Starting phenix.real_space_refine on Tue Aug 4 22:11:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iaz_35323/08_2026/8iaz_35323.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iaz_35323/08_2026/8iaz_35323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iaz_35323/08_2026/8iaz_35323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iaz_35323/08_2026/8iaz_35323.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iaz_35323/08_2026/8iaz_35323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iaz_35323/08_2026/8iaz_35323.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 Zn 1 6.06 5 P 203 5.49 5 S 16 5.16 5 C 3919 2.51 5 N 1333 2.21 5 O 1924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7396 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3110 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 374} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 3464 Classifications: {'RNA': 163} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 10, 'rna3p_pur': 74, 'rna3p_pyr': 61} Link IDs: {'rna2p': 22, 'rna3p': 140} Chain breaks: 3 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 490 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "C" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 331 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2769 SG CYS A 343 12.251 39.929 54.366 0.35 19.85 S ATOM 2791 SG CYS A 346 9.833 37.189 55.351 0.14 23.35 S ATOM 2917 SG CYS A 362 11.328 37.075 51.877 0.33 19.10 S ATOM 2929 SG CYS A 364 8.759 39.462 52.559 0.16 24.39 S Time building chain proxies: 1.63, per 1000 atoms: 0.22 Number of scatterers: 7396 At special positions: 0 Unit cell: (98.04, 123.84, 98.9, 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) Zn 1 29.99 S 16 16.00 P 203 15.00 O 1924 8.00 N 1333 7.00 C 3919 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: 0.55 Conformation dependent library (CDL) restraints added in 193.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 362 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 346 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 364 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 343 " Number of angles added : 6 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 732 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 3 sheets defined 47.4% alpha, 12.0% beta 52 base pairs and 111 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 15 through 47 Processing helix chain 'A' and resid 53 through 63 removed outlier: 3.657A pdb=" N VAL A 58 " --> pdb=" O LYS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.670A pdb=" N VAL A 77 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 98 removed outlier: 3.717A pdb=" N VAL A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 98 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 215 through 242 removed outlier: 3.751A pdb=" N ARG A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 282 Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.614A pdb=" N MET A 297 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN A 300 " --> pdb=" O GLY A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 311 removed outlier: 3.710A pdb=" N LYS A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 327 Processing helix chain 'A' and resid 370 through 380 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 119 removed outlier: 4.309A pdb=" N SER A 160 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TYR A 170 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 174 " --> pdb=" O PHE A 8 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG A 142 " --> pdb=" O ASN A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210 removed outlier: 6.155A pdb=" N ILE A 287 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 332 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 361 154 hydrogen bonds defined for protein. 435 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 124 hydrogen bonds 218 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 111 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 817 1.32 - 1.44: 3287 1.44 - 1.56: 3440 1.56 - 1.69: 396 1.69 - 1.81: 22 Bond restraints: 7962 Sorted by residual: bond pdb=" O3' C E 196 " pdb=" P C E 197 " ideal model delta sigma weight residual 1.607 1.432 0.175 1.20e-02 6.94e+03 2.13e+02 bond pdb=" P C E 196 " pdb=" OP2 C E 196 " ideal model delta sigma weight residual 1.485 1.363 0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" O3' DA C 3 " pdb=" P DG C 4 " ideal model delta sigma weight residual 1.607 1.543 0.064 1.20e-02 6.94e+03 2.81e+01 bond pdb=" C3' C E 196 " pdb=" O3' C E 196 " ideal model delta sigma weight residual 1.417 1.350 0.067 1.40e-02 5.10e+03 2.26e+01 bond pdb=" P C E 197 " pdb=" OP2 C E 197 " ideal model delta sigma weight residual 1.485 1.392 0.093 2.00e-02 2.50e+03 2.17e+01 ... (remaining 7957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.30: 11620 4.30 - 8.61: 46 8.61 - 12.91: 6 12.91 - 17.21: 1 17.21 - 21.52: 1 Bond angle restraints: 11674 Sorted by residual: angle pdb=" C2' C E 197 " pdb=" C1' C E 197 " pdb=" N1 C E 197 " ideal model delta sigma weight residual 112.00 120.95 -8.95 1.10e+00 8.26e-01 6.62e+01 angle pdb=" O2' C E 197 " pdb=" C2' C E 197 " pdb=" C1' C E 197 " ideal model delta sigma weight residual 110.60 89.08 21.52 3.00e+00 1.11e-01 5.14e+01 angle pdb=" C4' DG C 4 " pdb=" O4' DG C 4 " pdb=" C1' DG C 4 " ideal model delta sigma weight residual 110.10 103.27 6.83 1.00e+00 1.00e+00 4.67e+01 angle pdb=" O5' C E 196 " pdb=" C5' C E 196 " pdb=" C4' C E 196 " ideal model delta sigma weight residual 109.40 114.03 -4.63 8.00e-01 1.56e+00 3.35e+01 angle pdb=" C1' C E 26 " pdb=" N1 C E 26 " pdb=" C2 C E 26 " ideal model delta sigma weight residual 118.80 125.13 -6.33 1.10e+00 8.26e-01 3.32e+01 ... (remaining 11669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 4227 35.58 - 71.16: 592 71.16 - 106.74: 32 106.74 - 142.32: 6 142.32 - 177.89: 15 Dihedral angle restraints: 4872 sinusoidal: 3740 harmonic: 1132 Sorted by residual: dihedral pdb=" O4' U E 189 " pdb=" C1' U E 189 " pdb=" N1 U E 189 " pdb=" C2 U E 189 " ideal model delta sinusoidal sigma weight residual -160.00 17.31 -177.31 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U E 82 " pdb=" C1' U E 82 " pdb=" N1 U E 82 " pdb=" C2 U E 82 " ideal model delta sinusoidal sigma weight residual -160.00 16.45 -176.45 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U E 134 " pdb=" C1' U E 134 " pdb=" N1 U E 134 " pdb=" C2 U E 134 " ideal model delta sinusoidal sigma weight residual -160.00 7.65 -167.65 1 1.50e+01 4.44e-03 8.43e+01 ... (remaining 4869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1153 0.080 - 0.160: 248 0.160 - 0.240: 21 0.240 - 0.320: 2 0.320 - 0.400: 4 Chirality restraints: 1428 Sorted by residual: chirality pdb=" C2' A E 198 " pdb=" C3' A E 198 " pdb=" O2' A E 198 " pdb=" C1' A E 198 " both_signs ideal model delta sigma weight residual False -2.62 -3.02 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" P C E 196 " pdb=" OP1 C E 196 " pdb=" OP2 C E 196 " pdb=" O5' C E 196 " both_signs ideal model delta sigma weight residual True 2.41 -2.06 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" P C E 197 " pdb=" OP1 C E 197 " pdb=" OP2 C E 197 " pdb=" O5' C E 197 " both_signs ideal model delta sigma weight residual True 2.41 -2.06 0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 1425 not shown) Planarity restraints: 736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C E 196 " 0.066 2.00e-02 2.50e+03 3.51e-02 2.78e+01 pdb=" N1 C E 196 " -0.047 2.00e-02 2.50e+03 pdb=" C2 C E 196 " -0.036 2.00e-02 2.50e+03 pdb=" O2 C E 196 " 0.007 2.00e-02 2.50e+03 pdb=" N3 C E 196 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C E 196 " -0.022 2.00e-02 2.50e+03 pdb=" N4 C E 196 " 0.040 2.00e-02 2.50e+03 pdb=" C5 C E 196 " 0.017 2.00e-02 2.50e+03 pdb=" C6 C E 196 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C E 197 " 0.037 2.00e-02 2.50e+03 2.72e-02 1.66e+01 pdb=" N1 C E 197 " -0.032 2.00e-02 2.50e+03 pdb=" C2 C E 197 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C E 197 " 0.015 2.00e-02 2.50e+03 pdb=" N3 C E 197 " -0.050 2.00e-02 2.50e+03 pdb=" C4 C E 197 " 0.018 2.00e-02 2.50e+03 pdb=" N4 C E 197 " 0.032 2.00e-02 2.50e+03 pdb=" C5 C E 197 " -0.007 2.00e-02 2.50e+03 pdb=" C6 C E 197 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 4 " -0.021 2.00e-02 2.50e+03 1.78e-02 9.53e+00 pdb=" N9 DG C 4 " 0.038 2.00e-02 2.50e+03 pdb=" C8 DG C 4 " 0.023 2.00e-02 2.50e+03 pdb=" N7 DG C 4 " -0.013 2.00e-02 2.50e+03 pdb=" C5 DG C 4 " -0.021 2.00e-02 2.50e+03 pdb=" C6 DG C 4 " -0.011 2.00e-02 2.50e+03 pdb=" O6 DG C 4 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG C 4 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG C 4 " 0.011 2.00e-02 2.50e+03 pdb=" N2 DG C 4 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DG C 4 " -0.017 2.00e-02 2.50e+03 pdb=" C4 DG C 4 " -0.009 2.00e-02 2.50e+03 ... (remaining 733 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1414 2.77 - 3.30: 5910 3.30 - 3.84: 14132 3.84 - 4.37: 16748 4.37 - 4.90: 23310 Nonbonded interactions: 61514 Sorted by model distance: nonbonded pdb=" O2' C E 152 " pdb=" OP1 G E 153 " model vdw 2.239 3.040 nonbonded pdb=" O SER A 52 " pdb=" OG SER A 52 " model vdw 2.244 3.040 nonbonded pdb=" O MET A 298 " pdb=" OG SER A 304 " model vdw 2.284 3.040 nonbonded pdb=" O2' A E 48 " pdb=" OP1 C E 49 " model vdw 2.284 3.040 nonbonded pdb=" OE1 GLU A 11 " pdb=" O2' G E 30 " model vdw 2.288 3.040 ... (remaining 61509 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.96 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: 1.470 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: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.630 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 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 : 0.006 0.175 7966 Z= 0.536 Angle : 0.976 21.518 11680 Z= 0.766 Chirality : 0.066 0.400 1428 Planarity : 0.005 0.048 736 Dihedral : 26.191 177.894 4140 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.07 % Favored : 92.67 % Rotamer: Outliers : 4.37 % Allowed : 34.69 % Favored : 60.93 % 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: 0.24 (0.43), residues: 382 helix: 2.50 (0.40), residues: 167 sheet: -0.18 (0.89), residues: 41 loop : -2.29 (0.40), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 130 TYR 0.014 0.002 TYR A 44 PHE 0.014 0.002 PHE A 360 TRP 0.004 0.001 TRP A 140 HIS 0.005 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.54 ( 7962) covalent geometry : angle 0.96930 / 0.77 (11674) hydrogen bonds : bond 0.15517 / 9.73 ( 278) hydrogen bonds : angle 4.60152 / 3.49 ( 653) metal coordination : bond 0.00755 / 0.38 ( 4) metal coordination : angle 4.95686 / 2.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.8216 (ttm) cc_final: 0.7927 (ttm) REVERT: A 188 ASN cc_start: 0.6485 (m-40) cc_final: 0.6041 (m110) REVERT: A 210 LYS cc_start: 0.8479 (mtpm) cc_final: 0.8093 (mmtm) REVERT: A 228 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7980 (mm-30) REVERT: A 254 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7887 (mtm180) REVERT: A 301 ARG cc_start: 0.8431 (tpp-160) cc_final: 0.8197 (tpp-160) REVERT: A 336 TRP cc_start: 0.8144 (m-90) cc_final: 0.7833 (m100) outliers start: 15 outliers final: 10 residues processed: 63 average time/residue: 0.5652 time to fit residues: 37.6547 Evaluate side-chains 50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 362 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.185996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.151800 restraints weight = 7135.894| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 0.47 r_work: 0.3315 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 200 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 207 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7966 Z= 0.144 Angle : 0.613 12.424 11680 Z= 0.356 Chirality : 0.042 0.300 1428 Planarity : 0.004 0.040 736 Dihedral : 26.695 179.088 3352 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.07 % Favored : 92.67 % Rotamer: Outliers : 6.12 % Allowed : 30.32 % Favored : 63.56 % 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: 0.57 (0.43), residues: 382 helix: 2.94 (0.39), residues: 166 sheet: -0.14 (0.83), residues: 41 loop : -2.22 (0.40), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 95 TYR 0.010 0.001 TYR A 33 PHE 0.012 0.001 PHE A 200 TRP 0.002 0.001 TRP A 336 HIS 0.004 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.14 ( 7962) covalent geometry : angle 0.60343 / 0.36 (11674) hydrogen bonds : bond 0.06957 / 4.66 ( 278) hydrogen bonds : angle 3.66437 / 2.84 ( 653) metal coordination : bond 0.01009 / 0.50 ( 4) metal coordination : angle 4.86197 / 2.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 36 time to evaluate : 0.180 Fit side-chains REVERT: A 41 LYS cc_start: 0.6902 (OUTLIER) cc_final: 0.6406 (ttpt) REVERT: A 51 MET cc_start: 0.8088 (ttm) cc_final: 0.7807 (ttm) REVERT: A 62 ASN cc_start: 0.8564 (m-40) cc_final: 0.8329 (m110) REVERT: A 75 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7541 (ptpt) REVERT: A 152 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8879 (p) REVERT: A 188 ASN cc_start: 0.6820 (m-40) cc_final: 0.6437 (m110) REVERT: A 210 LYS cc_start: 0.8291 (mtpm) cc_final: 0.7929 (mmtm) REVERT: A 256 LYS cc_start: 0.8274 (ttmm) cc_final: 0.8020 (mtmm) REVERT: A 301 ARG cc_start: 0.8387 (tpp-160) cc_final: 0.8142 (tpp-160) REVERT: A 329 GLU cc_start: 0.8168 (pm20) cc_final: 0.7539 (pm20) outliers start: 21 outliers final: 9 residues processed: 56 average time/residue: 0.5770 time to fit residues: 34.1919 Evaluate side-chains 45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 362 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 28 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.180507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.145836 restraints weight = 6941.618| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 0.43 r_work: 0.3240 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 207 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 207 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7966 Z= 0.211 Angle : 0.694 11.692 11680 Z= 0.391 Chirality : 0.049 0.351 1428 Planarity : 0.005 0.043 736 Dihedral : 26.670 179.095 3344 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.07 % Favored : 92.67 % Rotamer: Outliers : 6.71 % Allowed : 28.57 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.43), residues: 382 helix: 2.42 (0.39), residues: 175 sheet: -0.17 (0.84), residues: 41 loop : -2.33 (0.40), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 95 TYR 0.010 0.002 TYR A 33 PHE 0.015 0.002 PHE A 35 TRP 0.004 0.002 TRP A 140 HIS 0.005 0.002 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.21 ( 7962) covalent geometry : angle 0.68658 / 0.39 (11674) hydrogen bonds : bond 0.08810 / 6.06 ( 278) hydrogen bonds : angle 3.58435 / 2.73 ( 653) metal coordination : bond 0.01066 / 0.53 ( 4) metal coordination : angle 4.46263 / 1.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 34 time to evaluate : 0.174 Fit side-chains REVERT: A 41 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6678 (ttpt) REVERT: A 51 MET cc_start: 0.8182 (ttm) cc_final: 0.7832 (ttm) REVERT: A 62 ASN cc_start: 0.8575 (m-40) cc_final: 0.8339 (m110) REVERT: A 75 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7368 (ptpt) REVERT: A 127 ARG cc_start: 0.8476 (ptt180) cc_final: 0.8108 (ptt-90) REVERT: A 210 LYS cc_start: 0.8281 (mtpm) cc_final: 0.7844 (mmtm) outliers start: 23 outliers final: 10 residues processed: 53 average time/residue: 0.6141 time to fit residues: 34.3894 Evaluate side-chains 43 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 383 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.181294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.145985 restraints weight = 7132.645| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 0.52 r_work: 0.3107 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 207 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 208 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7966 Z= 0.164 Angle : 0.627 11.809 11680 Z= 0.358 Chirality : 0.045 0.325 1428 Planarity : 0.004 0.041 736 Dihedral : 26.602 179.030 3340 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.81 % Favored : 92.93 % Rotamer: Outliers : 4.96 % Allowed : 30.32 % Favored : 64.72 % 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: 0.33 (0.43), residues: 382 helix: 2.51 (0.39), residues: 175 sheet: -0.08 (0.82), residues: 41 loop : -2.42 (0.40), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 95 TYR 0.011 0.001 TYR A 33 PHE 0.011 0.002 PHE A 35 TRP 0.003 0.001 TRP A 336 HIS 0.004 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 ( 7962) covalent geometry : angle 0.61802 / 0.36 (11674) hydrogen bonds : bond 0.07619 / 5.22 ( 278) hydrogen bonds : angle 3.45354 / 2.65 ( 653) metal coordination : bond 0.00834 / 0.41 ( 4) metal coordination : angle 4.75053 / 2.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 34 time to evaluate : 0.179 Fit side-chains REVERT: A 41 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6572 (ttpt) REVERT: A 51 MET cc_start: 0.8166 (ttm) cc_final: 0.7897 (ttm) REVERT: A 75 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7262 (ptpt) REVERT: A 127 ARG cc_start: 0.8514 (ptt180) cc_final: 0.8158 (ptt-90) REVERT: A 210 LYS cc_start: 0.8238 (mtpm) cc_final: 0.7791 (mmtm) REVERT: A 329 GLU cc_start: 0.8307 (pm20) cc_final: 0.7821 (pm20) REVERT: A 385 GLU cc_start: 0.6643 (pt0) cc_final: 0.6334 (pm20) outliers start: 17 outliers final: 8 residues processed: 47 average time/residue: 0.6626 time to fit residues: 32.7700 Evaluate side-chains 43 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 362 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 47 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 56 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.175105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.139195 restraints weight = 7067.072| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 0.53 r_work: 0.3086 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 208 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 207 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 7966 Z= 0.276 Angle : 0.800 11.409 11680 Z= 0.438 Chirality : 0.055 0.387 1428 Planarity : 0.005 0.044 736 Dihedral : 26.716 179.039 3340 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.12 % Favored : 91.62 % Rotamer: Outliers : 6.12 % Allowed : 27.99 % Favored : 65.89 % 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: -0.09 (0.42), residues: 382 helix: 2.00 (0.39), residues: 175 sheet: -0.02 (0.81), residues: 41 loop : -2.51 (0.40), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 130 TYR 0.012 0.002 TYR A 171 PHE 0.023 0.003 PHE A 35 TRP 0.006 0.002 TRP A 140 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.28 ( 7962) covalent geometry : angle 0.79209 / 0.44 (11674) hydrogen bonds : bond 0.10538 / 7.35 ( 278) hydrogen bonds : angle 3.67115 / 2.77 ( 653) metal coordination : bond 0.01142 / 0.56 ( 4) metal coordination : angle 5.10330 / 1.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 38 time to evaluate : 0.180 Fit side-chains REVERT: A 41 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6844 (ttpt) REVERT: A 106 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8229 (mp) REVERT: A 124 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7323 (tptt) REVERT: A 210 LYS cc_start: 0.8343 (mtpm) cc_final: 0.7840 (mttm) REVERT: A 385 GLU cc_start: 0.6618 (pt0) cc_final: 0.6274 (pm20) outliers start: 21 outliers final: 9 residues processed: 56 average time/residue: 0.6447 time to fit residues: 38.1251 Evaluate side-chains 45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 383 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 11 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.176254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.140601 restraints weight = 7062.177| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 0.50 r_work: 0.3094 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 207 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 208 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7966 Z= 0.234 Angle : 0.739 11.417 11680 Z= 0.411 Chirality : 0.052 0.372 1428 Planarity : 0.005 0.041 736 Dihedral : 26.675 179.368 3340 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.07 % Favored : 92.67 % Rotamer: Outliers : 6.41 % Allowed : 27.70 % Favored : 65.89 % 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: -0.13 (0.42), residues: 382 helix: 2.04 (0.39), residues: 174 sheet: -0.04 (0.81), residues: 41 loop : -2.60 (0.40), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 130 TYR 0.011 0.002 TYR A 33 PHE 0.019 0.002 PHE A 35 TRP 0.005 0.001 TRP A 336 HIS 0.004 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.23 ( 7962) covalent geometry : angle 0.73016 / 0.41 (11674) hydrogen bonds : bond 0.09483 / 6.60 ( 278) hydrogen bonds : angle 3.62392 / 2.76 ( 653) metal coordination : bond 0.00920 / 0.45 ( 4) metal coordination : angle 5.12631 / 2.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 34 time to evaluate : 0.185 Fit side-chains REVERT: A 41 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6703 (ttpt) REVERT: A 124 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7243 (ttpt) REVERT: A 138 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8669 (mt) REVERT: A 210 LYS cc_start: 0.8294 (mtpm) cc_final: 0.7799 (mttm) REVERT: A 385 GLU cc_start: 0.6579 (pt0) cc_final: 0.6250 (pm20) outliers start: 22 outliers final: 11 residues processed: 53 average time/residue: 0.6387 time to fit residues: 35.7474 Evaluate side-chains 44 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 383 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 33 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.179608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.144217 restraints weight = 7068.348| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 0.47 r_work: 0.3277 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 208 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 206 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7966 Z= 0.159 Angle : 0.630 11.126 11680 Z= 0.360 Chirality : 0.045 0.332 1428 Planarity : 0.004 0.039 736 Dihedral : 26.527 179.752 3339 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.07 % Favored : 92.67 % Rotamer: Outliers : 4.08 % Allowed : 29.74 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.43), residues: 382 helix: 2.42 (0.39), residues: 174 sheet: 0.16 (0.82), residues: 41 loop : -2.56 (0.40), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 130 TYR 0.012 0.001 TYR A 33 PHE 0.010 0.002 PHE A 35 TRP 0.004 0.001 TRP A 336 HIS 0.004 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.16 ( 7962) covalent geometry : angle 0.62017 / 0.36 (11674) hydrogen bonds : bond 0.07601 / 5.24 ( 278) hydrogen bonds : angle 3.48779 / 2.68 ( 653) metal coordination : bond 0.00633 / 0.31 ( 4) metal coordination : angle 4.86393 / 2.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.186 Fit side-chains REVERT: A 41 LYS cc_start: 0.7001 (OUTLIER) cc_final: 0.6566 (ttpt) REVERT: A 124 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7181 (ttpt) REVERT: A 210 LYS cc_start: 0.8210 (mtpm) cc_final: 0.7724 (mttm) REVERT: A 385 GLU cc_start: 0.6486 (pt0) cc_final: 0.6220 (pm20) outliers start: 14 outliers final: 7 residues processed: 47 average time/residue: 0.5808 time to fit residues: 28.8387 Evaluate side-chains 42 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 287 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 43 optimal weight: 30.0000 chunk 51 optimal weight: 30.0000 chunk 21 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.174231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.138000 restraints weight = 7100.194| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 0.50 r_work: 0.3096 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 206 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 206 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 7966 Z= 0.301 Angle : 0.839 10.891 11680 Z= 0.455 Chirality : 0.058 0.395 1428 Planarity : 0.005 0.043 736 Dihedral : 26.640 179.899 3339 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.38 % Favored : 91.36 % Rotamer: Outliers : 5.54 % Allowed : 28.28 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.42), residues: 382 helix: 2.03 (0.39), residues: 168 sheet: -0.03 (0.82), residues: 41 loop : -2.74 (0.40), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 130 TYR 0.013 0.002 TYR A 171 PHE 0.020 0.003 PHE A 35 TRP 0.007 0.002 TRP A 140 HIS 0.005 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.30 ( 7962) covalent geometry : angle 0.83136 / 0.45 (11674) hydrogen bonds : bond 0.10972 / 7.67 ( 278) hydrogen bonds : angle 3.71810 / 2.81 ( 653) metal coordination : bond 0.01019 / 0.50 ( 4) metal coordination : angle 5.04437 / 1.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 33 time to evaluate : 0.185 Fit side-chains REVERT: A 41 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6861 (ttpt) REVERT: A 124 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7315 (ttpt) REVERT: A 210 LYS cc_start: 0.8312 (mtpm) cc_final: 0.7812 (mttm) outliers start: 19 outliers final: 13 residues processed: 50 average time/residue: 0.5715 time to fit residues: 30.2687 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 383 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 54 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 38 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS A 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.181198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.145133 restraints weight = 7048.475| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 0.50 r_work: 0.3150 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 206 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 207 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7966 Z= 0.139 Angle : 0.611 11.091 11680 Z= 0.353 Chirality : 0.043 0.330 1428 Planarity : 0.004 0.037 736 Dihedral : 26.499 179.659 3339 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.07 % Favored : 92.67 % Rotamer: Outliers : 2.92 % Allowed : 30.90 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.44), residues: 382 helix: 2.49 (0.40), residues: 174 sheet: 0.21 (0.86), residues: 41 loop : -2.60 (0.40), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 217 TYR 0.012 0.001 TYR A 33 PHE 0.008 0.001 PHE A 312 TRP 0.006 0.001 TRP A 336 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.14 ( 7962) covalent geometry : angle 0.60188 / 0.35 (11674) hydrogen bonds : bond 0.06979 / 4.76 ( 278) hydrogen bonds : angle 3.45923 / 2.66 ( 653) metal coordination : bond 0.00518 / 0.26 ( 4) metal coordination : angle 4.79792 / 2.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7064 (tptm) cc_final: 0.6557 (ttpt) REVERT: A 210 LYS cc_start: 0.8170 (mtpm) cc_final: 0.7697 (mttm) outliers start: 10 outliers final: 7 residues processed: 42 average time/residue: 0.5998 time to fit residues: 26.5683 Evaluate side-chains 38 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 287 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 49 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS A 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.179075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.142692 restraints weight = 6943.293| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 0.48 r_work: 0.3067 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 207 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 208 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7966 Z= 0.200 Angle : 0.682 10.569 11680 Z= 0.383 Chirality : 0.048 0.367 1428 Planarity : 0.004 0.039 736 Dihedral : 26.479 179.229 3339 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.59 % Favored : 92.15 % Rotamer: Outliers : 2.62 % Allowed : 31.78 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.43), residues: 382 helix: 2.35 (0.39), residues: 174 sheet: 0.16 (0.83), residues: 41 loop : -2.63 (0.40), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 95 TYR 0.012 0.002 TYR A 33 PHE 0.013 0.002 PHE A 35 TRP 0.004 0.001 TRP A 336 HIS 0.005 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.20 ( 7962) covalent geometry : angle 0.67392 / 0.38 (11674) hydrogen bonds : bond 0.08529 / 5.90 ( 278) hydrogen bonds : angle 3.49821 / 2.68 ( 653) metal coordination : bond 0.00743 / 0.37 ( 4) metal coordination : angle 4.64116 / 1.97 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.181 Fit side-chains REVERT: A 41 LYS cc_start: 0.7228 (tptm) cc_final: 0.6697 (ttpt) REVERT: A 124 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7378 (ttpt) REVERT: A 210 LYS cc_start: 0.8266 (mtpm) cc_final: 0.7779 (mttm) outliers start: 9 outliers final: 7 residues processed: 41 average time/residue: 0.6306 time to fit residues: 27.3459 Evaluate side-chains 38 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 287 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 38 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS A 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.177462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.141057 restraints weight = 6979.506| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 0.49 r_work: 0.3094 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 208 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 208 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7966 Z= 0.192 Angle : 0.673 10.689 11680 Z= 0.380 Chirality : 0.048 0.365 1428 Planarity : 0.004 0.041 736 Dihedral : 26.440 179.391 3339 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.07 % Favored : 92.67 % Rotamer: Outliers : 2.92 % Allowed : 30.90 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.43), residues: 382 helix: 2.52 (0.40), residues: 168 sheet: 0.23 (0.82), residues: 41 loop : -2.70 (0.40), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 130 TYR 0.012 0.002 TYR A 33 PHE 0.014 0.002 PHE A 35 TRP 0.005 0.001 TRP A 336 HIS 0.005 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 ( 7962) covalent geometry : angle 0.66469 / 0.38 (11674) hydrogen bonds : bond 0.08407 / 5.81 ( 278) hydrogen bonds : angle 3.51094 / 2.69 ( 653) metal coordination : bond 0.00794 / 0.39 ( 4) metal coordination : angle 4.58956 / 1.97 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2117.03 seconds wall clock time: 37 minutes 0.94 seconds (2220.94 seconds total)