Starting phenix.real_space_refine on Thu Jun 12 17:16:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z4i_14498/06_2025/7z4i_14498.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4i_14498/06_2025/7z4i_14498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z4i_14498/06_2025/7z4i_14498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4i_14498/06_2025/7z4i_14498.map" model { file = "/net/cci-nas-00/data/ceres_data/7z4i_14498/06_2025/7z4i_14498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4i_14498/06_2025/7z4i_14498.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.008 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 134 5.49 5 S 22 5.16 5 C 8290 2.51 5 N 2417 2.21 5 O 2955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13820 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 2055 Classifications: {'RNA': 96} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 51, 'rna3p_pyr': 33} Link IDs: {'rna2p': 12, 'rna3p': 83} Chain: "C" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 565 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "D" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 249 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DT%5*END:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 10949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 10949 Classifications: {'peptide': 1338} Link IDs: {'PTRANS': 35, 'TRANS': 1302} Chain breaks: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.63, per 1000 atoms: 0.70 Number of scatterers: 13820 At special positions: 0 Unit cell: (90.35, 123.5, 120.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 22 16.00 P 134 15.00 O 2955 8.00 N 2417 7.00 C 8290 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: 3.78 Conformation dependent library (CDL) restraints added in 1.3 seconds 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2548 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 12 sheets defined 54.5% alpha, 9.7% beta 49 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 6.04 Creating SS restraints... Processing helix chain 'B' and resid 59 through 94 removed outlier: 5.222A pdb=" N ASN B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLU B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 103 Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 134 through 145 removed outlier: 3.621A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 217 through 229 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.738A pdb=" N PHE B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 282 Processing helix chain 'B' and resid 285 through 306 removed outlier: 4.219A pdb=" N LEU B 289 " --> pdb=" O GLN B 285 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 343 Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 368 through 382 Proline residue: B 378 - end of helix Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.527A pdb=" N ASN B 407 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 408 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 removed outlier: 4.159A pdb=" N HIS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 483 through 496 removed outlier: 4.109A pdb=" N MET B 495 " --> pdb=" O PHE B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 526 Processing helix chain 'B' and resid 541 through 552 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.554A pdb=" N TYR B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 604 through 609 Processing helix chain 'B' and resid 612 through 626 removed outlier: 3.631A pdb=" N LEU B 616 " --> pdb=" O ASN B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 637 removed outlier: 3.571A pdb=" N ILE B 632 " --> pdb=" O ASP B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 644 through 654 removed outlier: 3.671A pdb=" N ARG B 653 " --> pdb=" O LYS B 649 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 Processing helix chain 'B' and resid 678 through 685 Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 702 through 712 removed outlier: 4.486A pdb=" N GLU B 706 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 Processing helix chain 'B' and resid 730 through 751 Processing helix chain 'B' and resid 776 through 792 Processing helix chain 'B' and resid 794 through 799 removed outlier: 3.780A pdb=" N HIS B 799 " --> pdb=" O ILE B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 807 Processing helix chain 'B' and resid 808 through 817 Processing helix chain 'B' and resid 851 through 853 No H-bonds generated for 'chain 'B' and resid 851 through 853' Processing helix chain 'B' and resid 860 through 865 Processing helix chain 'B' and resid 872 through 889 removed outlier: 5.681A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TYR B 882 " --> pdb=" O LYS B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 901 Processing helix chain 'B' and resid 909 through 919 Processing helix chain 'B' and resid 925 through 940 Processing helix chain 'B' and resid 959 through 970 removed outlier: 3.970A pdb=" N VAL B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.238A pdb=" N ALA B 984 " --> pdb=" O ASN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1009 Processing helix chain 'B' and resid 1032 through 1041 Processing helix chain 'B' and resid 1078 through 1088 Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1168 through 1177 removed outlier: 4.595A pdb=" N SER B1172 " --> pdb=" O ILE B1168 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N SER B1173 " --> pdb=" O MET B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1186 Processing helix chain 'B' and resid 1229 through 1241 removed outlier: 3.571A pdb=" N HIS B1241 " --> pdb=" O TYR B1237 " (cutoff:3.500A) Processing helix chain 'B' and resid 1248 through 1262 Processing helix chain 'B' and resid 1263 through 1280 removed outlier: 4.305A pdb=" N ASP B1267 " --> pdb=" O LYS B1263 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1297 Processing helix chain 'B' and resid 1301 through 1313 removed outlier: 3.526A pdb=" N PHE B1313 " --> pdb=" O ILE B1309 " (cutoff:3.500A) Processing helix chain 'B' and resid 1314 through 1316 No H-bonds generated for 'chain 'B' and resid 1314 through 1316' Processing helix chain 'B' and resid 1340 through 1344 Processing helix chain 'B' and resid 1363 through 1365 No H-bonds generated for 'chain 'B' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'B' and resid 954 through 958 removed outlier: 6.238A pdb=" N ILE B 759 " --> pdb=" O ILE B 956 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU B 958 " --> pdb=" O ILE B 759 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE B 761 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 46 removed outlier: 9.873A pdb=" N GLU B1357 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS B 33 " --> pdb=" O GLU B1357 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ARG B1359 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU B 35 " --> pdb=" O ARG B1359 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ASP B1361 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU B1203 " --> pdb=" O ILE B1348 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER B1202 " --> pdb=" O LEU B1214 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU B1219 " --> pdb=" O ALA B1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 507 through 509 removed outlier: 5.146A pdb=" N LEU B 508 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 528 through 531 Processing sheet with id=AA5, first strand: chain 'B' and resid 837 through 840 Processing sheet with id=AA6, first strand: chain 'B' and resid 943 through 944 removed outlier: 3.708A pdb=" N LYS B 948 " --> pdb=" O ASP B 944 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1049 through 1050 Processing sheet with id=AA8, first strand: chain 'B' and resid 1063 through 1065 removed outlier: 3.911A pdb=" N TRP B1074 " --> pdb=" O GLU B1064 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AB1, first strand: chain 'B' and resid 1156 through 1163 Processing sheet with id=AB2, first strand: chain 'B' and resid 1156 through 1163 Processing sheet with id=AB3, first strand: chain 'B' and resid 1324 through 1326 528 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 120 hydrogen bonds 232 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 7.69 Time building geometry restraints manager: 4.44 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: 2499 1.33 - 1.45: 4103 1.45 - 1.57: 7443 1.57 - 1.69: 268 1.69 - 1.81: 42 Bond restraints: 14355 Sorted by residual: bond pdb=" N ASN B 77 " pdb=" CA ASN B 77 " ideal model delta sigma weight residual 1.458 1.407 0.052 1.26e-02 6.30e+03 1.68e+01 bond pdb=" CA SER B1109 " pdb=" C SER B1109 " ideal model delta sigma weight residual 1.524 1.482 0.042 1.30e-02 5.92e+03 1.03e+01 bond pdb=" C LYS B 76 " pdb=" N ASN B 77 " ideal model delta sigma weight residual 1.334 1.289 0.045 1.43e-02 4.89e+03 1.01e+01 bond pdb=" CA LYS B 209 " pdb=" C LYS B 209 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.24e-02 6.50e+03 4.32e+00 bond pdb=" N ASN B 588 " pdb=" CA ASN B 588 " ideal model delta sigma weight residual 1.459 1.435 0.024 1.20e-02 6.94e+03 4.15e+00 ... (remaining 14350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 19362 1.12 - 2.25: 483 2.25 - 3.37: 98 3.37 - 4.49: 13 4.49 - 5.62: 5 Bond angle restraints: 19961 Sorted by residual: angle pdb=" N ASN B 77 " pdb=" CA ASN B 77 " pdb=" C ASN B 77 " ideal model delta sigma weight residual 111.69 106.27 5.42 1.23e+00 6.61e-01 1.94e+01 angle pdb=" N ASN B 588 " pdb=" CA ASN B 588 " pdb=" C ASN B 588 " ideal model delta sigma weight residual 111.14 107.52 3.62 1.08e+00 8.57e-01 1.13e+01 angle pdb=" C LYS B 76 " pdb=" N ASN B 77 " pdb=" CA ASN B 77 " ideal model delta sigma weight residual 120.58 114.96 5.62 1.71e+00 3.42e-01 1.08e+01 angle pdb=" N TYR B 981 " pdb=" CA TYR B 981 " pdb=" C TYR B 981 " ideal model delta sigma weight residual 112.54 109.14 3.40 1.22e+00 6.72e-01 7.75e+00 angle pdb=" C PHE B 587 " pdb=" N ASN B 588 " pdb=" CA ASN B 588 " ideal model delta sigma weight residual 120.44 117.10 3.34 1.36e+00 5.41e-01 6.02e+00 ... (remaining 19956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.05: 8049 27.05 - 54.10: 505 54.10 - 81.15: 176 81.15 - 108.20: 4 108.20 - 135.25: 1 Dihedral angle restraints: 8735 sinusoidal: 4798 harmonic: 3937 Sorted by residual: dihedral pdb=" C4' DG C 16 " pdb=" C3' DG C 16 " pdb=" O3' DG C 16 " pdb=" P DA C 17 " ideal model delta sinusoidal sigma weight residual 220.00 84.75 135.25 1 3.50e+01 8.16e-04 1.34e+01 dihedral pdb=" O4' G A 82 " pdb=" C1' G A 82 " pdb=" N9 G A 82 " pdb=" C4 G A 82 " ideal model delta sinusoidal sigma weight residual 70.00 11.76 58.24 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ILE B 300 " pdb=" C ILE B 300 " pdb=" N LEU B 301 " pdb=" CA LEU B 301 " ideal model delta harmonic sigma weight residual -180.00 -164.15 -15.85 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 8732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1730 0.036 - 0.073: 435 0.073 - 0.109: 90 0.109 - 0.145: 27 0.145 - 0.182: 3 Chirality restraints: 2285 Sorted by residual: chirality pdb=" CA ASN B 77 " pdb=" N ASN B 77 " pdb=" C ASN B 77 " pdb=" CB ASN B 77 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" C1' A A 35 " pdb=" O4' A A 35 " pdb=" C2' A A 35 " pdb=" N9 A A 35 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" C1' A A 42 " pdb=" O4' A A 42 " pdb=" C2' A A 42 " pdb=" N9 A A 42 " both_signs ideal model delta sigma weight residual False 2.46 2.30 0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 2282 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 980 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C ASN B 980 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN B 980 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR B 981 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B1273 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C ILE B1273 " 0.033 2.00e-02 2.50e+03 pdb=" O ILE B1273 " -0.012 2.00e-02 2.50e+03 pdb=" N SER B1274 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 76 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.48e+00 pdb=" C LYS B 76 " 0.032 2.00e-02 2.50e+03 pdb=" O LYS B 76 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN B 77 " -0.011 2.00e-02 2.50e+03 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 3794 2.82 - 3.40: 14916 3.40 - 3.98: 29195 3.98 - 4.56: 39302 4.56 - 5.14: 53744 Nonbonded interactions: 140951 Sorted by model distance: nonbonded pdb=" O2' A A 47 " pdb=" O LEU B 101 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR B1232 " pdb=" OE1 GLU B1268 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASP B1361 " pdb=" OG SER B1363 " model vdw 2.256 3.040 nonbonded pdb=" OD1 ASN B 14 " pdb=" OG SER B 55 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR B 474 " pdb=" OD1 ASN B 477 " model vdw 2.263 3.040 ... (remaining 140946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 42.210 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 0.052 14355 Z= 0.182 Angle : 0.464 5.617 19961 Z= 0.258 Chirality : 0.036 0.182 2285 Planarity : 0.004 0.044 2055 Dihedral : 17.482 135.253 6187 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.58 % Allowed : 5.91 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.23), residues: 1330 helix: 1.18 (0.20), residues: 668 sheet: -0.27 (0.45), residues: 135 loop : 0.08 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 464 HIS 0.003 0.001 HIS B 328 PHE 0.010 0.001 PHE B1046 TYR 0.010 0.001 TYR B 155 ARG 0.003 0.001 ARG B 653 Details of bonding type rmsd hydrogen bonds : bond 0.12956 ( 640) hydrogen bonds : angle 5.33417 ( 1756) covalent geometry : bond 0.00336 (14355) covalent geometry : angle 0.46424 (19961) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 LEU cc_start: 0.8689 (tp) cc_final: 0.8312 (tp) REVERT: B 263 LYS cc_start: 0.9151 (mttt) cc_final: 0.8950 (mmmm) REVERT: B 470 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7443 (tp30) REVERT: B 610 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8078 (tp30) REVERT: B 795 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8105 (tt) REVERT: B 879 MET cc_start: 0.7247 (mmm) cc_final: 0.6935 (tpp) REVERT: B 911 LEU cc_start: 0.9610 (mt) cc_final: 0.9390 (tp) REVERT: B 1037 PHE cc_start: 0.8485 (p90) cc_final: 0.7947 (p90) outliers start: 7 outliers final: 2 residues processed: 135 average time/residue: 0.3729 time to fit residues: 68.2977 Evaluate side-chains 61 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 1145 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.5980 chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 37 optimal weight: 0.0570 chunk 74 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 43 optimal weight: 0.4980 chunk 69 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 HIS B 712 GLN B 807 GLN B 826 GLN B 854 ASN B 926 GLN B1041 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.088446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.064792 restraints weight = 47756.890| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.56 r_work: 0.3097 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14355 Z= 0.111 Angle : 0.474 6.754 19961 Z= 0.256 Chirality : 0.035 0.148 2285 Planarity : 0.004 0.049 2055 Dihedral : 18.700 137.457 3345 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.00 % Allowed : 9.23 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.23), residues: 1330 helix: 1.56 (0.20), residues: 685 sheet: 0.03 (0.47), residues: 126 loop : 0.05 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 464 HIS 0.006 0.001 HIS B 116 PHE 0.014 0.001 PHE B 196 TYR 0.021 0.001 TYR B1010 ARG 0.004 0.000 ARG B 653 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 640) hydrogen bonds : angle 4.23474 ( 1756) covalent geometry : bond 0.00233 (14355) covalent geometry : angle 0.47407 (19961) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 470 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7565 (tp30) REVERT: B 518 PHE cc_start: 0.8030 (t80) cc_final: 0.7683 (t80) REVERT: B 610 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8152 (tp30) REVERT: B 724 ILE cc_start: 0.9099 (mt) cc_final: 0.8889 (pt) REVERT: B 810 LYS cc_start: 0.7601 (mmtp) cc_final: 0.6889 (tttt) REVERT: B 882 TYR cc_start: 0.7278 (t80) cc_final: 0.6812 (t80) REVERT: B 911 LEU cc_start: 0.9597 (mt) cc_final: 0.9389 (tp) REVERT: B 919 ARG cc_start: 0.8656 (mtm110) cc_final: 0.8415 (ttp-110) REVERT: B 933 GLN cc_start: 0.9278 (tt0) cc_final: 0.8765 (tm-30) REVERT: B 1037 PHE cc_start: 0.8582 (p90) cc_final: 0.7969 (p90) outliers start: 12 outliers final: 4 residues processed: 77 average time/residue: 0.3657 time to fit residues: 39.2387 Evaluate side-chains 53 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 1145 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 51 optimal weight: 0.0470 chunk 85 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 57 optimal weight: 0.0980 chunk 45 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.0284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 826 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.085750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.061234 restraints weight = 48080.675| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.47 r_work: 0.3072 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14355 Z= 0.112 Angle : 0.450 6.137 19961 Z= 0.243 Chirality : 0.035 0.171 2285 Planarity : 0.003 0.043 2055 Dihedral : 18.633 137.838 3343 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.08 % Allowed : 9.90 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.23), residues: 1330 helix: 1.84 (0.20), residues: 681 sheet: 0.11 (0.48), residues: 126 loop : 0.08 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 883 HIS 0.004 0.001 HIS B 167 PHE 0.010 0.001 PHE B1046 TYR 0.018 0.001 TYR B1039 ARG 0.012 0.000 ARG B1298 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 640) hydrogen bonds : angle 3.99726 ( 1756) covalent geometry : bond 0.00239 (14355) covalent geometry : angle 0.44995 (19961) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 383 MET cc_start: 0.8423 (mtp) cc_final: 0.8161 (mtp) REVERT: B 470 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7454 (tp30) REVERT: B 610 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8202 (tp30) REVERT: B 724 ILE cc_start: 0.9101 (mt) cc_final: 0.8901 (pt) REVERT: B 795 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8483 (tt) REVERT: B 810 LYS cc_start: 0.7707 (mmtp) cc_final: 0.7004 (tttt) REVERT: B 911 LEU cc_start: 0.9596 (mt) cc_final: 0.9362 (tp) REVERT: B 933 GLN cc_start: 0.9289 (tt0) cc_final: 0.8763 (tm-30) REVERT: B 1037 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.7956 (p90) outliers start: 13 outliers final: 6 residues processed: 63 average time/residue: 0.3228 time to fit residues: 29.9296 Evaluate side-chains 54 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 85 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 65 optimal weight: 0.0980 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 511 HIS B 885 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.082214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.057170 restraints weight = 48618.687| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.48 r_work: 0.2963 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 14355 Z= 0.246 Angle : 0.535 6.997 19961 Z= 0.284 Chirality : 0.038 0.154 2285 Planarity : 0.004 0.101 2055 Dihedral : 18.743 138.712 3342 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.58 % Allowed : 9.90 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.23), residues: 1330 helix: 1.70 (0.20), residues: 679 sheet: 0.07 (0.51), residues: 116 loop : 0.07 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 659 HIS 0.007 0.001 HIS B 641 PHE 0.013 0.001 PHE B1204 TYR 0.018 0.002 TYR B 823 ARG 0.011 0.001 ARG B 691 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 640) hydrogen bonds : angle 4.08385 ( 1756) covalent geometry : bond 0.00542 (14355) covalent geometry : angle 0.53488 (19961) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 610 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8403 (tp30) REVERT: B 682 PHE cc_start: 0.7245 (OUTLIER) cc_final: 0.6625 (t80) REVERT: B 762 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7815 (tp30) REVERT: B 810 LYS cc_start: 0.7731 (mmtp) cc_final: 0.7056 (tttt) REVERT: B 911 LEU cc_start: 0.9607 (mt) cc_final: 0.9393 (tp) REVERT: B 1037 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8037 (p90) REVERT: B 1273 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8965 (mp) outliers start: 19 outliers final: 9 residues processed: 63 average time/residue: 0.2916 time to fit residues: 28.2688 Evaluate side-chains 56 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1273 ILE Chi-restraints excluded: chain B residue 1318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 138 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 27 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.082908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.057782 restraints weight = 48640.947| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.51 r_work: 0.2986 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14355 Z= 0.151 Angle : 0.462 7.799 19961 Z= 0.249 Chirality : 0.035 0.138 2285 Planarity : 0.003 0.041 2055 Dihedral : 18.664 137.784 3342 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.41 % Allowed : 10.15 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.23), residues: 1330 helix: 1.90 (0.20), residues: 676 sheet: 0.14 (0.51), residues: 115 loop : 0.09 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 476 HIS 0.006 0.001 HIS B 167 PHE 0.021 0.001 PHE B 518 TYR 0.013 0.001 TYR B 882 ARG 0.005 0.000 ARG B1298 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 640) hydrogen bonds : angle 3.96557 ( 1756) covalent geometry : bond 0.00334 (14355) covalent geometry : angle 0.46182 (19961) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 534 MET cc_start: 0.5238 (ptt) cc_final: 0.4574 (ptt) REVERT: B 682 PHE cc_start: 0.7187 (OUTLIER) cc_final: 0.6422 (t80) REVERT: B 810 LYS cc_start: 0.7803 (mmtp) cc_final: 0.7139 (tttt) REVERT: B 912 ASP cc_start: 0.9324 (m-30) cc_final: 0.8996 (t70) REVERT: B 1037 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8031 (p90) outliers start: 17 outliers final: 9 residues processed: 62 average time/residue: 0.2841 time to fit residues: 27.0237 Evaluate side-chains 52 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.082537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.057656 restraints weight = 48740.881| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.55 r_work: 0.2980 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14355 Z= 0.150 Angle : 0.462 6.101 19961 Z= 0.248 Chirality : 0.035 0.145 2285 Planarity : 0.003 0.039 2055 Dihedral : 18.637 137.990 3342 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.16 % Allowed : 11.40 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.23), residues: 1330 helix: 1.97 (0.20), residues: 677 sheet: 0.22 (0.52), residues: 115 loop : 0.10 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 476 HIS 0.005 0.001 HIS B 167 PHE 0.015 0.001 PHE B 518 TYR 0.013 0.001 TYR B 882 ARG 0.005 0.000 ARG B 586 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 640) hydrogen bonds : angle 3.90913 ( 1756) covalent geometry : bond 0.00330 (14355) covalent geometry : angle 0.46188 (19961) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 682 PHE cc_start: 0.7229 (OUTLIER) cc_final: 0.6509 (t80) REVERT: B 810 LYS cc_start: 0.7761 (mmtp) cc_final: 0.7134 (tttt) REVERT: B 912 ASP cc_start: 0.9326 (m-30) cc_final: 0.8999 (t70) REVERT: B 976 ARG cc_start: 0.8952 (mtm-85) cc_final: 0.8571 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7954 (p90) outliers start: 14 outliers final: 10 residues processed: 55 average time/residue: 0.3046 time to fit residues: 25.8765 Evaluate side-chains 54 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 0.1980 chunk 10 optimal weight: 4.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.081466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.056415 restraints weight = 48823.189| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.47 r_work: 0.2949 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 14355 Z= 0.203 Angle : 0.499 6.237 19961 Z= 0.266 Chirality : 0.036 0.149 2285 Planarity : 0.003 0.042 2055 Dihedral : 18.696 138.613 3342 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.25 % Allowed : 11.90 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.23), residues: 1330 helix: 1.88 (0.20), residues: 680 sheet: 0.31 (0.53), residues: 113 loop : 0.05 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 659 HIS 0.005 0.001 HIS B 167 PHE 0.021 0.001 PHE B 518 TYR 0.015 0.001 TYR B 823 ARG 0.005 0.000 ARG B 586 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 640) hydrogen bonds : angle 3.99674 ( 1756) covalent geometry : bond 0.00451 (14355) covalent geometry : angle 0.49889 (19961) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8225 (mm) REVERT: B 383 MET cc_start: 0.8736 (mtp) cc_final: 0.8529 (mtp) REVERT: B 495 MET cc_start: 0.8449 (mtt) cc_final: 0.8205 (mtp) REVERT: B 682 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6639 (t80) REVERT: B 810 LYS cc_start: 0.7819 (mmtp) cc_final: 0.7175 (tttt) REVERT: B 976 ARG cc_start: 0.9034 (mtm-85) cc_final: 0.8602 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7993 (p90) outliers start: 15 outliers final: 12 residues processed: 55 average time/residue: 0.2923 time to fit residues: 24.3135 Evaluate side-chains 56 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain B residue 781 MET Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1318 LEU Chi-restraints excluded: chain B residue 1342 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.082506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.057758 restraints weight = 48106.167| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.44 r_work: 0.2993 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14355 Z= 0.115 Angle : 0.437 6.878 19961 Z= 0.236 Chirality : 0.034 0.137 2285 Planarity : 0.003 0.041 2055 Dihedral : 18.613 138.197 3342 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.16 % Allowed : 12.06 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.23), residues: 1330 helix: 2.02 (0.20), residues: 679 sheet: 0.39 (0.53), residues: 113 loop : 0.08 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 476 HIS 0.005 0.001 HIS B 167 PHE 0.009 0.001 PHE B 518 TYR 0.014 0.001 TYR B 155 ARG 0.003 0.000 ARG B 586 Details of bonding type rmsd hydrogen bonds : bond 0.03297 ( 640) hydrogen bonds : angle 3.83654 ( 1756) covalent geometry : bond 0.00250 (14355) covalent geometry : angle 0.43747 (19961) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8215 (mm) REVERT: B 682 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6612 (t80) REVERT: B 751 MET cc_start: 0.8957 (mmm) cc_final: 0.8710 (mmm) REVERT: B 810 LYS cc_start: 0.7866 (mmtp) cc_final: 0.7197 (tttt) REVERT: B 976 ARG cc_start: 0.8997 (mtm-85) cc_final: 0.8585 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7964 (p90) outliers start: 14 outliers final: 9 residues processed: 57 average time/residue: 0.2880 time to fit residues: 25.3240 Evaluate side-chains 56 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 50 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 120 optimal weight: 0.3980 chunk 71 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.082943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.058165 restraints weight = 48322.968| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.49 r_work: 0.3009 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14355 Z= 0.106 Angle : 0.424 6.392 19961 Z= 0.229 Chirality : 0.034 0.133 2285 Planarity : 0.003 0.041 2055 Dihedral : 18.544 138.606 3342 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.08 % Allowed : 12.90 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.23), residues: 1330 helix: 2.11 (0.20), residues: 676 sheet: 0.46 (0.53), residues: 112 loop : 0.07 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 476 HIS 0.004 0.001 HIS B 167 PHE 0.010 0.001 PHE B 518 TYR 0.015 0.001 TYR B 823 ARG 0.005 0.000 ARG B 629 Details of bonding type rmsd hydrogen bonds : bond 0.03117 ( 640) hydrogen bonds : angle 3.76084 ( 1756) covalent geometry : bond 0.00231 (14355) covalent geometry : angle 0.42407 (19961) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8198 (mm) REVERT: B 383 MET cc_start: 0.8697 (mtp) cc_final: 0.8415 (mtp) REVERT: B 518 PHE cc_start: 0.8330 (t80) cc_final: 0.8117 (t80) REVERT: B 682 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.6654 (t80) REVERT: B 810 LYS cc_start: 0.7897 (mmtp) cc_final: 0.7211 (tttt) REVERT: B 976 ARG cc_start: 0.9009 (mtm-85) cc_final: 0.8588 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7962 (p90) outliers start: 13 outliers final: 8 residues processed: 57 average time/residue: 0.2820 time to fit residues: 24.5947 Evaluate side-chains 54 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 0.9980 chunk 87 optimal weight: 0.0980 chunk 83 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 854 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.083470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.058978 restraints weight = 48433.691| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.47 r_work: 0.3026 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14355 Z= 0.095 Angle : 0.411 8.339 19961 Z= 0.222 Chirality : 0.033 0.132 2285 Planarity : 0.003 0.041 2055 Dihedral : 18.471 138.929 3342 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.00 % Allowed : 12.90 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.23), residues: 1330 helix: 2.22 (0.20), residues: 669 sheet: 0.69 (0.51), residues: 122 loop : 0.14 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 476 HIS 0.004 0.001 HIS B1311 PHE 0.009 0.001 PHE B1258 TYR 0.013 0.001 TYR B 155 ARG 0.003 0.000 ARG B 655 Details of bonding type rmsd hydrogen bonds : bond 0.03009 ( 640) hydrogen bonds : angle 3.67682 ( 1756) covalent geometry : bond 0.00202 (14355) covalent geometry : angle 0.41088 (19961) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8100 (mm) REVERT: B 682 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.6673 (t80) REVERT: B 810 LYS cc_start: 0.7949 (mmtp) cc_final: 0.7256 (tttt) REVERT: B 976 ARG cc_start: 0.9000 (mtm-85) cc_final: 0.8580 (mtp-110) REVERT: B 1037 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.7955 (p90) outliers start: 12 outliers final: 9 residues processed: 55 average time/residue: 0.3227 time to fit residues: 27.4324 Evaluate side-chains 56 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 9 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 93 optimal weight: 30.0000 chunk 131 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.080190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.055184 restraints weight = 49156.542| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.42 r_work: 0.2921 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 14355 Z= 0.283 Angle : 0.557 6.083 19961 Z= 0.294 Chirality : 0.038 0.161 2285 Planarity : 0.003 0.043 2055 Dihedral : 18.707 141.123 3342 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.08 % Allowed : 13.06 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.23), residues: 1330 helix: 1.84 (0.20), residues: 686 sheet: 0.54 (0.52), residues: 123 loop : 0.01 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 659 HIS 0.005 0.001 HIS B 167 PHE 0.032 0.002 PHE B 518 TYR 0.017 0.002 TYR B1141 ARG 0.003 0.001 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.04159 ( 640) hydrogen bonds : angle 4.00677 ( 1756) covalent geometry : bond 0.00627 (14355) covalent geometry : angle 0.55669 (19961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8215.32 seconds wall clock time: 145 minutes 20.74 seconds (8720.74 seconds total)