Starting phenix.real_space_refine on Fri Jul 3 01:36:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9waw_65827/07_2026/9waw_65827.cif Found real_map, /net/cci-nas-00/data/ceres_data/9waw_65827/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9waw_65827/07_2026/9waw_65827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9waw_65827/07_2026/9waw_65827.map" model { file = "/net/cci-nas-00/data/ceres_data/9waw_65827/07_2026/9waw_65827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9waw_65827/07_2026/9waw_65827.cif" } 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-dev-6108/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: 2.31, per 1000 atoms: 0.21 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: 0.78 Conformation dependent library (CDL) restraints added in 343.4 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: 0.96 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: 2.38 Time building geometry restraints manager: 1.08 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: 15337 1.02 - 2.04: 880 2.04 - 3.07: 168 3.07 - 4.09: 27 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=" N3 DT B 4 " pdb=" C4 DT B 4 " pdb=" O4 DT B 4 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+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 - 0.031: 1311 0.031 - 0.062: 375 0.062 - 0.093: 139 0.093 - 0.124: 59 0.124 - 0.155: 10 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 2.46 2.30 0.15 2.00e-01 2.50e+01 5.97e-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 2.46 2.31 0.15 2.00e-01 2.50e+01 5.79e-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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.820 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.570 ------------------------------------------------------------------------------- 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= 0.254 Angle : 0.549 5.111 16421 Z= 0.430 Chirality : 0.038 0.155 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 0.00306 / 0.25 (11733) covalent geometry : angle 0.54897 / 0.43 (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 : 0.372 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: 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: 0.8897 (m-80) REVERT: A 651 LEU cc_start: 0.9346 (mt) cc_final: 0.8956 (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: 0.5567 (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: 0.1279 time to fit residues: 38.7137 Evaluate side-chains 137 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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: 30.0000 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 30.0000 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 556 ASN ** A 595 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 = 0.3337 r_free = 0.3337 target = 0.059478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.040509 restraints weight = 74508.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.042070 restraints weight = 41196.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.043086 restraints weight = 28665.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.043653 restraints weight = 22773.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.044178 restraints weight = 19916.568| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 11733 Z= 0.200 Angle : 0.681 10.669 16421 Z= 0.379 Chirality : 0.044 0.303 1894 Planarity : 0.005 0.069 1599 Dihedral : 19.871 157.549 2981 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.07 % Allowed : 9.46 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.26), residues: 1017 helix: 1.64 (0.23), residues: 512 sheet: 1.16 (0.68), residues: 65 loop : 0.06 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 635 TYR 0.014 0.002 TYR A 973 PHE 0.021 0.002 PHE A1324 TRP 0.007 0.002 TRP A 18 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.20 (11733) covalent geometry : angle 0.68136 / 0.38 (16421) hydrogen bonds : bond 0.06948 / 4.71 ( 521) hydrogen bonds : angle 4.81534 / 3.45 ( 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 161 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.230 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: A 90 MET cc_start: 0.9261 (tpt) cc_final: 0.9030 (tpt) REVERT: A 383 MET cc_start: 0.7960 (ttm) cc_final: 0.7714 (tpp) REVERT: A 398 LEU cc_start: 0.9387 (mt) cc_final: 0.9128 (mt) REVERT: A 399 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8711 (tp) REVERT: A 423 LEU cc_start: 0.9755 (OUTLIER) cc_final: 0.9543 (mt) REVERT: A 484 LYS cc_start: 0.9668 (mtpt) cc_final: 0.9158 (mmtm) REVERT: A 651 LEU cc_start: 0.9208 (mt) cc_final: 0.8989 (mt) REVERT: A 746 GLU cc_start: 0.9400 (tp30) cc_final: 0.9150 (tp30) REVERT: A 929 LYS cc_start: 0.9690 (mttt) cc_final: 0.9477 (mmtt) REVERT: A 1089 MET cc_start: 0.8056 (tpp) cc_final: 0.7579 (tpp) REVERT: A 1097 LYS cc_start: 0.9386 (tptp) cc_final: 0.8998 (tptt) REVERT: A 1213 MET cc_start: 0.9348 (ttm) cc_final: 0.8863 (tpp) REVERT: A 1214 LEU cc_start: 0.9845 (tp) cc_final: 0.9587 (tp) REVERT: A 1258 PHE cc_start: 0.9380 (OUTLIER) cc_final: 0.9012 (m-80) REVERT: A 1365 LEU cc_start: 0.9568 (mt) cc_final: 0.8968 (pp) outliers start: 19 outliers final: 10 residues processed: 153 average time/residue: 0.1157 time to fit residues: 23.9571 Evaluate side-chains 124 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 1347 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 84 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 103 optimal weight: 30.0000 chunk 41 optimal weight: 40.0000 chunk 24 optimal weight: 8.9990 chunk 112 optimal weight: 40.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- 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** ** 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 = 0.3265 r_free = 0.3265 target = 0.055580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.037154 restraints weight = 79311.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.038580 restraints weight = 44311.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.039458 restraints weight = 31048.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.040074 restraints weight = 25044.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.040499 restraints weight = 21748.859| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 11733 Z= 0.307 Angle : 0.729 8.264 16421 Z= 0.416 Chirality : 0.045 0.221 1894 Planarity : 0.006 0.056 1599 Dihedral : 20.130 169.797 2981 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.39 % Allowed : 11.30 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.26), residues: 1017 helix: 0.84 (0.22), residues: 515 sheet: 0.58 (0.67), residues: 66 loop : -0.18 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 494 TYR 0.034 0.003 TYR A 517 PHE 0.024 0.002 PHE A1324 TRP 0.029 0.003 TRP A 659 HIS 0.008 0.002 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.31 (11733) covalent geometry : angle 0.72864 / 0.42 (16421) hydrogen bonds : bond 0.07649 / 5.12 ( 521) hydrogen bonds : angle 5.04906 / 3.59 ( 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 130 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.295 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 32 PHE cc_start: 0.9482 (m-80) cc_final: 0.9223 (m-80) REVERT: A 90 MET cc_start: 0.9301 (tpt) cc_final: 0.9053 (tpp) REVERT: A 321 MET cc_start: 0.9847 (mmp) cc_final: 0.9570 (mmm) REVERT: A 383 MET cc_start: 0.8090 (ttm) cc_final: 0.7694 (ttm) REVERT: A 398 LEU cc_start: 0.9499 (mt) cc_final: 0.9209 (mt) REVERT: A 399 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9060 (tp) REVERT: A 484 LYS cc_start: 0.9726 (mtpt) cc_final: 0.9192 (mmtp) REVERT: A 534 MET cc_start: 0.6571 (mtt) cc_final: 0.6132 (mtp) REVERT: A 651 LEU cc_start: 0.9261 (mt) cc_final: 0.9009 (mt) REVERT: A 746 GLU cc_start: 0.9515 (tp30) cc_final: 0.9245 (tp30) REVERT: A 1089 MET cc_start: 0.8042 (tpp) cc_final: 0.7806 (tpp) REVERT: A 1097 LYS cc_start: 0.9358 (tptp) cc_final: 0.8894 (tptt) REVERT: A 1213 MET cc_start: 0.9281 (ttm) cc_final: 0.8863 (tpp) REVERT: A 1268 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8808 (mp0) REVERT: A 1313 PHE cc_start: 0.9565 (m-80) cc_final: 0.9223 (m-10) REVERT: A 1324 PHE cc_start: 0.8063 (p90) cc_final: 0.7821 (p90) outliers start: 22 outliers final: 12 residues processed: 121 average time/residue: 0.0991 time to fit residues: 16.7394 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 : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU 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 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 1318 LEU 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: 9.9990 chunk 52 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.3275 r_free = 0.3275 target = 0.055878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.037640 restraints weight = 78938.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.039121 restraints weight = 42386.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.040071 restraints weight = 29203.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.040621 restraints weight = 23218.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.041024 restraints weight = 20204.251| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11733 Z= 0.211 Angle : 0.634 9.106 16421 Z= 0.359 Chirality : 0.042 0.222 1894 Planarity : 0.004 0.054 1599 Dihedral : 20.225 171.879 2981 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.39 % Allowed : 11.74 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.26), residues: 1017 helix: 0.93 (0.23), residues: 505 sheet: 0.34 (0.66), residues: 66 loop : -0.14 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 494 TYR 0.032 0.002 TYR A 517 PHE 0.020 0.002 PHE A1324 TRP 0.009 0.002 TRP A 18 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.21 (11733) covalent geometry : angle 0.63378 / 0.36 (16421) hydrogen bonds : bond 0.06370 / 4.36 ( 521) hydrogen bonds : angle 4.78536 / 3.41 ( 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 124 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.331 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 32 PHE cc_start: 0.9493 (m-80) cc_final: 0.9148 (m-80) REVERT: A 90 MET cc_start: 0.9289 (tpt) cc_final: 0.9061 (tpp) REVERT: A 321 MET cc_start: 0.9783 (mmp) cc_final: 0.9318 (mmm) REVERT: A 383 MET cc_start: 0.8204 (ttm) cc_final: 0.7840 (ttm) REVERT: A 398 LEU cc_start: 0.9534 (mt) cc_final: 0.9216 (mt) REVERT: A 399 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8952 (tp) REVERT: A 484 LYS cc_start: 0.9717 (mtpt) cc_final: 0.9155 (mmtp) REVERT: A 534 MET cc_start: 0.6677 (mtt) cc_final: 0.6162 (mtp) REVERT: A 746 GLU cc_start: 0.9537 (tp30) cc_final: 0.9228 (tp30) REVERT: A 1089 MET cc_start: 0.8014 (tpp) cc_final: 0.7752 (tpp) REVERT: A 1097 LYS cc_start: 0.9360 (tptp) cc_final: 0.8917 (tptt) REVERT: A 1213 MET cc_start: 0.9303 (ttm) cc_final: 0.8883 (tpp) REVERT: A 1313 PHE cc_start: 0.9548 (m-80) cc_final: 0.9102 (m-10) outliers start: 22 outliers final: 13 residues processed: 117 average time/residue: 0.0947 time to fit residues: 15.8589 Evaluate side-chains 114 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 128 TYR 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 667 ILE 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 1263 LYS Chi-restraints excluded: chain A residue 1318 LEU 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: 5.9990 chunk 54 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 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 = 0.3246 r_free = 0.3246 target = 0.054368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.036457 restraints weight = 79254.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.037866 restraints weight = 43156.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.038750 restraints weight = 29846.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.039349 restraints weight = 23876.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.039672 restraints weight = 20691.810| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 11733 Z= 0.233 Angle : 0.646 10.346 16421 Z= 0.365 Chirality : 0.043 0.237 1894 Planarity : 0.005 0.053 1599 Dihedral : 20.319 172.308 2981 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.07 % Allowed : 13.37 % Favored : 84.57 % 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: 0.45 (0.26), residues: 1017 helix: 0.83 (0.23), residues: 507 sheet: 0.53 (0.71), residues: 56 loop : -0.22 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 494 TYR 0.034 0.002 TYR A 517 PHE 0.019 0.002 PHE A 164 TRP 0.010 0.002 TRP A 659 HIS 0.006 0.002 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.23 (11733) covalent geometry : angle 0.64550 / 0.36 (16421) hydrogen bonds : bond 0.06630 / 4.49 ( 521) hydrogen bonds : angle 4.84734 / 3.44 ( 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 118 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.293 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: A 32 PHE cc_start: 0.9500 (m-80) cc_final: 0.9141 (m-80) REVERT: A 90 MET cc_start: 0.9318 (tpt) cc_final: 0.9069 (tpt) REVERT: A 321 MET cc_start: 0.9802 (mmp) cc_final: 0.9512 (mmm) REVERT: A 399 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9058 (tp) REVERT: A 484 LYS cc_start: 0.9738 (mtpt) cc_final: 0.9182 (mmtp) REVERT: A 534 MET cc_start: 0.6632 (mtt) cc_final: 0.6147 (mtp) REVERT: A 569 PHE cc_start: 0.9551 (m-80) cc_final: 0.9309 (m-80) REVERT: A 746 GLU cc_start: 0.9560 (tp30) cc_final: 0.9216 (tp30) REVERT: A 751 MET cc_start: 0.9278 (ttm) cc_final: 0.9042 (ttm) REVERT: A 1089 MET cc_start: 0.7924 (tpp) cc_final: 0.7678 (tpp) REVERT: A 1097 LYS cc_start: 0.9369 (tptp) cc_final: 0.8923 (tptt) REVERT: A 1213 MET cc_start: 0.9310 (ttm) cc_final: 0.8937 (tpt) REVERT: A 1313 PHE cc_start: 0.9575 (m-80) cc_final: 0.9104 (m-10) REVERT: A 1326 TYR cc_start: 0.9371 (t80) cc_final: 0.9131 (t80) outliers start: 19 outliers final: 14 residues processed: 114 average time/residue: 0.0978 time to fit residues: 15.6887 Evaluate side-chains 108 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 70 ARG 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 440 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 625 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 1263 LYS Chi-restraints excluded: chain A residue 1318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** A 595 HIS ** 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 = 0.3262 r_free = 0.3262 target = 0.055093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.037199 restraints weight = 79323.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.038661 restraints weight = 42602.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.039607 restraints weight = 29186.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.040146 restraints weight = 23123.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.040548 restraints weight = 20072.424| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11733 Z= 0.169 Angle : 0.620 12.212 16421 Z= 0.344 Chirality : 0.041 0.235 1894 Planarity : 0.004 0.052 1599 Dihedral : 20.301 171.919 2981 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.85 % Allowed : 13.80 % Favored : 84.35 % 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: 0.96 (0.23), residues: 508 sheet: 0.39 (0.67), residues: 64 loop : -0.13 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 494 TYR 0.030 0.002 TYR A 517 PHE 0.016 0.002 PHE A 164 TRP 0.008 0.001 TRP A 18 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (11733) covalent geometry : angle 0.62029 / 0.34 (16421) hydrogen bonds : bond 0.05810 / 3.99 ( 521) hydrogen bonds : angle 4.67890 / 3.31 ( 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: 17 poor density : 102 time to evaluate : 0.362 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 32 PHE cc_start: 0.9496 (m-80) cc_final: 0.9115 (m-80) REVERT: A 125 GLU cc_start: 0.9381 (OUTLIER) cc_final: 0.8829 (mm-30) REVERT: A 161 MET cc_start: 0.9706 (mmp) cc_final: 0.9113 (mmp) REVERT: A 398 LEU cc_start: 0.9539 (mt) cc_final: 0.9224 (mt) REVERT: A 399 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8973 (tp) REVERT: A 484 LYS cc_start: 0.9721 (mtpt) cc_final: 0.9159 (mmtp) REVERT: A 534 MET cc_start: 0.6672 (mtt) cc_final: 0.6275 (mtp) REVERT: A 746 GLU cc_start: 0.9567 (tp30) cc_final: 0.9322 (tp30) REVERT: A 1089 MET cc_start: 0.7940 (tpp) cc_final: 0.7491 (tpp) REVERT: A 1097 LYS cc_start: 0.9408 (tptp) cc_final: 0.8692 (tptt) REVERT: A 1099 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8505 (mt-10) REVERT: A 1169 MET cc_start: 0.8580 (tpt) cc_final: 0.8321 (tpt) REVERT: A 1213 MET cc_start: 0.9302 (ttm) cc_final: 0.8899 (tpt) REVERT: A 1313 PHE cc_start: 0.9531 (m-80) cc_final: 0.9024 (m-10) outliers start: 17 outliers final: 11 residues processed: 113 average time/residue: 0.0938 time to fit residues: 15.1751 Evaluate side-chains 109 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 416 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 743 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 1318 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: 9.9990 chunk 50 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 56 optimal weight: 0.0010 chunk 108 optimal weight: 30.0000 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 overall best weight: 3.5992 ------------------------------------------------------------------------------- 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** ** 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 = 0.3266 r_free = 0.3266 target = 0.055166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.037198 restraints weight = 78027.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.038662 restraints weight = 41628.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.039581 restraints weight = 28444.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.040193 restraints weight = 22533.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.040616 restraints weight = 19436.268| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11733 Z= 0.153 Angle : 0.594 12.700 16421 Z= 0.332 Chirality : 0.041 0.235 1894 Planarity : 0.004 0.050 1599 Dihedral : 20.250 170.402 2981 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.85 % Allowed : 14.89 % Favored : 83.26 % 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: 0.68 (0.26), residues: 1017 helix: 1.06 (0.23), residues: 505 sheet: 0.56 (0.70), residues: 64 loop : -0.16 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 494 TYR 0.031 0.002 TYR A 517 PHE 0.016 0.002 PHE A 164 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 0.00292 / 0.15 (11733) covalent geometry : angle 0.59401 / 0.33 (16421) hydrogen bonds : bond 0.05404 / 3.73 ( 521) hydrogen bonds : angle 4.58060 / 3.25 ( 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 117 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 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: A 32 PHE cc_start: 0.9501 (m-80) cc_final: 0.9124 (m-80) REVERT: A 125 GLU cc_start: 0.9383 (OUTLIER) cc_final: 0.8820 (mm-30) REVERT: A 161 MET cc_start: 0.9710 (mmp) cc_final: 0.9144 (mmp) REVERT: A 398 LEU cc_start: 0.9505 (mt) cc_final: 0.9198 (mt) REVERT: A 399 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8951 (tp) REVERT: A 484 LYS cc_start: 0.9716 (mtpt) cc_final: 0.9131 (mmtp) REVERT: A 534 MET cc_start: 0.6672 (mtt) cc_final: 0.6163 (mtp) REVERT: A 746 GLU cc_start: 0.9621 (tp30) cc_final: 0.9297 (tp30) REVERT: A 1089 MET cc_start: 0.8019 (tpp) cc_final: 0.7567 (tpp) REVERT: A 1097 LYS cc_start: 0.9418 (tptp) cc_final: 0.8713 (tptt) REVERT: A 1099 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8563 (mt-10) REVERT: A 1169 MET cc_start: 0.8548 (tpt) cc_final: 0.8236 (tpt) REVERT: A 1213 MET cc_start: 0.9280 (ttm) cc_final: 0.8864 (tpt) REVERT: A 1313 PHE cc_start: 0.9554 (m-80) cc_final: 0.9013 (m-10) REVERT: A 1326 TYR cc_start: 0.9348 (t80) cc_final: 0.9075 (t80) outliers start: 17 outliers final: 10 residues processed: 110 average time/residue: 0.1011 time to fit residues: 15.7366 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 : 0.349 ------------------------------------------------------------------------------- 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 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 1318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 107 optimal weight: 30.0000 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 113 optimal weight: 30.0000 chunk 110 optimal weight: 20.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- 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 394 ASN ** A 595 HIS ** 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 = 0.3195 r_free = 0.3195 target = 0.051664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.034217 restraints weight = 82449.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.035532 restraints weight = 45468.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.036346 restraints weight = 31684.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.036910 restraints weight = 25488.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.037236 restraints weight = 22100.475| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 11733 Z= 0.332 Angle : 0.766 14.026 16421 Z= 0.427 Chirality : 0.045 0.242 1894 Planarity : 0.005 0.051 1599 Dihedral : 20.588 175.129 2981 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 24.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.28 % Allowed : 15.43 % 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: -0.17 (0.25), residues: 1017 helix: 0.25 (0.22), residues: 512 sheet: 0.10 (0.69), residues: 54 loop : -0.43 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 494 TYR 0.026 0.002 TYR A 517 PHE 0.020 0.003 PHE A 164 TRP 0.021 0.003 TRP A 659 HIS 0.007 0.003 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.33 (11733) covalent geometry : angle 0.76573 / 0.43 (16421) hydrogen bonds : bond 0.07884 / 5.24 ( 521) hydrogen bonds : angle 5.18680 / 3.70 ( 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 112 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.328 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 32 PHE cc_start: 0.9482 (m-80) cc_final: 0.9121 (m-80) REVERT: A 70 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8122 (ttp-170) REVERT: A 125 GLU cc_start: 0.9228 (OUTLIER) cc_final: 0.8735 (mm-30) REVERT: A 399 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9116 (tp) REVERT: A 484 LYS cc_start: 0.9763 (mtpt) cc_final: 0.9251 (mtmm) REVERT: A 534 MET cc_start: 0.6567 (mtt) cc_final: 0.6020 (mtp) REVERT: A 746 GLU cc_start: 0.9635 (tp30) cc_final: 0.9403 (tp30) REVERT: A 1097 LYS cc_start: 0.9362 (tptp) cc_final: 0.8644 (tptt) REVERT: A 1099 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8505 (mt-10) REVERT: A 1122 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8291 (mtm110) REVERT: A 1169 MET cc_start: 0.8649 (tpt) cc_final: 0.8330 (tpt) REVERT: A 1213 MET cc_start: 0.9303 (ttm) cc_final: 0.8890 (tpt) REVERT: A 1313 PHE cc_start: 0.9563 (m-80) cc_final: 0.9054 (m-10) REVERT: A 1326 TYR cc_start: 0.9386 (t80) cc_final: 0.9154 (t80) outliers start: 21 outliers final: 15 residues processed: 104 average time/residue: 0.0984 time to fit residues: 14.1211 Evaluate side-chains 107 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 70 ARG 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 474 THR Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 741 VAL 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 1122 ARG Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** A 595 HIS ** 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 = 0.3244 r_free = 0.3244 target = 0.054241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.036555 restraints weight = 79854.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.038006 restraints weight = 42725.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.038881 restraints weight = 29167.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.039501 restraints weight = 23257.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.039827 restraints weight = 20061.166| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11733 Z= 0.157 Angle : 0.648 15.677 16421 Z= 0.357 Chirality : 0.042 0.292 1894 Planarity : 0.004 0.049 1599 Dihedral : 20.523 171.742 2981 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.41 % Allowed : 16.09 % Favored : 82.50 % 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: 0.32 (0.26), residues: 1017 helix: 0.83 (0.23), residues: 505 sheet: -0.44 (0.66), residues: 62 loop : -0.29 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 494 TYR 0.058 0.002 TYR A 517 PHE 0.017 0.002 PHE A 164 TRP 0.006 0.001 TRP A 18 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (11733) covalent geometry : angle 0.64767 / 0.36 (16421) hydrogen bonds : bond 0.05660 / 3.92 ( 521) hydrogen bonds : angle 4.73689 / 3.36 ( 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 110 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.253 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 32 PHE cc_start: 0.9437 (m-80) cc_final: 0.9036 (m-80) REVERT: A 125 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8750 (mm-30) REVERT: A 399 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9057 (tp) REVERT: A 484 LYS cc_start: 0.9715 (mtpt) cc_final: 0.9182 (mtmm) REVERT: A 534 MET cc_start: 0.6714 (mtt) cc_final: 0.6207 (mtp) REVERT: A 746 GLU cc_start: 0.9611 (tp30) cc_final: 0.9334 (tp30) REVERT: A 1089 MET cc_start: 0.8105 (mmt) cc_final: 0.7479 (tpp) REVERT: A 1097 LYS cc_start: 0.9405 (tptp) cc_final: 0.8690 (tptt) REVERT: A 1099 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8572 (mt-10) REVERT: A 1169 MET cc_start: 0.8599 (tpt) cc_final: 0.8289 (tpt) REVERT: A 1213 MET cc_start: 0.9309 (ttm) cc_final: 0.8797 (tpp) REVERT: A 1313 PHE cc_start: 0.9533 (m-80) cc_final: 0.8962 (m-10) REVERT: A 1326 TYR cc_start: 0.9393 (t80) cc_final: 0.9104 (t80) outliers start: 13 outliers final: 10 residues processed: 104 average time/residue: 0.0978 time to fit residues: 14.3456 Evaluate side-chains 106 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 174 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 510 LYS 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 1318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 66 optimal weight: 8.9990 chunk 107 optimal weight: 30.0000 chunk 65 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 44 optimal weight: 30.0000 chunk 40 optimal weight: 5.9990 chunk 46 optimal weight: 30.0000 chunk 83 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** A 595 HIS ** 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 = 0.3211 r_free = 0.3211 target = 0.052468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.035003 restraints weight = 81956.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.036354 restraints weight = 44652.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.037204 restraints weight = 30874.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.037800 restraints weight = 24675.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.038013 restraints weight = 21318.192| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 11733 Z= 0.253 Angle : 0.702 16.583 16421 Z= 0.389 Chirality : 0.043 0.241 1894 Planarity : 0.004 0.050 1599 Dihedral : 20.593 171.979 2981 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.52 % Allowed : 16.30 % Favored : 82.17 % 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: 0.08 (0.26), residues: 1017 helix: 0.57 (0.23), residues: 512 sheet: 0.15 (0.70), residues: 54 loop : -0.45 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1122 TYR 0.023 0.002 TYR A 517 PHE 0.014 0.002 PHE A1080 TRP 0.011 0.002 TRP A 659 HIS 0.007 0.002 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.25 (11733) covalent geometry : angle 0.70234 / 0.39 (16421) hydrogen bonds : bond 0.06505 / 4.41 ( 521) hydrogen bonds : angle 4.95722 / 3.54 ( 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 103 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.306 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 32 PHE cc_start: 0.9459 (m-80) cc_final: 0.9012 (m-80) REVERT: A 125 GLU cc_start: 0.9210 (OUTLIER) cc_final: 0.8588 (mm-30) REVERT: A 383 MET cc_start: 0.8248 (tpt) cc_final: 0.8000 (tpt) REVERT: A 399 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9160 (tp) REVERT: A 484 LYS cc_start: 0.9743 (mtpt) cc_final: 0.9539 (ttmm) REVERT: A 534 MET cc_start: 0.6809 (mtt) cc_final: 0.6319 (mtp) REVERT: A 1089 MET cc_start: 0.8072 (mmt) cc_final: 0.7252 (tpp) REVERT: A 1097 LYS cc_start: 0.9368 (tptp) cc_final: 0.8641 (tptt) REVERT: A 1099 GLU cc_start: 0.9308 (mt-10) cc_final: 0.8540 (mt-10) REVERT: A 1169 MET cc_start: 0.8563 (tpt) cc_final: 0.8247 (tpt) REVERT: A 1213 MET cc_start: 0.9328 (ttm) cc_final: 0.8889 (tpt) REVERT: A 1313 PHE cc_start: 0.9551 (m-80) cc_final: 0.9265 (m-10) REVERT: A 1326 TYR cc_start: 0.9452 (t80) cc_final: 0.9196 (t80) outliers start: 14 outliers final: 12 residues processed: 97 average time/residue: 0.0999 time to fit residues: 13.6470 Evaluate side-chains 101 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 174 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 517 TYR 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 1318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 95 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 102 optimal weight: 40.0000 chunk 57 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** A 595 HIS ** 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 = 0.3215 r_free = 0.3215 target = 0.052554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.035239 restraints weight = 82878.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.036638 restraints weight = 44827.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.037540 restraints weight = 30787.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.037956 restraints weight = 24326.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.038325 restraints weight = 21495.319| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.176 11733 Z= 0.313 Angle : 0.924 59.194 16421 Z= 0.553 Chirality : 0.044 0.268 1894 Planarity : 0.004 0.050 1599 Dihedral : 20.597 171.953 2981 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.85 % Allowed : 15.87 % Favored : 82.28 % Cbeta Deviations : 0.10 % 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: 0.08 (0.26), residues: 1017 helix: 0.56 (0.23), residues: 512 sheet: 0.14 (0.70), residues: 54 loop : -0.44 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1122 TYR 0.021 0.002 TYR A 517 PHE 0.015 0.002 PHE A 164 TRP 0.011 0.002 TRP A 659 HIS 0.006 0.002 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.31 (11733) covalent geometry : angle 0.92404 / 0.55 (16421) hydrogen bonds : bond 0.06501 / 4.41 ( 521) hydrogen bonds : angle 4.95815 / 3.54 ( 1394) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1714.66 seconds wall clock time: 30 minutes 24.10 seconds (1824.10 seconds total)