Starting phenix.real_space_refine on Wed Aug 5 21:01:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h4k_51862/08_2026/9h4k_51862.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h4k_51862/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9h4k_51862/08_2026/9h4k_51862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h4k_51862/08_2026/9h4k_51862.map" model { file = "/net/cci-nas-00/data/ceres_data/9h4k_51862/08_2026/9h4k_51862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h4k_51862/08_2026/9h4k_51862.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.68, per 1000 atoms: 0.23 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: 0.99 Conformation dependent library (CDL) restraints added in 492.5 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: 1.33 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: 2.89 Time building geometry restraints manager: 1.26 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=" C3' DT D 44 " pdb=" C2' DT D 44 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DG D 37 " pdb=" C2' DG D 37 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DT C 10 " pdb=" C2' DT C 10 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.84e+00 bond pdb=" C1' DT C 23 " pdb=" N1 DT C 23 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 7.12e+00 bond pdb=" C3' DG D 35 " pdb=" C2' DG D 35 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.59e+00 ... (remaining 11961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 16247 2.02 - 4.03: 500 4.03 - 6.05: 13 6.05 - 8.07: 3 8.07 - 10.08: 3 Bond angle restraints: 16766 Sorted by residual: angle pdb=" O5' A B 14 " pdb=" C5' A B 14 " pdb=" C4' A B 14 " ideal model delta sigma weight residual 109.40 114.57 -5.17 8.00e-01 1.56e+00 4.18e+01 angle pdb=" C3' A B 13 " pdb=" O3' A B 13 " pdb=" P A B 14 " ideal model delta sigma weight residual 119.70 126.16 -6.46 1.20e+00 6.94e-01 2.90e+01 angle pdb=" O4' DT C 21 " pdb=" C4' DT C 21 " pdb=" C3' DT C 21 " ideal model delta sigma weight residual 106.00 103.41 2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT C 23 " pdb=" C4 DT C 23 " pdb=" O4 DT C 23 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT C 29 " pdb=" C4 DT C 29 " pdb=" O4 DT C 29 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+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 - 0.040: 1299 0.040 - 0.079: 414 0.079 - 0.119: 126 0.119 - 0.158: 97 0.158 - 0.198: 3 Chirality restraints: 1939 Sorted by residual: chirality pdb=" C2' A B 13 " pdb=" C3' A B 13 " pdb=" O2' A B 13 " pdb=" C1' A B 13 " both_signs ideal model delta sigma weight residual False -2.62 -2.82 0.20 2.00e-01 2.50e+01 9.79e-01 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 2.47 2.30 0.17 2.00e-01 2.50e+01 7.58e-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: 3.410 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.260 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:9.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 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= 0.294 Angle : 0.676 10.083 16766 Z= 0.522 Chirality : 0.050 0.198 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/Z covalent geometry : bond 0.00409 / 0.29 (11966) covalent geometry : angle 0.67558 / 0.52 (16766) hydrogen bonds : bond 0.15417 / 10.59 ( 470) hydrogen bonds : angle 5.28384 / 3.95 ( 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 : 0.382 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: 0.5386 time to fit residues: 96.1171 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 : 0.530 ------------------------------------------------------------------------------- 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: 6.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 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: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 641 HIS A 690 ASN A 990 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.129915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.091059 restraints weight = 18542.048| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.01 r_work: 0.3217 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11966 Z= 0.182 Angle : 0.651 9.148 16766 Z= 0.364 Chirality : 0.043 0.319 1939 Planarity : 0.005 0.050 1604 Dihedral : 19.930 164.269 3055 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.78 % Allowed : 19.44 % Favored : 76.78 % 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: -0.44 (0.25), residues: 1010 helix: 0.80 (0.24), residues: 479 sheet: 0.31 (0.50), residues: 97 loop : -1.73 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 655 TYR 0.012 0.001 TYR A 155 PHE 0.024 0.002 PHE A1276 TRP 0.020 0.001 TRP A1074 HIS 0.012 0.002 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.18 (11966) covalent geometry : angle 0.65111 / 0.36 (16766) hydrogen bonds : bond 0.05935 / 4.20 ( 470) hydrogen bonds : angle 4.35177 / 3.28 ( 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 116 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 81 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 495 MET cc_start: 0.8141 (mtt) cc_final: 0.7635 (mtt) REVERT: A 650 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7865 (mm-40) REVERT: A 1044 ASN cc_start: 0.8380 (m-40) cc_final: 0.7923 (t0) REVERT: A 1047 LYS cc_start: 0.8816 (mttm) cc_final: 0.8340 (mmtp) REVERT: A 1304 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8132 (mp0) outliers start: 35 outliers final: 7 residues processed: 109 average time/residue: 0.4827 time to fit residues: 57.1945 Evaluate side-chains 75 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 620 VAL Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1304 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 2 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 0.0010 chunk 67 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS A 504 ASN ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1221 GLN A1256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.131589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.098112 restraints weight = 18513.660| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.29 r_work: 0.3220 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11966 Z= 0.156 Angle : 0.568 8.874 16766 Z= 0.323 Chirality : 0.042 0.304 1939 Planarity : 0.004 0.053 1604 Dihedral : 19.697 169.833 3049 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.35 % Allowed : 19.87 % Favored : 76.78 % 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: 1.01 (0.23), residues: 487 sheet: 0.27 (0.51), residues: 98 loop : -1.48 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 655 TYR 0.011 0.001 TYR A 639 PHE 0.032 0.002 PHE A 518 TRP 0.005 0.001 TRP A 476 HIS 0.007 0.001 HIS A 985 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (11966) covalent geometry : angle 0.56776 / 0.32 (16766) hydrogen bonds : bond 0.06103 / 4.33 ( 470) hydrogen bonds : angle 4.17462 / 3.13 ( 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 106 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 75 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 526 LYS cc_start: 0.6676 (mmmt) cc_final: 0.6327 (mmtp) REVERT: A 555 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8271 (t) REVERT: A 709 GLN cc_start: 0.7430 (tm-30) cc_final: 0.7166 (mm110) REVERT: A 751 MET cc_start: 0.8716 (tpt) cc_final: 0.8479 (tpt) REVERT: A 1038 PHE cc_start: 0.0895 (OUTLIER) cc_final: 0.0102 (t80) REVERT: A 1242 TYR cc_start: 0.6779 (OUTLIER) cc_final: 0.6520 (t80) REVERT: A 1299 ASP cc_start: 0.8104 (m-30) cc_final: 0.7345 (t0) REVERT: A 1304 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8131 (mp0) outliers start: 31 outliers final: 6 residues processed: 100 average time/residue: 0.6064 time to fit residues: 65.2956 Evaluate side-chains 65 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 1038 PHE Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1304 GLU 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: 2.9990 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 77 ASN A 116 HIS A 342 GLN A 501 ASN A 504 ASN ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 HIS A1221 GLN A1256 GLN A1264 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.123653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.082454 restraints weight = 18437.230| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.02 r_work: 0.3067 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.6876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.128 11966 Z= 0.346 Angle : 0.844 12.257 16766 Z= 0.456 Chirality : 0.056 0.499 1939 Planarity : 0.006 0.067 1604 Dihedral : 20.060 173.669 3049 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.54 % Allowed : 20.09 % Favored : 75.38 % 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 are not related in a simple way. whole: -0.97 (0.24), residues: 1010 helix: 0.15 (0.22), residues: 488 sheet: -0.04 (0.49), residues: 105 loop : -1.72 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1060 TYR 0.021 0.002 TYR A 362 PHE 0.020 0.003 PHE A 966 TRP 0.012 0.003 TRP A 18 HIS 0.015 0.003 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00798 / 0.35 (11966) covalent geometry : angle 0.84362 / 0.46 (16766) hydrogen bonds : bond 0.10305 / 7.11 ( 470) hydrogen bonds : angle 4.60342 / 3.46 ( 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 97 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 55 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7094 (pm20) cc_final: 0.6812 (pm20) REVERT: A 395 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7764 (ttm-80) REVERT: A 495 MET cc_start: 0.9004 (mtt) cc_final: 0.8795 (mtt) REVERT: A 606 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.6985 (t80) REVERT: A 976 ARG cc_start: 0.8257 (ttm110) cc_final: 0.7967 (ttm110) REVERT: A 1038 PHE cc_start: 0.0696 (OUTLIER) cc_final: -0.0161 (t80) outliers start: 42 outliers final: 16 residues processed: 92 average time/residue: 0.5822 time to fit residues: 57.5648 Evaluate side-chains 65 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 310 THR Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 1038 PHE Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1251 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 6 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 0 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 63 optimal weight: 0.2980 chunk 109 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 ASN A 504 ASN ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.126660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.085863 restraints weight = 18193.128| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.01 r_work: 0.3112 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.6829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11966 Z= 0.131 Angle : 0.550 9.500 16766 Z= 0.318 Chirality : 0.040 0.313 1939 Planarity : 0.004 0.054 1604 Dihedral : 19.790 168.627 3049 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.38 % Allowed : 21.81 % 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: -0.26 (0.25), residues: 1010 helix: 0.88 (0.23), residues: 490 sheet: 0.26 (0.51), residues: 96 loop : -1.55 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 655 TYR 0.012 0.001 TYR A 155 PHE 0.010 0.001 PHE A 966 TRP 0.009 0.001 TRP A 476 HIS 0.004 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (11966) covalent geometry : angle 0.54955 / 0.32 (16766) hydrogen bonds : bond 0.06105 / 4.24 ( 470) hydrogen bonds : angle 4.14097 / 3.12 ( 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 70 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 122 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.8012 (tp) REVERT: A 171 GLU cc_start: 0.6942 (pm20) cc_final: 0.6613 (pm20) REVERT: A 395 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7761 (ttm-80) REVERT: A 495 MET cc_start: 0.9014 (mtt) cc_final: 0.8780 (mtt) REVERT: A 606 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.6928 (t80) REVERT: A 661 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7594 (mmp-170) REVERT: A 745 ASP cc_start: 0.8472 (t0) cc_final: 0.8168 (m-30) REVERT: A 976 ARG cc_start: 0.8207 (ttm110) cc_final: 0.7920 (ttm110) outliers start: 22 outliers final: 7 residues processed: 67 average time/residue: 0.5491 time to fit residues: 39.9815 Evaluate side-chains 55 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1138 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 77 optimal weight: 0.0870 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3862 r_free = 0.3862 target = 0.121867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.080863 restraints weight = 18418.297| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.00 r_work: 0.3028 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.7029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 11966 Z= 0.276 Angle : 0.687 11.137 16766 Z= 0.379 Chirality : 0.048 0.430 1939 Planarity : 0.005 0.056 1604 Dihedral : 19.885 172.073 3049 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.13 % Allowed : 21.49 % Favored : 75.38 % 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 are not related in a simple way. whole: -0.56 (0.25), residues: 1010 helix: 0.65 (0.23), residues: 486 sheet: -0.11 (0.47), residues: 105 loop : -1.66 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 635 TYR 0.019 0.002 TYR A 362 PHE 0.015 0.002 PHE A 446 TRP 0.014 0.002 TRP A 476 HIS 0.010 0.002 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.28 (11966) covalent geometry : angle 0.68667 / 0.38 (16766) hydrogen bonds : bond 0.08437 / 5.81 ( 470) hydrogen bonds : angle 4.28818 / 3.23 ( 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 72 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 43 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 122 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8181 (tp) REVERT: A 171 GLU cc_start: 0.7205 (pm20) cc_final: 0.6881 (pm20) REVERT: A 395 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7904 (ttm-80) REVERT: A 564 LEU cc_start: 0.3187 (OUTLIER) cc_final: 0.2753 (pt) REVERT: A 606 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.6938 (t80) REVERT: A 649 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8091 (mptm) REVERT: A 745 ASP cc_start: 0.8588 (t0) cc_final: 0.8261 (m-30) REVERT: A 746 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: A 926 GLN cc_start: 0.8363 (tp40) cc_final: 0.8140 (mm110) REVERT: A 976 ARG cc_start: 0.8251 (ttm110) cc_final: 0.7964 (ttm110) outliers start: 29 outliers final: 14 residues processed: 66 average time/residue: 0.5954 time to fit residues: 42.3484 Evaluate side-chains 62 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 661 ARG 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 1038 PHE Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1138 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: 1.9990 chunk 0 optimal weight: 0.6980 chunk 79 optimal weight: 0.0030 chunk 75 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.124744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.084086 restraints weight = 18401.043| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.99 r_work: 0.3087 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.7100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11966 Z= 0.136 Angle : 0.547 9.299 16766 Z= 0.317 Chirality : 0.040 0.338 1939 Planarity : 0.004 0.052 1604 Dihedral : 19.757 168.801 3049 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.59 % Allowed : 21.71 % Favored : 75.70 % 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 (0.25), residues: 1010 helix: 1.05 (0.24), residues: 485 sheet: 0.13 (0.50), residues: 96 loop : -1.59 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 655 TYR 0.013 0.001 TYR A 155 PHE 0.010 0.001 PHE A1258 TRP 0.011 0.001 TRP A 476 HIS 0.004 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (11966) covalent geometry : angle 0.54743 / 0.32 (16766) hydrogen bonds : bond 0.06195 / 4.31 ( 470) hydrogen bonds : angle 4.06876 / 3.07 ( 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 68 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 44 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 122 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8139 (tp) REVERT: A 171 GLU cc_start: 0.7162 (pm20) cc_final: 0.6831 (pm20) REVERT: A 395 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8228 (ttp80) REVERT: A 606 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.6895 (t80) REVERT: A 745 ASP cc_start: 0.8451 (t0) cc_final: 0.8239 (m-30) REVERT: A 976 ARG cc_start: 0.8191 (ttm110) cc_final: 0.7970 (ttm110) REVERT: A 1256 GLN cc_start: 0.8431 (mm110) cc_final: 0.8052 (mm-40) outliers start: 24 outliers final: 12 residues processed: 65 average time/residue: 0.5329 time to fit residues: 37.4319 Evaluate side-chains 58 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 1038 PHE Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1190 VAL 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: 0.7980 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3900 r_free = 0.3900 target = 0.124593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.083611 restraints weight = 18352.984| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.02 r_work: 0.3079 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.7216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11966 Z= 0.152 Angle : 0.560 9.177 16766 Z= 0.318 Chirality : 0.041 0.347 1939 Planarity : 0.004 0.066 1604 Dihedral : 19.735 169.843 3049 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.16 % Allowed : 22.25 % Favored : 75.59 % 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: -0.05 (0.25), residues: 1010 helix: 1.14 (0.24), residues: 485 sheet: 0.40 (0.51), residues: 91 loop : -1.52 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 655 TYR 0.013 0.001 TYR A 155 PHE 0.016 0.001 PHE A 553 TRP 0.012 0.001 TRP A 476 HIS 0.005 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (11966) covalent geometry : angle 0.55994 / 0.32 (16766) hydrogen bonds : bond 0.06206 / 4.30 ( 470) hydrogen bonds : angle 3.98602 / 3.01 ( 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 71 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 122 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8159 (tp) REVERT: A 171 GLU cc_start: 0.7185 (pm20) cc_final: 0.6845 (pm20) REVERT: A 395 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8202 (ttp80) REVERT: A 606 PHE cc_start: 0.7557 (OUTLIER) cc_final: 0.6900 (t80) REVERT: A 745 ASP cc_start: 0.8458 (t0) cc_final: 0.8235 (m-30) REVERT: A 746 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7546 (tp30) REVERT: A 976 ARG cc_start: 0.8208 (ttm110) cc_final: 0.7885 (ttm110) REVERT: A 1256 GLN cc_start: 0.8447 (mm110) cc_final: 0.8153 (mm-40) outliers start: 20 outliers final: 12 residues processed: 69 average time/residue: 0.5995 time to fit residues: 44.7010 Evaluate side-chains 62 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 661 ARG 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 1050 ILE Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1190 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 20 optimal weight: 0.0050 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 44 optimal weight: 0.0170 chunk 33 optimal weight: 0.0670 chunk 22 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 overall best weight: 0.3570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS A 595 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.127241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.086953 restraints weight = 18290.904| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.01 r_work: 0.3141 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.7269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11966 Z= 0.115 Angle : 0.523 10.872 16766 Z= 0.300 Chirality : 0.038 0.298 1939 Planarity : 0.004 0.080 1604 Dihedral : 19.647 168.541 3049 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.73 % Allowed : 22.68 % Favored : 75.59 % 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: 0.20 (0.26), residues: 1010 helix: 1.38 (0.24), residues: 484 sheet: 0.30 (0.50), residues: 97 loop : -1.40 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 655 TYR 0.011 0.001 TYR A 155 PHE 0.010 0.001 PHE A1258 TRP 0.010 0.001 TRP A 476 HIS 0.010 0.001 HIS A 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.11 (11966) covalent geometry : angle 0.52341 / 0.30 (16766) hydrogen bonds : bond 0.05130 / 3.60 ( 470) hydrogen bonds : angle 3.87870 / 2.93 ( 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 67 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7170 (pm20) cc_final: 0.6853 (pm20) REVERT: A 555 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8268 (t) REVERT: A 600 ILE cc_start: 0.7510 (tt) cc_final: 0.7213 (tt) REVERT: A 606 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.6829 (t80) REVERT: A 655 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7363 (mmm160) REVERT: A 745 ASP cc_start: 0.8269 (t0) cc_final: 0.8068 (m-30) REVERT: A 976 ARG cc_start: 0.8164 (ttm110) cc_final: 0.7933 (ttm110) REVERT: A 1256 GLN cc_start: 0.8454 (mm110) cc_final: 0.8133 (mm-40) outliers start: 16 outliers final: 10 residues processed: 65 average time/residue: 0.6700 time to fit residues: 46.9741 Evaluate side-chains 60 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1190 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3913 r_free = 0.3913 target = 0.125538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.084723 restraints weight = 18326.455| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.02 r_work: 0.3099 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.7321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11966 Z= 0.143 Angle : 0.548 9.876 16766 Z= 0.311 Chirality : 0.040 0.336 1939 Planarity : 0.004 0.070 1604 Dihedral : 19.655 170.241 3049 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.40 % Allowed : 23.00 % Favored : 75.59 % 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: 0.21 (0.26), residues: 1010 helix: 1.35 (0.24), residues: 484 sheet: 0.53 (0.52), residues: 92 loop : -1.38 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 655 TYR 0.013 0.001 TYR A 155 PHE 0.010 0.001 PHE A1045 TRP 0.010 0.001 TRP A 476 HIS 0.005 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (11966) covalent geometry : angle 0.54838 / 0.31 (16766) hydrogen bonds : bond 0.05697 / 3.96 ( 470) hydrogen bonds : angle 3.88516 / 2.94 ( 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 64 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7197 (pm20) cc_final: 0.6857 (pm20) REVERT: A 600 ILE cc_start: 0.7573 (tt) cc_final: 0.7276 (tt) REVERT: A 606 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.6828 (t80) REVERT: A 745 ASP cc_start: 0.8403 (t0) cc_final: 0.8201 (m-30) REVERT: A 746 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7479 (tp30) REVERT: A 976 ARG cc_start: 0.8187 (ttm110) cc_final: 0.7855 (ttm110) REVERT: A 1256 GLN cc_start: 0.8472 (mm110) cc_final: 0.8138 (mm-40) outliers start: 13 outliers final: 11 residues processed: 62 average time/residue: 0.6263 time to fit residues: 41.7589 Evaluate side-chains 62 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 661 ARG 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 1050 ILE Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1190 VAL 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: 20.0000 chunk 76 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 668 ASN ** 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 = 0.3891 r_free = 0.3891 target = 0.124044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.083123 restraints weight = 18289.584| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.99 r_work: 0.3068 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.7436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11966 Z= 0.175 Angle : 0.586 10.007 16766 Z= 0.329 Chirality : 0.042 0.371 1939 Planarity : 0.004 0.064 1604 Dihedral : 19.705 170.208 3049 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.16 % Allowed : 22.46 % Favored : 75.38 % 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 are not related in a simple way. whole: 0.03 (0.26), residues: 1010 helix: 1.13 (0.24), residues: 490 sheet: 0.43 (0.51), residues: 92 loop : -1.41 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 655 TYR 0.015 0.001 TYR A 362 PHE 0.011 0.002 PHE A 105 TRP 0.011 0.002 TRP A 476 HIS 0.005 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (11966) covalent geometry : angle 0.58591 / 0.33 (16766) hydrogen bonds : bond 0.06485 / 4.50 ( 470) hydrogen bonds : angle 3.96091 / 3.00 ( 1267) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4833.24 seconds wall clock time: 82 minutes 33.41 seconds (4953.41 seconds total)