Starting phenix.real_space_refine on Wed Aug 5 19:31:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9waw_65827/08_2026/9waw_65827.cif Found real_map, /net/cci-nas-00/data/ceres_data/9waw_65827/08_2026/9waw_65827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9waw_65827/08_2026/9waw_65827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9waw_65827/08_2026/9waw_65827.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9waw_65827/08_2026/9waw_65827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9waw_65827/08_2026/9waw_65827.map" } resolution = 3.95 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= 0.005 sd= 0.037 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 135 5.49 5 S 19 5.16 5 C 6647 2.51 5 N 1985 2.21 5 O 2454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 11240 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8391 Classifications: {'peptide': 1025} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 997} Chain breaks: 3 Chain: "B" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 582 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "C" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 308 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "D" Number of atoms: 1959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1959 Classifications: {'RNA': 92} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 43, 'rna3p_pyr': 35} Link IDs: {'rna2p': 13, 'rna3p': 78} Time building chain proxies: 1.82, per 1000 atoms: 0.16 Number of scatterers: 11240 At special positions: 0 Unit cell: (120.736, 101.332, 150.92, 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 19 16.00 P 135 15.00 O 2454 8.00 N 1985 7.00 C 6647 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 287.4 milliseconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1950 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 6 sheets defined 54.4% alpha, 9.3% beta 49 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.567A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.555A 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 293 through 306 removed outlier: 3.581A pdb=" N ILE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.704A pdb=" N ALA A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.122A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.824A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLU A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 512 through 526 removed outlier: 3.999A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 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 654 removed outlier: 3.519A pdb=" N ARG A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 654 " --> pdb=" O GLN A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 668 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 703 through 712 Processing helix chain 'A' and resid 721 through 727 Processing helix chain 'A' and resid 730 through 751 Processing helix chain 'A' and resid 925 through 940 removed outlier: 3.685A pdb=" N LYS A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.838A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1000 removed outlier: 4.457A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1088 removed outlier: 3.579A pdb=" N SER A1088 " --> pdb=" O ARG A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.735A 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 1281 removed outlier: 3.662A pdb=" N GLU A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.718A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1316 No H-bonds generated for 'chain 'A' and resid 1314 through 1316' Processing helix chain 'A' and resid 1340 through 1344 Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.610A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A1093 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A1095 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 9.752A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.275A 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: 4.141A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 509 removed outlier: 5.259A pdb=" N LEU A 508 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.612A pdb=" N ALA A 538 " --> pdb=" O TYR A 529 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 528 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.532A pdb=" N ALA A1147 " --> pdb=" O VAL A1160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1324 through 1326 removed outlier: 3.560A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 230 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 0.86 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: 2477 1.33 - 1.45: 3068 1.45 - 1.57: 5885 1.57 - 1.69: 267 1.69 - 1.81: 36 Bond restraints: 11733 Sorted by residual: bond pdb=" C3' DA B 27 " pdb=" C2' DA B 27 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.50e+00 bond pdb=" C3' DC B 3 " pdb=" C2' DC B 3 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.67e+00 bond pdb=" C3' DC C 5 " pdb=" C2' DC C 5 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.49e+00 bond pdb=" C3' DG B 28 " pdb=" C2' DG B 28 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.34e+00 bond pdb=" C3' DC B 14 " pdb=" C2' DC B 14 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.90e+00 ... (remaining 11728 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 15058 1.02 - 2.04: 956 2.04 - 3.07: 369 3.07 - 4.09: 29 4.09 - 5.11: 9 Bond angle restraints: 16421 Sorted by residual: angle pdb=" O2 C D 11 " pdb=" C2 C D 11 " pdb=" N3 C D 11 " ideal model delta sigma weight residual 121.90 117.80 4.10 7.00e-01 2.04e+00 3.43e+01 angle pdb=" C2 C D 11 " pdb=" N1 C D 11 " pdb=" C6 C D 11 " ideal model delta sigma weight residual 120.30 118.12 2.18 4.00e-01 6.25e+00 2.96e+01 angle pdb=" N1 C D 11 " pdb=" C2 C D 11 " pdb=" O2 C D 11 " ideal model delta sigma weight residual 118.90 121.95 -3.05 6.00e-01 2.78e+00 2.58e+01 angle pdb=" O4' DT B 19 " pdb=" C4' DT B 19 " pdb=" C3' DT B 19 " ideal model delta sigma weight residual 106.00 103.15 2.85 6.00e-01 2.78e+00 2.25e+01 angle pdb=" O5' U D 14 " pdb=" C5' U D 14 " pdb=" C4' U D 14 " ideal model delta sigma weight residual 109.40 112.73 -3.33 8.00e-01 1.56e+00 1.73e+01 ... (remaining 16416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.85: 6673 30.85 - 61.70: 367 61.70 - 92.55: 72 92.55 - 123.40: 1 123.40 - 154.25: 1 Dihedral angle restraints: 7114 sinusoidal: 4103 harmonic: 3011 Sorted by residual: dihedral pdb=" C4' DG B 7 " pdb=" C3' DG B 7 " pdb=" O3' DG B 7 " pdb=" P DA B 8 " ideal model delta sinusoidal sigma weight residual -140.00 14.25 -154.25 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA PHE A 446 " pdb=" C PHE A 446 " pdb=" N ARG A 447 " pdb=" CA ARG A 447 " ideal model delta harmonic sigma weight residual 180.00 161.51 18.49 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA LEU A 625 " pdb=" C LEU A 625 " pdb=" N PHE A 626 " pdb=" CA PHE A 626 " ideal model delta harmonic sigma weight residual -180.00 -162.97 -17.03 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 7111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1264 0.034 - 0.067: 366 0.067 - 0.101: 134 0.101 - 0.134: 106 0.134 - 0.168: 24 Chirality restraints: 1894 Sorted by residual: chirality pdb=" C1' A D 34 " pdb=" O4' A D 34 " pdb=" C2' A D 34 " pdb=" N9 A D 34 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.04e-01 chirality pdb=" C1' A D 42 " pdb=" O4' A D 42 " pdb=" C2' A D 42 " pdb=" N9 A D 42 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" C4' U D 12 " pdb=" C5' U D 12 " pdb=" O4' U D 12 " pdb=" C3' U D 12 " both_signs ideal model delta sigma weight residual False -2.50 -2.35 -0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 1891 not shown) Planarity restraints: 1599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D 34 " -0.026 2.00e-02 2.50e+03 1.20e-02 3.97e+00 pdb=" N9 A D 34 " 0.028 2.00e-02 2.50e+03 pdb=" C8 A D 34 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A D 34 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A D 34 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A D 34 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A D 34 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A D 34 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A D 34 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A D 34 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A D 34 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 42 " 0.025 2.00e-02 2.50e+03 1.12e-02 3.43e+00 pdb=" N9 A D 42 " -0.025 2.00e-02 2.50e+03 pdb=" C8 A D 42 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A D 42 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A D 42 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A D 42 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A D 42 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A D 42 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A D 42 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A D 42 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A D 42 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U D 10 " 0.023 2.00e-02 2.50e+03 1.23e-02 3.40e+00 pdb=" N1 U D 10 " -0.026 2.00e-02 2.50e+03 pdb=" C2 U D 10 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U D 10 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U D 10 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U D 10 " 0.007 2.00e-02 2.50e+03 pdb=" O4 U D 10 " 0.006 2.00e-02 2.50e+03 pdb=" C5 U D 10 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U D 10 " -0.006 2.00e-02 2.50e+03 ... (remaining 1596 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 5 2.02 - 2.74: 936 2.74 - 3.46: 15538 3.46 - 4.18: 28453 4.18 - 4.90: 45587 Nonbonded interactions: 90519 Sorted by model distance: nonbonded pdb=" NZ LYS A 742 " pdb=" OP1 C D 67 " model vdw 1.296 3.120 nonbonded pdb=" NZ LYS A 44 " pdb=" O6 G D 92 " model vdw 1.297 3.120 nonbonded pdb=" ND2 ASN A 77 " pdb=" O2 U D 59 " model vdw 1.298 3.120 nonbonded pdb=" NH1 ARG A 340 " pdb=" OP1 A D 41 " model vdw 1.298 3.120 nonbonded pdb=" NH2 ARG A1122 " pdb=" N3 A D 49 " model vdw 1.353 3.200 ... (remaining 90514 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.380 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.790 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 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 : 0.003 0.026 11733 Z= 0.260 Angle : 0.624 5.111 16421 Z= 0.490 Chirality : 0.047 0.168 1894 Planarity : 0.003 0.035 1599 Dihedral : 17.165 154.251 5164 Min Nonbonded Distance : 1.296 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.85 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.85 (0.27), residues: 1017 helix: 2.09 (0.24), residues: 511 sheet: 1.02 (0.66), residues: 68 loop : 0.29 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 71 TYR 0.008 0.001 TYR A 451 PHE 0.009 0.001 PHE A 491 TRP 0.015 0.002 TRP A1126 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.26 (11733) covalent geometry : angle 0.62351 / 0.49 (16421) hydrogen bonds : bond 0.16176 / 10.59 ( 521) hydrogen bonds : angle 5.57888 / 4.07 ( 1394) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 TYR cc_start: 0.8381 (m-80) cc_final: 0.7870 (m-80) REVERT: A 569 PHE cc_start: 0.9184 (m-80) cc_final: 0.8898 (m-80) REVERT: A 651 LEU cc_start: 0.9346 (mt) cc_final: 0.8955 (pp) REVERT: A 948 LYS cc_start: 0.9194 (tttt) cc_final: 0.8826 (mptt) REVERT: A 1099 GLU cc_start: 0.7386 (mt-10) cc_final: 0.5569 (mt-10) REVERT: A 1365 LEU cc_start: 0.9051 (mt) cc_final: 0.8699 (pp) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1211 time to fit residues: 36.6736 Evaluate side-chains 136 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 40.0000 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 40.0000 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.060593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.041471 restraints weight = 73974.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.043066 restraints weight = 40898.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.044179 restraints weight = 28506.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.044719 restraints weight = 22550.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.045227 restraints weight = 19592.407| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11733 Z= 0.174 Angle : 0.669 10.682 16421 Z= 0.370 Chirality : 0.044 0.292 1894 Planarity : 0.005 0.078 1599 Dihedral : 19.748 157.012 2981 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.96 % Allowed : 8.91 % Favored : 89.13 % 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: 1.49 (0.27), residues: 1017 helix: 1.76 (0.23), residues: 511 sheet: 1.34 (0.62), residues: 78 loop : 0.05 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 635 TYR 0.012 0.001 TYR A 973 PHE 0.020 0.002 PHE A1324 TRP 0.007 0.001 TRP A 18 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (11733) covalent geometry : angle 0.66883 / 0.37 (16421) hydrogen bonds : bond 0.06776 / 4.60 ( 521) hydrogen bonds : angle 4.73748 / 3.39 ( 1394) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9215 (tpt) cc_final: 0.9007 (tpt) REVERT: A 383 MET cc_start: 0.7827 (ttm) cc_final: 0.7587 (tpp) REVERT: A 398 LEU cc_start: 0.9345 (mt) cc_final: 0.9086 (mt) REVERT: A 399 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8684 (tp) REVERT: A 423 LEU cc_start: 0.9739 (OUTLIER) cc_final: 0.9527 (mt) REVERT: A 651 LEU cc_start: 0.9207 (mt) cc_final: 0.8978 (mt) REVERT: A 683 LEU cc_start: 0.9411 (mt) cc_final: 0.8879 (tp) REVERT: A 746 GLU cc_start: 0.9357 (tp30) cc_final: 0.9115 (tp30) REVERT: A 1089 MET cc_start: 0.8049 (tpp) cc_final: 0.7570 (tpp) REVERT: A 1096 LYS cc_start: 0.9575 (tptt) cc_final: 0.9230 (tptm) REVERT: A 1097 LYS cc_start: 0.9409 (tptp) cc_final: 0.8962 (tptt) REVERT: A 1108 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8952 (mp0) REVERT: A 1213 MET cc_start: 0.9313 (ttm) cc_final: 0.8835 (tpp) REVERT: A 1214 LEU cc_start: 0.9845 (tp) cc_final: 0.9630 (tp) REVERT: A 1258 PHE cc_start: 0.9384 (OUTLIER) cc_final: 0.9027 (m-80) REVERT: A 1365 LEU cc_start: 0.9567 (mt) cc_final: 0.8965 (pp) outliers start: 18 outliers final: 9 residues processed: 161 average time/residue: 0.0984 time to fit residues: 21.8949 Evaluate side-chains 130 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1258 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 84 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 103 optimal weight: 40.0000 chunk 41 optimal weight: 50.0000 chunk 24 optimal weight: 5.9990 chunk 112 optimal weight: 50.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** A 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.057359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.038764 restraints weight = 77906.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.040244 restraints weight = 42978.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.041171 restraints weight = 29892.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.041700 restraints weight = 23933.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.042153 restraints weight = 20991.982| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 11733 Z= 0.243 Angle : 0.684 8.082 16421 Z= 0.385 Chirality : 0.044 0.210 1894 Planarity : 0.005 0.055 1599 Dihedral : 19.910 168.329 2981 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.28 % Allowed : 11.20 % Favored : 86.52 % 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: 0.89 (0.26), residues: 1017 helix: 1.22 (0.23), residues: 510 sheet: 0.97 (0.63), residues: 76 loop : -0.15 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 139 TYR 0.029 0.002 TYR A 517 PHE 0.015 0.002 PHE A 970 TRP 0.023 0.003 TRP A 659 HIS 0.008 0.002 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.24 (11733) covalent geometry : angle 0.68427 / 0.39 (16421) hydrogen bonds : bond 0.07030 / 4.72 ( 521) hydrogen bonds : angle 4.82818 / 3.43 ( 1394) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.9553 (pm20) cc_final: 0.9233 (pm20) REVERT: A 76 LYS cc_start: 0.9637 (ptpp) cc_final: 0.9430 (ptpp) REVERT: A 90 MET cc_start: 0.9286 (tpt) cc_final: 0.9059 (tpp) REVERT: A 321 MET cc_start: 0.9815 (mmp) cc_final: 0.9486 (mmm) REVERT: A 383 MET cc_start: 0.8020 (ttm) cc_final: 0.7621 (ttm) REVERT: A 398 LEU cc_start: 0.9479 (mt) cc_final: 0.9167 (mt) REVERT: A 399 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8941 (tp) REVERT: A 484 LYS cc_start: 0.9721 (mtpt) cc_final: 0.9162 (mmtm) REVERT: A 534 MET cc_start: 0.6515 (mtt) cc_final: 0.6135 (mtm) REVERT: A 562 LYS cc_start: 0.9629 (pttm) cc_final: 0.9365 (mmmt) REVERT: A 651 LEU cc_start: 0.9303 (mt) cc_final: 0.9100 (mt) REVERT: A 662 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9249 (tp) REVERT: A 746 GLU cc_start: 0.9491 (tp30) cc_final: 0.9218 (tp30) REVERT: A 751 MET cc_start: 0.9079 (tpp) cc_final: 0.8869 (mtp) REVERT: A 1089 MET cc_start: 0.8096 (tpp) cc_final: 0.7859 (tpp) REVERT: A 1097 LYS cc_start: 0.9366 (tptp) cc_final: 0.8900 (tptt) REVERT: A 1213 MET cc_start: 0.9256 (ttm) cc_final: 0.8818 (tpp) REVERT: A 1268 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8742 (mp0) REVERT: A 1313 PHE cc_start: 0.9493 (m-80) cc_final: 0.9192 (m-10) REVERT: A 1324 PHE cc_start: 0.8549 (p90) cc_final: 0.8267 (p90) outliers start: 21 outliers final: 11 residues processed: 130 average time/residue: 0.1090 time to fit residues: 19.4064 Evaluate side-chains 116 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1347 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 40 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 75 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 HIS ** 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 = 0.3293 r_free = 0.3293 target = 0.056905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.038344 restraints weight = 77673.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.039840 restraints weight = 42333.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.040775 restraints weight = 29329.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.041416 restraints weight = 23418.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.041703 restraints weight = 20180.831| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11733 Z= 0.195 Angle : 0.623 9.544 16421 Z= 0.353 Chirality : 0.042 0.212 1894 Planarity : 0.004 0.053 1599 Dihedral : 19.992 172.182 2981 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.17 % Allowed : 10.98 % Favored : 86.85 % 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: 0.72 (0.26), residues: 1017 helix: 1.10 (0.23), residues: 511 sheet: 0.61 (0.66), residues: 66 loop : -0.18 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 661 TYR 0.033 0.002 TYR A 517 PHE 0.014 0.002 PHE A 970 TRP 0.009 0.002 TRP A 659 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.19 (11733) covalent geometry : angle 0.62307 / 0.35 (16421) hydrogen bonds : bond 0.06186 / 4.22 ( 521) hydrogen bonds : angle 4.65542 / 3.32 ( 1394) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.9648 (ptpp) cc_final: 0.9430 (pttm) REVERT: A 90 MET cc_start: 0.9327 (tpt) cc_final: 0.9083 (tpp) REVERT: A 321 MET cc_start: 0.9800 (mmp) cc_final: 0.9366 (mmm) REVERT: A 383 MET cc_start: 0.8164 (ttm) cc_final: 0.7802 (ttm) REVERT: A 398 LEU cc_start: 0.9498 (mt) cc_final: 0.9164 (mt) REVERT: A 399 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8947 (tp) REVERT: A 484 LYS cc_start: 0.9709 (mtpt) cc_final: 0.9137 (mmtp) REVERT: A 534 MET cc_start: 0.6704 (mtt) cc_final: 0.6278 (mtp) REVERT: A 651 LEU cc_start: 0.9261 (mt) cc_final: 0.9050 (mt) REVERT: A 662 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9330 (tp) REVERT: A 746 GLU cc_start: 0.9516 (tp30) cc_final: 0.9222 (tp30) REVERT: A 1089 MET cc_start: 0.8002 (tpp) cc_final: 0.7750 (tpp) REVERT: A 1097 LYS cc_start: 0.9361 (tptp) cc_final: 0.8911 (tptt) REVERT: A 1213 MET cc_start: 0.9328 (ttm) cc_final: 0.8942 (tpt) REVERT: A 1313 PHE cc_start: 0.9504 (m-80) cc_final: 0.9129 (m-10) REVERT: A 1324 PHE cc_start: 0.8630 (p90) cc_final: 0.8292 (p90) REVERT: A 1365 LEU cc_start: 0.9652 (mm) cc_final: 0.8964 (pp) outliers start: 20 outliers final: 13 residues processed: 118 average time/residue: 0.1013 time to fit residues: 16.7601 Evaluate side-chains 118 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1317 ASN Chi-restraints excluded: chain A residue 1347 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 2 optimal weight: 0.1980 chunk 54 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 109 optimal weight: 30.0000 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 HIS ** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.057270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.038811 restraints weight = 76936.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.040331 restraints weight = 41848.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.041264 restraints weight = 28777.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.041903 restraints weight = 22968.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.042135 restraints weight = 19911.464| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11733 Z= 0.147 Angle : 0.575 9.713 16421 Z= 0.327 Chirality : 0.040 0.214 1894 Planarity : 0.004 0.052 1599 Dihedral : 20.005 171.354 2981 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.28 % Allowed : 11.74 % Favored : 85.98 % 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: 0.88 (0.26), residues: 1017 helix: 1.28 (0.23), residues: 508 sheet: 0.53 (0.65), residues: 66 loop : -0.13 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 139 TYR 0.036 0.002 TYR A 517 PHE 0.014 0.002 PHE A1327 TRP 0.014 0.002 TRP A 464 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (11733) covalent geometry : angle 0.57543 / 0.33 (16421) hydrogen bonds : bond 0.05554 / 3.82 ( 521) hydrogen bonds : angle 4.48629 / 3.19 ( 1394) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.9615 (ptpp) cc_final: 0.9312 (pttm) REVERT: A 90 MET cc_start: 0.9330 (tpt) cc_final: 0.9125 (tpp) REVERT: A 321 MET cc_start: 0.9811 (mmp) cc_final: 0.9465 (mmm) REVERT: A 383 MET cc_start: 0.8146 (ttm) cc_final: 0.7856 (ttm) REVERT: A 398 LEU cc_start: 0.9491 (mt) cc_final: 0.9166 (mt) REVERT: A 399 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8903 (tp) REVERT: A 484 LYS cc_start: 0.9704 (mtpt) cc_final: 0.9103 (mmtp) REVERT: A 534 MET cc_start: 0.6713 (mtt) cc_final: 0.6311 (mtp) REVERT: A 651 LEU cc_start: 0.9256 (mt) cc_final: 0.9055 (mt) REVERT: A 662 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9266 (tp) REVERT: A 746 GLU cc_start: 0.9531 (tp30) cc_final: 0.9261 (tp30) REVERT: A 929 LYS cc_start: 0.9631 (mttt) cc_final: 0.9378 (mmtt) REVERT: A 1089 MET cc_start: 0.8044 (tpp) cc_final: 0.7763 (tpp) REVERT: A 1097 LYS cc_start: 0.9387 (tptp) cc_final: 0.8922 (tptt) REVERT: A 1213 MET cc_start: 0.9307 (ttm) cc_final: 0.8918 (tpt) REVERT: A 1258 PHE cc_start: 0.9437 (OUTLIER) cc_final: 0.9142 (m-80) REVERT: A 1313 PHE cc_start: 0.9549 (m-80) cc_final: 0.9083 (m-10) REVERT: A 1324 PHE cc_start: 0.8683 (p90) cc_final: 0.8334 (p90) REVERT: A 1326 TYR cc_start: 0.9241 (t80) cc_final: 0.8983 (t80) REVERT: A 1365 LEU cc_start: 0.9670 (mm) cc_final: 0.9025 (pp) outliers start: 21 outliers final: 10 residues processed: 121 average time/residue: 0.0854 time to fit residues: 14.8830 Evaluate side-chains 114 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1258 PHE Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1317 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 85 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 ASN A 412 HIS ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1262 HIS ** 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 = 0.3263 r_free = 0.3263 target = 0.055384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.037382 restraints weight = 79783.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.038846 restraints weight = 43072.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.039794 restraints weight = 29568.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.040261 restraints weight = 23458.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.040703 restraints weight = 20635.656| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11733 Z= 0.221 Angle : 0.639 11.151 16421 Z= 0.358 Chirality : 0.042 0.220 1894 Planarity : 0.004 0.053 1599 Dihedral : 20.087 172.957 2981 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.96 % Allowed : 13.80 % Favored : 84.24 % 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: 0.61 (0.26), residues: 1017 helix: 1.00 (0.23), residues: 518 sheet: 0.69 (0.69), residues: 56 loop : -0.25 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 494 TYR 0.031 0.002 TYR A 517 PHE 0.017 0.002 PHE A 970 TRP 0.011 0.002 TRP A 659 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.22 (11733) covalent geometry : angle 0.63920 / 0.36 (16421) hydrogen bonds : bond 0.06245 / 4.22 ( 521) hydrogen bonds : angle 4.67377 / 3.32 ( 1394) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.9655 (ptpp) cc_final: 0.9444 (pttm) REVERT: A 161 MET cc_start: 0.9734 (mmp) cc_final: 0.9150 (mmp) REVERT: A 321 MET cc_start: 0.9807 (mmp) cc_final: 0.9597 (mmm) REVERT: A 383 MET cc_start: 0.8320 (ttm) cc_final: 0.7974 (ttm) REVERT: A 399 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9036 (tp) REVERT: A 484 LYS cc_start: 0.9727 (mtpt) cc_final: 0.9156 (mmtp) REVERT: A 534 MET cc_start: 0.6705 (mtt) cc_final: 0.6250 (mtp) REVERT: A 569 PHE cc_start: 0.9537 (m-80) cc_final: 0.9322 (m-80) REVERT: A 651 LEU cc_start: 0.9261 (mt) cc_final: 0.9058 (mt) REVERT: A 662 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9276 (tp) REVERT: A 746 GLU cc_start: 0.9607 (tp30) cc_final: 0.9294 (tp30) REVERT: A 751 MET cc_start: 0.9147 (ttm) cc_final: 0.8232 (ppp) REVERT: A 1089 MET cc_start: 0.8006 (tpp) cc_final: 0.7740 (tpp) REVERT: A 1097 LYS cc_start: 0.9388 (tptp) cc_final: 0.8927 (tptt) REVERT: A 1213 MET cc_start: 0.9281 (ttm) cc_final: 0.8931 (tpt) REVERT: A 1313 PHE cc_start: 0.9511 (m-80) cc_final: 0.9025 (m-10) REVERT: A 1324 PHE cc_start: 0.8750 (p90) cc_final: 0.8363 (p90) REVERT: A 1326 TYR cc_start: 0.9333 (t80) cc_final: 0.9023 (t80) outliers start: 18 outliers final: 15 residues processed: 111 average time/residue: 0.1101 time to fit residues: 17.1592 Evaluate side-chains 114 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1317 ASN Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 97 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 56 optimal weight: 40.0000 chunk 108 optimal weight: 40.0000 chunk 33 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** 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 = 0.3239 r_free = 0.3239 target = 0.054230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.036539 restraints weight = 80169.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.037983 restraints weight = 42862.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.038932 restraints weight = 29265.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.039430 restraints weight = 23089.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.039625 restraints weight = 20207.801| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11733 Z= 0.213 Angle : 0.635 10.887 16421 Z= 0.358 Chirality : 0.042 0.229 1894 Planarity : 0.004 0.052 1599 Dihedral : 20.265 174.280 2981 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.50 % Allowed : 13.59 % Favored : 83.91 % 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: 0.50 (0.26), residues: 1017 helix: 0.88 (0.23), residues: 517 sheet: 0.57 (0.69), residues: 54 loop : -0.25 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 671 TYR 0.031 0.002 TYR A 517 PHE 0.020 0.002 PHE A 643 TRP 0.011 0.002 TRP A 659 HIS 0.005 0.002 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.21 (11733) covalent geometry : angle 0.63485 / 0.36 (16421) hydrogen bonds : bond 0.06186 / 4.23 ( 521) hydrogen bonds : angle 4.66465 / 3.32 ( 1394) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9554 (tpp) cc_final: 0.9302 (tpp) REVERT: A 125 GLU cc_start: 0.9347 (OUTLIER) cc_final: 0.8780 (mm-30) REVERT: A 321 MET cc_start: 0.9787 (mmp) cc_final: 0.9567 (mmm) REVERT: A 383 MET cc_start: 0.8634 (ttm) cc_final: 0.8297 (ttm) REVERT: A 399 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9102 (tp) REVERT: A 484 LYS cc_start: 0.9725 (mtpt) cc_final: 0.9203 (mtmm) REVERT: A 534 MET cc_start: 0.6699 (mtt) cc_final: 0.6316 (mtp) REVERT: A 651 LEU cc_start: 0.9211 (mt) cc_final: 0.8998 (mt) REVERT: A 662 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9285 (tp) REVERT: A 746 GLU cc_start: 0.9608 (tp30) cc_final: 0.9326 (tp30) REVERT: A 1097 LYS cc_start: 0.9389 (tptp) cc_final: 0.8710 (tptt) REVERT: A 1099 GLU cc_start: 0.9317 (mt-10) cc_final: 0.8547 (mt-10) REVERT: A 1213 MET cc_start: 0.9316 (ttm) cc_final: 0.8846 (tpp) REVERT: A 1313 PHE cc_start: 0.9527 (m-80) cc_final: 0.9255 (m-10) REVERT: A 1326 TYR cc_start: 0.9325 (t80) cc_final: 0.9107 (t80) outliers start: 23 outliers final: 17 residues processed: 113 average time/residue: 0.1103 time to fit residues: 17.3906 Evaluate side-chains 111 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1317 ASN Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1347 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 107 optimal weight: 40.0000 chunk 1 optimal weight: 0.4980 chunk 74 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 109 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 113 optimal weight: 40.0000 chunk 110 optimal weight: 30.0000 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.054211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.036430 restraints weight = 79969.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.037852 restraints weight = 42797.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.038757 restraints weight = 29410.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.039351 restraints weight = 23376.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.039570 restraints weight = 20214.057| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11733 Z= 0.190 Angle : 0.623 13.850 16421 Z= 0.347 Chirality : 0.041 0.231 1894 Planarity : 0.004 0.050 1599 Dihedral : 20.297 172.694 2981 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.96 % Allowed : 15.22 % Favored : 82.83 % 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: 0.51 (0.26), residues: 1017 helix: 0.96 (0.23), residues: 517 sheet: -0.23 (0.61), residues: 70 loop : -0.21 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 671 TYR 0.029 0.002 TYR A 517 PHE 0.015 0.002 PHE A 970 TRP 0.010 0.002 TRP A 659 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.19 (11733) covalent geometry : angle 0.62257 / 0.35 (16421) hydrogen bonds : bond 0.05965 / 4.08 ( 521) hydrogen bonds : angle 4.61401 / 3.29 ( 1394) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.9352 (OUTLIER) cc_final: 0.8776 (mm-30) REVERT: A 321 MET cc_start: 0.9773 (mmp) cc_final: 0.9505 (mmm) REVERT: A 383 MET cc_start: 0.8676 (ttm) cc_final: 0.8338 (ttm) REVERT: A 399 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9094 (tp) REVERT: A 484 LYS cc_start: 0.9721 (mtpt) cc_final: 0.9189 (mtmm) REVERT: A 510 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9251 (ptmm) REVERT: A 534 MET cc_start: 0.6753 (mtt) cc_final: 0.6271 (mtp) REVERT: A 651 LEU cc_start: 0.9248 (mt) cc_final: 0.9030 (mt) REVERT: A 662 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9257 (tp) REVERT: A 746 GLU cc_start: 0.9610 (tp30) cc_final: 0.9336 (tp30) REVERT: A 751 MET cc_start: 0.9195 (ttm) cc_final: 0.8964 (ttm) REVERT: A 1089 MET cc_start: 0.7703 (tpp) cc_final: 0.7132 (tpp) REVERT: A 1097 LYS cc_start: 0.9386 (tptp) cc_final: 0.8683 (tptt) REVERT: A 1099 GLU cc_start: 0.9297 (mt-10) cc_final: 0.8571 (mt-10) REVERT: A 1213 MET cc_start: 0.9289 (ttm) cc_final: 0.8887 (tpt) REVERT: A 1313 PHE cc_start: 0.9529 (m-80) cc_final: 0.9197 (m-10) outliers start: 18 outliers final: 11 residues processed: 103 average time/residue: 0.0940 time to fit residues: 14.0450 Evaluate side-chains 105 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1317 ASN Chi-restraints excluded: chain A residue 1318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 0.4980 chunk 79 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1262 HIS ** 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 = 0.3284 r_free = 0.3284 target = 0.055835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.038044 restraints weight = 77412.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.039528 restraints weight = 40975.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.040266 restraints weight = 27882.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.040906 restraints weight = 22752.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.041161 restraints weight = 19734.232| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11733 Z= 0.124 Angle : 0.617 15.033 16421 Z= 0.336 Chirality : 0.040 0.226 1894 Planarity : 0.004 0.048 1599 Dihedral : 20.219 170.371 2981 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.41 % Allowed : 16.20 % Favored : 82.39 % 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: 0.72 (0.26), residues: 1017 helix: 1.12 (0.23), residues: 516 sheet: 0.50 (0.66), residues: 64 loop : -0.20 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1212 TYR 0.064 0.002 TYR A 517 PHE 0.012 0.001 PHE A 164 TRP 0.006 0.001 TRP A 18 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (11733) covalent geometry : angle 0.61666 / 0.34 (16421) hydrogen bonds : bond 0.05031 / 3.53 ( 521) hydrogen bonds : angle 4.39606 / 3.14 ( 1394) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.9618 (ptpp) cc_final: 0.9374 (pttm) REVERT: A 125 GLU cc_start: 0.9410 (OUTLIER) cc_final: 0.8891 (mm-30) REVERT: A 398 LEU cc_start: 0.9493 (mt) cc_final: 0.9193 (mt) REVERT: A 399 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8884 (tp) REVERT: A 484 LYS cc_start: 0.9698 (mtpt) cc_final: 0.9229 (mttm) REVERT: A 534 MET cc_start: 0.6793 (mtt) cc_final: 0.6327 (mtp) REVERT: A 651 LEU cc_start: 0.9233 (mt) cc_final: 0.9016 (mt) REVERT: A 662 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9183 (tp) REVERT: A 751 MET cc_start: 0.9160 (ttm) cc_final: 0.8671 (ppp) REVERT: A 1089 MET cc_start: 0.7740 (tpp) cc_final: 0.7171 (tpp) REVERT: A 1097 LYS cc_start: 0.9426 (tptp) cc_final: 0.8744 (tptt) REVERT: A 1099 GLU cc_start: 0.9343 (mt-10) cc_final: 0.8599 (mt-10) REVERT: A 1213 MET cc_start: 0.9274 (ttm) cc_final: 0.8802 (tpp) REVERT: A 1313 PHE cc_start: 0.9491 (m-80) cc_final: 0.8868 (m-10) REVERT: A 1326 TYR cc_start: 0.9296 (t80) cc_final: 0.9070 (t80) REVERT: A 1365 LEU cc_start: 0.9661 (mm) cc_final: 0.9090 (pp) outliers start: 13 outliers final: 9 residues processed: 109 average time/residue: 0.0997 time to fit residues: 15.8533 Evaluate side-chains 108 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1317 ASN Chi-restraints excluded: chain A residue 1318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 66 optimal weight: 6.9990 chunk 107 optimal weight: 40.0000 chunk 65 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 33 optimal weight: 0.0870 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 83 optimal weight: 9.9990 overall best weight: 2.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1262 HIS ** 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 = 0.3279 r_free = 0.3279 target = 0.055621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.037774 restraints weight = 78320.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.039260 restraints weight = 41392.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.040190 restraints weight = 28158.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.040844 restraints weight = 22187.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.041226 restraints weight = 19035.240| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11733 Z= 0.126 Angle : 0.614 16.500 16421 Z= 0.332 Chirality : 0.039 0.218 1894 Planarity : 0.004 0.048 1599 Dihedral : 20.185 169.464 2981 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.63 % Allowed : 15.98 % Favored : 82.39 % 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: 0.80 (0.26), residues: 1017 helix: 1.19 (0.23), residues: 512 sheet: 0.65 (0.66), residues: 64 loop : -0.17 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 494 TYR 0.040 0.001 TYR A 517 PHE 0.010 0.001 PHE A 970 TRP 0.006 0.001 TRP A 18 HIS 0.005 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 (11733) covalent geometry : angle 0.61386 / 0.33 (16421) hydrogen bonds : bond 0.04931 / 3.44 ( 521) hydrogen bonds : angle 4.37268 / 3.12 ( 1394) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.9615 (ptpp) cc_final: 0.9373 (pttm) REVERT: A 125 GLU cc_start: 0.9405 (OUTLIER) cc_final: 0.8885 (mm-30) REVERT: A 398 LEU cc_start: 0.9494 (mt) cc_final: 0.9266 (mt) REVERT: A 484 LYS cc_start: 0.9701 (mtpt) cc_final: 0.9227 (mttm) REVERT: A 534 MET cc_start: 0.6711 (mtt) cc_final: 0.6215 (mtp) REVERT: A 651 LEU cc_start: 0.9224 (mt) cc_final: 0.9009 (mt) REVERT: A 662 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9156 (tp) REVERT: A 746 GLU cc_start: 0.9580 (tp30) cc_final: 0.9276 (tp30) REVERT: A 751 MET cc_start: 0.9210 (ttm) cc_final: 0.8714 (ppp) REVERT: A 1089 MET cc_start: 0.7744 (tpp) cc_final: 0.7164 (tpp) REVERT: A 1097 LYS cc_start: 0.9432 (tptp) cc_final: 0.8730 (tptt) REVERT: A 1099 GLU cc_start: 0.9356 (mt-10) cc_final: 0.8611 (mt-10) REVERT: A 1213 MET cc_start: 0.9243 (ttm) cc_final: 0.8766 (tpp) REVERT: A 1313 PHE cc_start: 0.9473 (m-80) cc_final: 0.8910 (m-10) REVERT: A 1365 LEU cc_start: 0.9660 (mm) cc_final: 0.9096 (pp) outliers start: 15 outliers final: 9 residues processed: 108 average time/residue: 0.0998 time to fit residues: 16.1291 Evaluate side-chains 108 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1317 ASN Chi-restraints excluded: chain A residue 1318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 95 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 102 optimal weight: 40.0000 chunk 57 optimal weight: 40.0000 chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 50.0000 chunk 81 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 85 optimal weight: 0.1980 chunk 54 optimal weight: 6.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1262 HIS ** 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 = 0.3247 r_free = 0.3247 target = 0.054183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.036500 restraints weight = 80212.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.037917 restraints weight = 42857.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.038801 restraints weight = 29374.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.039425 restraints weight = 23350.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.039712 restraints weight = 20074.535| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11733 Z= 0.186 Angle : 0.639 16.568 16421 Z= 0.351 Chirality : 0.040 0.221 1894 Planarity : 0.004 0.049 1599 Dihedral : 20.281 171.547 2981 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.30 % Allowed : 16.41 % Favored : 82.28 % 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: 0.61 (0.26), residues: 1017 helix: 1.05 (0.23), residues: 511 sheet: 0.53 (0.66), residues: 64 loop : -0.29 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 400 TYR 0.048 0.002 TYR A 517 PHE 0.015 0.002 PHE A 970 TRP 0.008 0.001 TRP A 659 HIS 0.011 0.002 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.19 (11733) covalent geometry : angle 0.63949 / 0.35 (16421) hydrogen bonds : bond 0.05668 / 3.88 ( 521) hydrogen bonds : angle 4.56048 / 3.27 ( 1394) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1736.92 seconds wall clock time: 30 minutes 50.58 seconds (1850.58 seconds total)