Starting phenix.real_space_refine on Sun May 3 07:48:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h4k_51862/05_2026/9h4k_51862.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h4k_51862/05_2026/9h4k_51862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9h4k_51862/05_2026/9h4k_51862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h4k_51862/05_2026/9h4k_51862.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h4k_51862/05_2026/9h4k_51862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h4k_51862/05_2026/9h4k_51862.map" } resolution = 2.6 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= 0.002 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 140 5.49 5 S 17 5.16 5 C 6792 2.51 5 N 2006 2.21 5 O 2500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11455 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8459 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 27, 'TRANS': 1000} Chain breaks: 8 Chain: "B" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2105 Classifications: {'RNA': 98} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 31} Link IDs: {'rna2p': 11, 'rna3p': 86} Chain: "C" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 618 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "D" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 273 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Time building chain proxies: 2.78, per 1000 atoms: 0.24 Number of scatterers: 11455 At special positions: 0 Unit cell: (113.9, 122.4, 118.15, 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 17 16.00 P 140 15.00 O 2500 8.00 N 2006 7.00 C 6792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 548.6 milliseconds 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 7 sheets defined 50.5% alpha, 8.9% beta 44 base pairs and 93 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.809A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.997A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 382 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 406 through 410 removed outlier: 4.044A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.329A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.601A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 562 through 573 removed outlier: 3.857A pdb=" N GLU A 566 " --> pdb=" O LYS A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 removed outlier: 3.841A pdb=" N HIS A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.560A pdb=" N LEU A 616 " --> pdb=" O ASN A 612 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 637 removed outlier: 4.006A pdb=" N GLU A 634 " --> pdb=" O GLU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 652 removed outlier: 3.512A pdb=" N MET A 648 " --> pdb=" O ASP A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 685 removed outlier: 3.666A pdb=" N SER A 685 " --> pdb=" O ASP A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 703 through 712 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.745A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 922 removed outlier: 3.678A pdb=" N LEU A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 940 removed outlier: 3.962A pdb=" N LYS A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 4.048A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 Processing helix chain 'A' and resid 1002 through 1005 Processing helix chain 'A' and resid 1078 through 1088 removed outlier: 3.509A pdb=" N THR A1082 " --> pdb=" O ARG A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.646A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1280 Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.630A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A1312 " --> pdb=" O ASN A1308 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1343 removed outlier: 3.766A pdb=" N VAL A1342 " --> pdb=" O THR A1339 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1339 through 1343' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.257A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.434A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLU A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 507 through 509 removed outlier: 5.339A pdb=" N LEU A 508 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1063 through 1065 Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 6.080A pdb=" N LYS A1156 " --> pdb=" O GLU A1150 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU A1150 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LYS A1158 " --> pdb=" O LYS A1148 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS A1148 " --> pdb=" O LYS A1158 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A1160 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL A1146 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLU A1162 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LEU A1144 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU A1164 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER A1142 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE A1166 " --> pdb=" O ALA A1140 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1325 361 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 109 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 93 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.31 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: 2549 1.33 - 1.45: 3160 1.45 - 1.57: 5945 1.57 - 1.69: 279 1.69 - 1.81: 33 Bond restraints: 11966 Sorted by residual: bond pdb=" CB GLN A 341 " pdb=" CG GLN A 341 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.49e+00 bond pdb=" CB LYS A1059 " pdb=" CG LYS A1059 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" C HIS A 754 " pdb=" N LYS A 755 " ideal model delta sigma weight residual 1.339 1.285 0.055 5.57e-02 3.22e+02 9.68e-01 bond pdb=" C3' DA C 9 " pdb=" O3' DA C 9 " ideal model delta sigma weight residual 1.422 1.450 -0.028 3.00e-02 1.11e+03 8.61e-01 bond pdb=" CA THR A 703 " pdb=" C THR A 703 " ideal model delta sigma weight residual 1.518 1.554 -0.036 4.01e-02 6.22e+02 7.88e-01 ... (remaining 11961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 16563 2.02 - 4.03: 185 4.03 - 6.05: 13 6.05 - 8.07: 2 8.07 - 10.08: 3 Bond angle restraints: 16766 Sorted by residual: angle pdb=" CA LYS A1059 " pdb=" CB LYS A1059 " pdb=" CG LYS A1059 " ideal model delta sigma weight residual 114.10 122.27 -8.17 2.00e+00 2.50e-01 1.67e+01 angle pdb=" C3' A B 13 " pdb=" O3' A B 13 " pdb=" P A B 14 " ideal model delta sigma weight residual 120.20 126.16 -5.96 1.50e+00 4.44e-01 1.58e+01 angle pdb=" O3' A B 13 " pdb=" C3' A B 13 " pdb=" C2' A B 13 " ideal model delta sigma weight residual 113.70 119.51 -5.81 1.50e+00 4.44e-01 1.50e+01 angle pdb=" CA GLN A 341 " pdb=" CB GLN A 341 " pdb=" CG GLN A 341 " ideal model delta sigma weight residual 114.10 121.12 -7.02 2.00e+00 2.50e-01 1.23e+01 angle pdb=" C4' A B 13 " pdb=" C3' A B 13 " pdb=" C2' A B 13 " ideal model delta sigma weight residual 102.60 99.40 3.20 1.00e+00 1.00e+00 1.02e+01 ... (remaining 16761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.40: 6659 32.40 - 64.81: 511 64.81 - 97.21: 37 97.21 - 129.62: 1 129.62 - 162.02: 3 Dihedral angle restraints: 7211 sinusoidal: 4190 harmonic: 3021 Sorted by residual: dihedral pdb=" O4' C B 70 " pdb=" C1' C B 70 " pdb=" N1 C B 70 " pdb=" C2 C B 70 " ideal model delta sinusoidal sigma weight residual 200.00 41.91 158.09 1 1.50e+01 4.44e-03 8.23e+01 dihedral pdb=" O4' U B 56 " pdb=" C1' U B 56 " pdb=" N1 U B 56 " pdb=" C2 U B 56 " ideal model delta sinusoidal sigma weight residual -128.00 34.02 -162.02 1 1.70e+01 3.46e-03 6.48e+01 dihedral pdb=" C4' DA C 9 " pdb=" C3' DA C 9 " pdb=" O3' DA C 9 " pdb=" P DT C 10 " ideal model delta sinusoidal sigma weight residual 220.00 68.30 151.70 1 3.50e+01 8.16e-04 1.47e+01 ... (remaining 7208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1386 0.035 - 0.070: 405 0.070 - 0.106: 105 0.106 - 0.141: 41 0.141 - 0.176: 2 Chirality restraints: 1939 Sorted by residual: chirality pdb=" C3' A B 13 " pdb=" C4' A B 13 " pdb=" O3' A B 13 " pdb=" C2' A B 13 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" C1' A B 51 " pdb=" O4' A B 51 " pdb=" C2' A B 51 " pdb=" N9 A B 51 " both_signs ideal model delta sigma weight residual False 2.46 2.30 0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CB ILE A 615 " pdb=" CA ILE A 615 " pdb=" CG1 ILE A 615 " pdb=" CG2 ILE A 615 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 1936 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 430 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO A 431 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 431 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 431 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 31 " 0.007 2.00e-02 2.50e+03 1.11e-02 3.06e+00 pdb=" N1 DT C 31 " -0.026 2.00e-02 2.50e+03 pdb=" C2 DT C 31 " 0.022 2.00e-02 2.50e+03 pdb=" O2 DT C 31 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT C 31 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT C 31 " -0.001 2.00e-02 2.50e+03 pdb=" O4 DT C 31 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DT C 31 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT C 31 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DT C 31 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 518 " -0.011 2.00e-02 2.50e+03 1.32e-02 3.06e+00 pdb=" CG PHE A 518 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 518 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 518 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 518 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 518 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 518 " -0.001 2.00e-02 2.50e+03 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1633 2.76 - 3.29: 9880 3.29 - 3.83: 19472 3.83 - 4.36: 23778 4.36 - 4.90: 36913 Nonbonded interactions: 91676 Sorted by model distance: nonbonded pdb=" NZ LYS A 526 " pdb=" O ASN A 690 " model vdw 2.220 3.120 nonbonded pdb=" NZ LYS A1148 " pdb=" OG SER A1159 " model vdw 2.234 3.120 nonbonded pdb=" NH1 ARG A 100 " pdb=" O PRO A 117 " model vdw 2.273 3.120 nonbonded pdb=" OE2 GLU A1357 " pdb=" NH1 ARG A1359 " model vdw 2.289 3.120 nonbonded pdb=" O LYS A 554 " pdb=" NE2 HIS A 595 " model vdw 2.291 3.120 ... (remaining 91671 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=0.00 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: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.480 Find NCS groups from input model: 0.050 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:10.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 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 : 0.004 0.055 11966 Z= 0.162 Angle : 0.555 10.083 16766 Z= 0.309 Chirality : 0.039 0.176 1939 Planarity : 0.004 0.050 1604 Dihedral : 19.859 162.022 5251 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.97 % Allowed : 16.85 % Favored : 82.18 % 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 are not related in a simple way. whole: -0.56 (0.25), residues: 1010 helix: 0.76 (0.24), residues: 473 sheet: 0.11 (0.47), residues: 113 loop : -1.84 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 655 TYR 0.015 0.001 TYR A1242 PHE 0.031 0.002 PHE A 518 TRP 0.007 0.001 TRP A 18 HIS 0.006 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00361 (11966) covalent geometry : angle 0.55463 (16766) hydrogen bonds : bond 0.15417 ( 470) hydrogen bonds : angle 5.28384 ( 1267) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 422 ILE cc_start: 0.6234 (mt) cc_final: 0.5775 (mt) REVERT: A 650 GLN cc_start: 0.8206 (mp10) cc_final: 0.7836 (mm-40) REVERT: A 761 ILE cc_start: 0.7282 (mt) cc_final: 0.7005 (mm) REVERT: A 1044 ASN cc_start: 0.8061 (m-40) cc_final: 0.7721 (t0) REVERT: A 1047 LYS cc_start: 0.8794 (mttm) cc_final: 0.8457 (mmtp) REVERT: A 1308 ASN cc_start: 0.6901 (m110) cc_final: 0.6562 (m110) outliers start: 9 outliers final: 4 residues processed: 165 average time/residue: 0.6024 time to fit residues: 106.7233 Evaluate side-chains 77 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 1275 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.0570 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 990 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.133968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.097197 restraints weight = 18667.987| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.05 r_work: 0.3274 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11966 Z= 0.152 Angle : 0.596 8.547 16766 Z= 0.320 Chirality : 0.038 0.233 1939 Planarity : 0.004 0.053 1604 Dihedral : 19.680 161.403 3055 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.35 % Allowed : 20.19 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.25), residues: 1010 helix: 0.71 (0.23), residues: 490 sheet: 0.33 (0.53), residues: 96 loop : -1.79 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1333 TYR 0.021 0.001 TYR A 639 PHE 0.010 0.002 PHE A1045 TRP 0.012 0.001 TRP A1074 HIS 0.007 0.001 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00326 (11966) covalent geometry : angle 0.59649 (16766) hydrogen bonds : bond 0.04760 ( 470) hydrogen bonds : angle 4.29441 ( 1267) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 75 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 709 GLN cc_start: 0.7511 (tm-30) cc_final: 0.7257 (mm-40) REVERT: A 976 ARG cc_start: 0.8211 (ttm110) cc_final: 0.7970 (ttm110) REVERT: A 1038 PHE cc_start: 0.0720 (OUTLIER) cc_final: -0.0012 (t80) REVERT: A 1299 ASP cc_start: 0.8168 (m-30) cc_final: 0.7446 (t0) outliers start: 31 outliers final: 7 residues processed: 99 average time/residue: 0.6866 time to fit residues: 72.6920 Evaluate side-chains 64 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1038 PHE Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1138 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 2 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 77 ASN A 504 ASN ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN A1264 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.125013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.083887 restraints weight = 18140.770| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.99 r_work: 0.3077 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.6862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 11966 Z= 0.193 Angle : 0.615 9.445 16766 Z= 0.336 Chirality : 0.041 0.291 1939 Planarity : 0.004 0.053 1604 Dihedral : 19.742 170.550 3049 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.89 % Allowed : 20.30 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.25), residues: 1010 helix: 0.72 (0.23), residues: 490 sheet: 0.18 (0.49), residues: 101 loop : -1.63 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 655 TYR 0.016 0.002 TYR A 155 PHE 0.016 0.002 PHE A 966 TRP 0.009 0.001 TRP A 18 HIS 0.007 0.002 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00433 (11966) covalent geometry : angle 0.61500 (16766) hydrogen bonds : bond 0.07262 ( 470) hydrogen bonds : angle 4.20735 ( 1267) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 59 time to evaluate : 0.386 Fit side-chains REVERT: A 122 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8050 (tp) REVERT: A 171 GLU cc_start: 0.7024 (pm20) cc_final: 0.6763 (pm20) REVERT: A 395 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7774 (ttm-80) REVERT: A 695 GLN cc_start: 0.5079 (OUTLIER) cc_final: 0.4632 (mp10) REVERT: A 746 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: A 926 GLN cc_start: 0.8314 (tp40) cc_final: 0.8113 (mm110) REVERT: A 976 ARG cc_start: 0.8083 (ttm110) cc_final: 0.7797 (ttm110) outliers start: 36 outliers final: 6 residues processed: 91 average time/residue: 0.7254 time to fit residues: 70.4137 Evaluate side-chains 58 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 695 GLN Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1251 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 39 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.121696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.080568 restraints weight = 18471.483| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.04 r_work: 0.3019 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.7413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 11966 Z= 0.283 Angle : 0.674 8.172 16766 Z= 0.364 Chirality : 0.044 0.310 1939 Planarity : 0.005 0.055 1604 Dihedral : 19.853 166.691 3049 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.54 % Allowed : 20.30 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.25), residues: 1010 helix: 0.67 (0.23), residues: 484 sheet: 0.22 (0.49), residues: 97 loop : -1.75 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1060 TYR 0.017 0.002 TYR A 362 PHE 0.015 0.002 PHE A1181 TRP 0.012 0.002 TRP A 476 HIS 0.009 0.002 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00654 (11966) covalent geometry : angle 0.67371 (16766) hydrogen bonds : bond 0.07843 ( 470) hydrogen bonds : angle 4.31592 ( 1267) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 49 time to evaluate : 0.379 Fit side-chains REVERT: A 122 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8317 (tp) REVERT: A 171 GLU cc_start: 0.7364 (pm20) cc_final: 0.7029 (pm20) REVERT: A 567 ASP cc_start: 0.6470 (OUTLIER) cc_final: 0.6000 (m-30) REVERT: A 695 GLN cc_start: 0.5689 (OUTLIER) cc_final: 0.4765 (mp10) REVERT: A 746 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.7817 (tp30) REVERT: A 1256 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7960 (mm-40) outliers start: 42 outliers final: 12 residues processed: 81 average time/residue: 0.7092 time to fit residues: 61.4138 Evaluate side-chains 63 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 695 GLN Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1038 PHE Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1256 GLN Chi-restraints excluded: chain A residue 1339 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 6 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 109 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 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 116 HIS A 595 HIS A 712 GLN ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.126132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.085580 restraints weight = 18267.134| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.02 r_work: 0.3118 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.7522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11966 Z= 0.120 Angle : 0.512 6.788 16766 Z= 0.284 Chirality : 0.037 0.248 1939 Planarity : 0.004 0.053 1604 Dihedral : 19.550 162.206 3049 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.92 % Allowed : 21.17 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.26), residues: 1010 helix: 1.09 (0.23), residues: 491 sheet: 0.19 (0.50), residues: 97 loop : -1.58 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1060 TYR 0.011 0.001 TYR A 155 PHE 0.025 0.001 PHE A 518 TRP 0.009 0.001 TRP A 476 HIS 0.014 0.001 HIS A 595 Details of bonding type rmsd covalent geometry : bond 0.00255 (11966) covalent geometry : angle 0.51174 (16766) hydrogen bonds : bond 0.04925 ( 470) hydrogen bonds : angle 3.96537 ( 1267) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 53 time to evaluate : 0.427 Fit side-chains REVERT: A 171 GLU cc_start: 0.7352 (pm20) cc_final: 0.7004 (pm20) REVERT: A 606 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7176 (t80) REVERT: A 695 GLN cc_start: 0.5264 (OUTLIER) cc_final: 0.4402 (mp10) REVERT: A 976 ARG cc_start: 0.8236 (ttm110) cc_final: 0.7964 (ttm110) REVERT: A 1060 ARG cc_start: 0.8393 (mtp-110) cc_final: 0.7863 (ttt180) REVERT: A 1256 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7993 (mm-40) outliers start: 27 outliers final: 11 residues processed: 73 average time/residue: 0.6681 time to fit residues: 52.3541 Evaluate side-chains 57 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 695 GLN Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 87 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.122340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.081365 restraints weight = 18326.783| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.03 r_work: 0.3037 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.7679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11966 Z= 0.224 Angle : 0.609 9.295 16766 Z= 0.332 Chirality : 0.041 0.296 1939 Planarity : 0.004 0.054 1604 Dihedral : 19.716 165.841 3049 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.35 % Allowed : 21.38 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.25), residues: 1010 helix: 1.07 (0.23), residues: 483 sheet: 0.36 (0.52), residues: 92 loop : -1.59 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1060 TYR 0.016 0.002 TYR A 362 PHE 0.024 0.002 PHE A 518 TRP 0.010 0.002 TRP A 476 HIS 0.007 0.002 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00515 (11966) covalent geometry : angle 0.60931 (16766) hydrogen bonds : bond 0.06968 ( 470) hydrogen bonds : angle 4.08361 ( 1267) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 40 time to evaluate : 0.347 Fit side-chains REVERT: A 171 GLU cc_start: 0.7314 (pm20) cc_final: 0.6976 (pm20) REVERT: A 606 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7341 (t80) REVERT: A 746 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.7691 (tp30) REVERT: A 1256 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7930 (mm-40) outliers start: 31 outliers final: 14 residues processed: 66 average time/residue: 0.7520 time to fit residues: 53.1204 Evaluate side-chains 56 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1256 GLN Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 79 optimal weight: 0.0270 chunk 75 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.124902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.084224 restraints weight = 18327.638| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.00 r_work: 0.3092 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.7745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11966 Z= 0.136 Angle : 0.527 8.790 16766 Z= 0.291 Chirality : 0.038 0.260 1939 Planarity : 0.004 0.054 1604 Dihedral : 19.554 162.511 3049 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.59 % Allowed : 22.68 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.26), residues: 1010 helix: 1.18 (0.24), residues: 490 sheet: 0.47 (0.52), residues: 92 loop : -1.47 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1060 TYR 0.012 0.001 TYR A 155 PHE 0.025 0.001 PHE A 518 TRP 0.009 0.001 TRP A 476 HIS 0.004 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00299 (11966) covalent geometry : angle 0.52681 (16766) hydrogen bonds : bond 0.05340 ( 470) hydrogen bonds : angle 3.90070 ( 1267) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7358 (pm20) cc_final: 0.7006 (pm20) REVERT: A 606 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.7331 (t80) REVERT: A 746 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7451 (tp30) REVERT: A 1256 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7912 (mm-40) outliers start: 24 outliers final: 14 residues processed: 64 average time/residue: 0.7196 time to fit residues: 49.4049 Evaluate side-chains 61 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 695 GLN Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1256 GLN Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 69 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.125298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.084591 restraints weight = 18280.737| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.01 r_work: 0.3099 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.7857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11966 Z= 0.134 Angle : 0.518 8.572 16766 Z= 0.286 Chirality : 0.038 0.260 1939 Planarity : 0.004 0.060 1604 Dihedral : 19.469 163.144 3049 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.81 % Allowed : 22.68 % Favored : 74.51 % 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 are not related in a simple way. whole: 0.19 (0.26), residues: 1010 helix: 1.30 (0.24), residues: 490 sheet: 0.50 (0.52), residues: 93 loop : -1.40 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1060 TYR 0.013 0.001 TYR A 155 PHE 0.027 0.001 PHE A 518 TRP 0.009 0.001 TRP A 476 HIS 0.004 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00293 (11966) covalent geometry : angle 0.51798 (16766) hydrogen bonds : bond 0.05211 ( 470) hydrogen bonds : angle 3.82480 ( 1267) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 46 time to evaluate : 0.342 Fit side-chains REVERT: A 171 GLU cc_start: 0.7350 (pm20) cc_final: 0.7000 (pm20) REVERT: A 746 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7424 (tp30) REVERT: A 1256 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7961 (mm-40) outliers start: 26 outliers final: 12 residues processed: 67 average time/residue: 0.7226 time to fit residues: 51.9429 Evaluate side-chains 57 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1256 GLN Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.0170 chunk 39 optimal weight: 0.4980 chunk 44 optimal weight: 0.0980 chunk 33 optimal weight: 0.0870 chunk 22 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.127992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.087819 restraints weight = 18147.493| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.99 r_work: 0.3158 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.7904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11966 Z= 0.105 Angle : 0.496 9.109 16766 Z= 0.273 Chirality : 0.036 0.239 1939 Planarity : 0.004 0.060 1604 Dihedral : 19.379 160.988 3049 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.51 % Allowed : 23.87 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.26), residues: 1010 helix: 1.41 (0.24), residues: 491 sheet: 0.57 (0.52), residues: 93 loop : -1.29 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1060 TYR 0.010 0.001 TYR A 155 PHE 0.026 0.001 PHE A 518 TRP 0.008 0.001 TRP A 476 HIS 0.004 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00213 (11966) covalent geometry : angle 0.49560 (16766) hydrogen bonds : bond 0.04219 ( 470) hydrogen bonds : angle 3.73993 ( 1267) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7327 (pm20) cc_final: 0.6975 (pm20) REVERT: A 606 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7294 (t80) REVERT: A 951 ARG cc_start: 0.7559 (ttm170) cc_final: 0.6531 (mmt90) REVERT: A 1256 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7947 (mm-40) outliers start: 14 outliers final: 9 residues processed: 57 average time/residue: 0.7212 time to fit residues: 44.1603 Evaluate side-chains 57 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 695 GLN Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1256 GLN Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.124793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.084013 restraints weight = 18174.786| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.99 r_work: 0.3088 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.7939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11966 Z= 0.150 Angle : 0.540 9.956 16766 Z= 0.296 Chirality : 0.038 0.268 1939 Planarity : 0.004 0.057 1604 Dihedral : 19.472 164.012 3049 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.05 % Allowed : 23.65 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.26), residues: 1010 helix: 1.37 (0.24), residues: 488 sheet: 0.60 (0.52), residues: 92 loop : -1.29 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 655 TYR 0.014 0.001 TYR A 155 PHE 0.024 0.001 PHE A 518 TRP 0.008 0.001 TRP A 476 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00335 (11966) covalent geometry : angle 0.53988 (16766) hydrogen bonds : bond 0.05533 ( 470) hydrogen bonds : angle 3.85409 ( 1267) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.374 Fit side-chains REVERT: A 171 GLU cc_start: 0.7372 (pm20) cc_final: 0.7029 (pm20) REVERT: A 606 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.7317 (t80) REVERT: A 1256 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7881 (mm-40) outliers start: 19 outliers final: 11 residues processed: 62 average time/residue: 0.6803 time to fit residues: 45.4269 Evaluate side-chains 59 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1256 GLN Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 22 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.123129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.082176 restraints weight = 18284.051| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.00 r_work: 0.3052 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.8009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11966 Z= 0.187 Angle : 0.583 10.209 16766 Z= 0.319 Chirality : 0.040 0.285 1939 Planarity : 0.004 0.058 1604 Dihedral : 19.592 164.117 3049 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.73 % Allowed : 23.87 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.26), residues: 1010 helix: 1.26 (0.23), residues: 482 sheet: 0.53 (0.52), residues: 92 loop : -1.31 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 655 TYR 0.014 0.001 TYR A 362 PHE 0.026 0.002 PHE A 518 TRP 0.009 0.001 TRP A 476 HIS 0.006 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00427 (11966) covalent geometry : angle 0.58270 (16766) hydrogen bonds : bond 0.06400 ( 470) hydrogen bonds : angle 3.98443 ( 1267) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5527.02 seconds wall clock time: 94 minutes 33.99 seconds (5673.99 seconds total)