.151967 restraints weight = 10001.819| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.59 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3176 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= 0.151 Angle : 0.586 11.329 14705 Z= 0.303 Chirality : 0.038 0.156 1706 Planarity : 0.003 0.031 1364 Dihedral : 23.021 176.184 2921 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 6.35 % Allowed : 36.01 % Favored : 57.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.28), residues: 841 helix: 1.57 (0.26), residues: 376 sheet: 0.04 (0.59), residues: 70 loop : -0.30 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 734 TYR 0.020 0.001 TYR A 358 PHE 0.017 0.002 PHE A 758 TRP 0.006 0.001 TRP A 229 HIS 0.007 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00327 (10429) covalent geometry : angle 0.58588 (14705) hydrogen bonds : bond 0.03872 ( 417) hydrogen bonds : angle 4.00968 ( 1133) *********************** 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 128 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 79 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 346 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6856 (tp30) REVERT: A 406 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6417 (tp30) REVERT: A 619 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6857 (m-30) REVERT: A 729 ASP cc_start: 0.7918 (m-30) cc_final: 0.7630 (m-30) REVERT: A 824 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8238 (ptp90) outliers start: 49 outliers final: 34 residues processed: 121 average time/residue: 0.4653 time to fit residues: 60.9638 Evaluate side-chains 109 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 71 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU 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 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 277 TYR 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 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 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 653 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 66 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 0.0870 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 42 optimal weight: 0.0870 chunk 89 optimal weight: 2.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.188963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.155538 restraints weight = 9970.321| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.52 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3293 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= 0.145 Angle : 0.581 10.819 14705 Z= 0.300 Chirality : 0.038 0.156 1706 Planarity : 0.003 0.029 1364 Dihedral : 22.978 176.226 2921 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 6.35 % Allowed : 36.27 % Favored : 57.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.28), residues: 841 helix: 1.63 (0.26), residues: 374 sheet: 0.08 (0.59), residues: 70 loop : -0.28 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 734 TYR 0.021 0.001 TYR A 358 PHE 0.016 0.002 PHE A 758 TRP 0.006 0.001 TRP A 229 HIS 0.006 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00315 (10429) covalent geometry : angle 0.58094 (14705) hydrogen bonds : bond 0.03806 ( 417) hydrogen bonds : angle 3.98871 ( 1133) *********************** 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 127 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 78 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: A 346 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6863 (tp30) REVERT: A 505 LYS cc_start: 0.7431 (mptt) cc_final: 0.7017 (mmmt) REVERT: A 619 ASP cc_start: 0.7222 (OUTLIER) cc_final: 0.6853 (m-30) REVERT: A 729 ASP cc_start: 0.7954 (m-30) cc_final: 0.7682 (m-30) REVERT: A 824 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8197 (ptp90) outliers start: 49 outliers final: 33 residues processed: 118 average time/residue: 0.4410 time to fit residues: 56.5493 Evaluate side-chains 111 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 74 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU 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 102 GLU 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 357 ILE Chi-restraints excluded: chain A residue 376 THR 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 524 LYS Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 653 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 12 optimal weight: 0.0170 chunk 80 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 0.0050 chunk 66 optimal weight: 3.9990 overall best weight: 0.7434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN A 472 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.189283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.156369 restraints weight = 9949.534| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.54 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3445 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= 0.142 Angle : 0.577 10.112 14705 Z= 0.297 Chirality : 0.038 0.152 1706 Planarity : 0.003 0.028 1364 Dihedral : 22.904 176.338 2921 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 5.31 % Allowed : 37.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.28), residues: 841 helix: 1.63 (0.26), residues: 374 sheet: 0.10 (0.60), residues: 70 loop : -0.25 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 734 TYR 0.022 0.001 TYR A 358 PHE 0.015 0.001 PHE A 758 TRP 0.005 0.001 TRP A 229 HIS 0.007 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00307 (10429) covalent geometry : angle 0.57664 (14705) hydrogen bonds : bond 0.03745 ( 417) hydrogen bonds : angle 3.97452 ( 1133) ********************** 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 115 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 74 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6631 (mp0) REVERT: A 346 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6760 (tp30) REVERT: A 490 MET cc_start: 0.7162 (mmm) cc_final: 0.6790 (mtt) REVERT: A 619 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6821 (m-30) REVERT: A 729 ASP cc_start: 0.7954 (m-30) cc_final: 0.7694 (m-30) REVERT: A 824 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8035 (ptp90) outliers start: 41 outliers final: 31 residues processed: 109 average time/residue: 0.4708 time to fit residues: 55.9750 Evaluate side-chains 102 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 67 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 102 GLU 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 357 ILE 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 524 LYS Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 653 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 0.0270 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.190291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.155403 restraints weight = 9977.612| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.60 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3540 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= 0.135 Angle : 0.573 9.855 14705 Z= 0.296 Chirality : 0.037 0.153 1706 Planarity : 0.003 0.028 1364 Dihedral : 22.805 176.253 2921 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.05 % Allowed : 38.47 % Favored : 56.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.28), residues: 841 helix: 1.69 (0.26), residues: 373 sheet: 0.09 (0.60), residues: 70 loop : -0.19 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 734 TYR 0.020 0.001 TYR A 358 PHE 0.014 0.001 PHE A 758 TRP 0.005 0.001 TRP A 229 HIS 0.007 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00290 (10429) covalent geometry : angle 0.57345 (14705) hydrogen bonds : bond 0.03671 ( 417) hydrogen bonds : angle 3.94816 ( 1133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2211.92 seconds wall clock time: 38 minutes 44.98 seconds (2324.98 seconds total)