Starting phenix.real_space_refine on Fri Jul 3 16:00:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t2r_40985/07_2026/8t2r_40985.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t2r_40985/07_2026/8t2r_40985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8t2r_40985/07_2026/8t2r_40985.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t2r_40985/07_2026/8t2r_40985.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t2r_40985/07_2026/8t2r_40985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t2r_40985/07_2026/8t2r_40985.map" model { file = "/net/cci-nas-00/data/ceres_data/8t2r_40985/07_2026/8t2r_40985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t2r_40985/07_2026/8t2r_40985.cif" } resolution = 3.1 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= 0.001 sd= 0.028 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 Ca 13 9.91 5 P 552 5.49 5 S 21 5.16 5 C 7314 2.51 5 N 2782 2.21 5 O 4381 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15063 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 3184 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 388, 3142 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 10, 'TRANS': 377} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 388, 3142 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 10, 'TRANS': 377} Chain breaks: 2 bond proxies already assigned to first conformer: 3149 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 3, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 3} Chain: "B" Number of atoms: 11724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 11724 Classifications: {'RNA': 545} Modifications used: {'rna2p_pur': 39, 'rna2p_pyr': 10, 'rna3p_pur': 291, 'rna3p_pyr': 205} Link IDs: {'rna2p': 48, 'rna3p': 496} Chain breaks: 6 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' CA': 13, 'NH4': 2} Classifications: {'undetermined': 15} Link IDs: {None: 14} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG D 347 " occ=0.25 ... (20 atoms not shown) pdb=" NH2BARG D 347 " occ=0.75 residue: pdb=" N AGLN D 359 " occ=0.72 ... (16 atoms not shown) pdb=" NE2BGLN D 359 " occ=0.28 residue: pdb=" N AARG D 382 " occ=0.67 ... (20 atoms not shown) pdb=" NH2BARG D 382 " occ=0.33 residue: pdb=" N AARG D 407 " occ=0.48 ... (20 atoms not shown) pdb=" NH2BARG D 407 " occ=0.52 Time building chain proxies: 3.27, per 1000 atoms: 0.22 Number of scatterers: 15063 At special positions: 0 Unit cell: (97.904, 134.196, 160.36, 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) Ca 13 19.99 S 21 16.00 P 552 15.00 O 4381 8.00 N 2782 7.00 C 7314 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: 1.08 Conformation dependent library (CDL) restraints added in 380.6 milliseconds 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 736 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 2 sheets defined 70.9% alpha, 5.9% beta 177 base pairs and 312 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'D' and resid 4 through 11 Processing helix chain 'D' and resid 12 through 27 Processing helix chain 'D' and resid 36 through 57 removed outlier: 6.619A pdb=" N GLU D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 118 through 132 removed outlier: 3.601A pdb=" N ALA D 122 " --> pdb=" O CYS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 150 through 162 removed outlier: 3.589A pdb=" N LEU D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 177 removed outlier: 3.681A pdb=" N ILE D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 218 removed outlier: 4.304A pdb=" N LEU D 201 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU D 210 " --> pdb=" O MET D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 252 Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 313 through 333 Processing helix chain 'D' and resid 337 through 361 removed outlier: 3.658A pdb=" N LYS D 361 " --> pdb=" O TRP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 374 Processing helix chain 'D' and resid 376 through 385 removed outlier: 4.381A pdb=" N AARG D 382 " --> pdb=" O ASN D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 396 removed outlier: 4.032A pdb=" N LYS D 396 " --> pdb=" O TYR D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 403 Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 415 through 424 Processing sheet with id=AA1, first strand: chain 'D' and resid 220 through 224 removed outlier: 4.374A pdb=" N ASN D 220 " --> pdb=" O MET D 231 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N CYS D 228 " --> pdb=" O ILE D 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 275 through 279 205 hydrogen bonds defined for protein. 613 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 439 hydrogen bonds 692 hydrogen bond angles 0 basepair planarities 177 basepair parallelities 312 stacking parallelities Total time for adding SS restraints: 3.45 Time building geometry restraints manager: 1.55 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: 1878 1.33 - 1.45: 7659 1.45 - 1.57: 5863 1.57 - 1.69: 1096 1.69 - 1.82: 35 Bond restraints: 16531 Sorted by residual: bond pdb=" C ASP D 265 " pdb=" N ARG D 266 " ideal model delta sigma weight residual 1.335 1.250 0.084 3.04e-02 1.08e+03 7.69e+00 bond pdb=" CB MET D 354 " pdb=" CG MET D 354 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.90e+00 bond pdb=" SD MET D 354 " pdb=" CE MET D 354 " ideal model delta sigma weight residual 1.791 1.743 0.048 2.50e-02 1.60e+03 3.75e+00 bond pdb=" C2' A B 370 " pdb=" O2' A B 370 " ideal model delta sigma weight residual 1.420 1.395 0.025 1.50e-02 4.44e+03 2.82e+00 bond pdb=" SD MET D 337 " pdb=" CE MET D 337 " ideal model delta sigma weight residual 1.791 1.749 0.042 2.50e-02 1.60e+03 2.78e+00 ... (remaining 16526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 24936 4.84 - 9.68: 125 9.68 - 14.52: 4 14.52 - 19.36: 0 19.36 - 24.20: 1 Bond angle restraints: 25066 Sorted by residual: angle pdb=" C ASP D 265 " pdb=" N ARG D 266 " pdb=" CA ARG D 266 " ideal model delta sigma weight residual 121.95 146.15 -24.20 3.74e+00 7.15e-02 4.19e+01 angle pdb=" C ALA D 225 " pdb=" N ASP D 226 " pdb=" CA ASP D 226 " ideal model delta sigma weight residual 122.61 131.23 -8.62 1.56e+00 4.11e-01 3.05e+01 angle pdb=" O3' C B 206 " pdb=" C3' C B 206 " pdb=" C2' C B 206 " ideal model delta sigma weight residual 113.70 121.28 -7.58 1.50e+00 4.44e-01 2.56e+01 angle pdb=" C3' A B 67 " pdb=" O3' A B 67 " pdb=" P U B 68 " ideal model delta sigma weight residual 120.20 127.49 -7.29 1.50e+00 4.44e-01 2.36e+01 angle pdb=" O3' U B 46 " pdb=" C3' U B 46 " pdb=" C2' U B 46 " ideal model delta sigma weight residual 113.70 120.78 -7.08 1.50e+00 4.44e-01 2.23e+01 ... (remaining 25061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 8656 35.34 - 70.68: 1167 70.68 - 106.02: 158 106.02 - 141.36: 8 141.36 - 176.70: 9 Dihedral angle restraints: 9998 sinusoidal: 8853 harmonic: 1145 Sorted by residual: dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N ILE D 101 " pdb=" CA ILE D 101 " ideal model delta harmonic sigma weight residual -180.00 -128.31 -51.69 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" O4' C B 138 " pdb=" C1' C B 138 " pdb=" N1 C B 138 " pdb=" C2 C B 138 " ideal model delta sinusoidal sigma weight residual -160.00 16.70 -176.70 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U B 361 " pdb=" C1' U B 361 " pdb=" N1 U B 361 " pdb=" C2 U B 361 " ideal model delta sinusoidal sigma weight residual 200.00 48.56 151.44 1 1.50e+01 4.44e-03 8.01e+01 ... (remaining 9995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2960 0.074 - 0.148: 241 0.148 - 0.221: 18 0.221 - 0.295: 6 0.295 - 0.369: 7 Chirality restraints: 3232 Sorted by residual: chirality pdb=" C1' A B 51 " pdb=" O4' A B 51 " pdb=" C2' A B 51 " pdb=" N9 A B 51 " both_signs ideal model delta sigma weight residual False 2.46 2.09 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" C3' U B 46 " pdb=" C4' U B 46 " pdb=" O3' U B 46 " pdb=" C2' U B 46 " both_signs ideal model delta sigma weight residual False -2.48 -2.13 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C3' G B 348 " pdb=" C4' G B 348 " pdb=" O3' G B 348 " pdb=" C2' G B 348 " both_signs ideal model delta sigma weight residual False -2.74 -2.40 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 3229 not shown) Planarity restraints: 1108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 99 " -0.057 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO D 100 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A B 51 " 0.038 2.00e-02 2.50e+03 1.81e-02 9.05e+00 pdb=" N9 A B 51 " -0.045 2.00e-02 2.50e+03 pdb=" C8 A B 51 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A B 51 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A B 51 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 51 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 51 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A B 51 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A B 51 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A B 51 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A B 51 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 436 " 0.037 2.00e-02 2.50e+03 1.93e-02 8.37e+00 pdb=" N1 U B 436 " -0.040 2.00e-02 2.50e+03 pdb=" C2 U B 436 " -0.007 2.00e-02 2.50e+03 pdb=" O2 U B 436 " -0.000 2.00e-02 2.50e+03 pdb=" N3 U B 436 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U B 436 " 0.008 2.00e-02 2.50e+03 pdb=" O4 U B 436 " 0.012 2.00e-02 2.50e+03 pdb=" C5 U B 436 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U B 436 " -0.007 2.00e-02 2.50e+03 ... (remaining 1105 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1629 2.72 - 3.26: 12266 3.26 - 3.81: 32606 3.81 - 4.35: 39407 4.35 - 4.90: 50689 Nonbonded interactions: 136597 Sorted by model distance: nonbonded pdb=" O2' A B 370 " pdb=" O4' G B 371 " model vdw 2.174 3.040 nonbonded pdb=" O2' G B 136 " pdb=" OP1 U B 148 " model vdw 2.239 3.040 nonbonded pdb=" OG SER D 415 " pdb=" OD2 ASP D 418 " model vdw 2.285 3.040 nonbonded pdb=" OP2 A B 137 " pdb=" O2' A B 147 " model vdw 2.290 3.040 nonbonded pdb=" OG SER D 110 " pdb=" OD2 ASP D 211 " model vdw 2.295 3.040 ... (remaining 136592 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.760 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: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.830 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 0.084 16531 Z= 0.294 Angle : 0.956 24.199 25066 Z= 0.456 Chirality : 0.045 0.369 3232 Planarity : 0.007 0.086 1108 Dihedral : 24.254 176.698 9262 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.14 % Favored : 96.34 % Rotamer: Outliers : 1.15 % Allowed : 23.34 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -2.13 (0.34), residues: 394 helix: -0.97 (0.26), residues: 272 sheet: -1.11 (1.04), residues: 20 loop : -2.29 (0.49), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 217 TYR 0.029 0.003 TYR D 350 PHE 0.018 0.003 PHE D 221 TRP 0.009 0.002 TRP D 328 HIS 0.003 0.001 HIS D 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.29 (16531) covalent geometry : angle 0.95636 / 0.46 (25066) hydrogen bonds : bond 0.13901 / 8.70 ( 644) hydrogen bonds : angle 5.28168 / 3.78 ( 1305) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.217 Fit side-chains REVERT: D 197 ASN cc_start: 0.6283 (t0) cc_final: 0.5914 (t0) REVERT: D 216 LYS cc_start: 0.8625 (tmtt) cc_final: 0.8217 (tttt) REVERT: D 236 MET cc_start: 0.5233 (ppp) cc_final: 0.4107 (ttp) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1523 time to fit residues: 8.3004 Evaluate side-chains 33 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.172964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.115533 restraints weight = 46834.726| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.14 r_work: 0.3003 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 16531 Z= 0.367 Angle : 0.769 10.333 25066 Z= 0.384 Chirality : 0.041 0.315 3232 Planarity : 0.006 0.079 1108 Dihedral : 24.337 176.211 8440 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.93 % Favored : 95.55 % Rotamer: Outliers : 3.46 % Allowed : 22.48 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 (0.39), residues: 394 helix: 0.37 (0.30), residues: 272 sheet: -0.77 (1.06), residues: 20 loop : -2.17 (0.54), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 353 TYR 0.024 0.002 TYR D 385 PHE 0.013 0.002 PHE D 298 TRP 0.011 0.002 TRP D 136 HIS 0.005 0.002 HIS D 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.37 (16531) covalent geometry : angle 0.76926 / 0.38 (25066) hydrogen bonds : bond 0.08201 / 5.37 ( 644) hydrogen bonds : angle 3.60717 / 2.60 ( 1305) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.268 Fit side-chains REVERT: D 88 ARG cc_start: 0.7509 (ttm110) cc_final: 0.6872 (mtm110) REVERT: D 216 LYS cc_start: 0.8729 (tmtt) cc_final: 0.8407 (tttt) REVERT: D 236 MET cc_start: 0.5672 (ppp) cc_final: 0.5298 (ttp) REVERT: D 247 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7611 (tmm-80) outliers start: 8 outliers final: 5 residues processed: 32 average time/residue: 0.1382 time to fit residues: 6.5486 Evaluate side-chains 31 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 399 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.176140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.134490 restraints weight = 53142.714| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.53 r_work: 0.3069 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 16531 Z= 0.290 Angle : 0.689 8.200 25066 Z= 0.347 Chirality : 0.038 0.310 3232 Planarity : 0.005 0.078 1108 Dihedral : 24.188 177.348 8440 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.19 % Favored : 95.29 % Rotamer: Outliers : 4.61 % Allowed : 22.19 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 0.16 (0.41), residues: 394 helix: 0.93 (0.31), residues: 273 sheet: -0.91 (0.96), residues: 22 loop : -1.90 (0.57), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 247 TYR 0.024 0.002 TYR D 385 PHE 0.013 0.002 PHE D 145 TRP 0.009 0.002 TRP D 136 HIS 0.004 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.29 (16531) covalent geometry : angle 0.68864 / 0.35 (25066) hydrogen bonds : bond 0.07393 / 4.84 ( 644) hydrogen bonds : angle 3.43519 / 2.47 ( 1305) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.266 Fit side-chains REVERT: D 88 ARG cc_start: 0.7482 (ttm110) cc_final: 0.6781 (mtm110) REVERT: D 216 LYS cc_start: 0.8717 (tmtt) cc_final: 0.8416 (tttt) REVERT: D 236 MET cc_start: 0.5973 (ppp) cc_final: 0.5523 (ttp) REVERT: D 247 ARG cc_start: 0.7987 (ttp80) cc_final: 0.7660 (tmm-80) outliers start: 12 outliers final: 10 residues processed: 37 average time/residue: 0.1301 time to fit residues: 7.1645 Evaluate side-chains 38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 399 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.178853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.136260 restraints weight = 50171.888| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 0.99 r_work: 0.3133 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16531 Z= 0.159 Angle : 0.598 7.090 25066 Z= 0.301 Chirality : 0.033 0.311 3232 Planarity : 0.005 0.081 1108 Dihedral : 24.123 175.535 8440 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.52 % Allowed : 2.88 % Favored : 96.60 % Rotamer: Outliers : 4.61 % Allowed : 22.19 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 0.75 (0.43), residues: 394 helix: 1.47 (0.32), residues: 273 sheet: -0.90 (0.98), residues: 22 loop : -1.91 (0.58), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 247 TYR 0.016 0.002 TYR D 350 PHE 0.010 0.001 PHE D 145 TRP 0.008 0.001 TRP D 136 HIS 0.003 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (16531) covalent geometry : angle 0.59769 / 0.30 (25066) hydrogen bonds : bond 0.06216 / 4.07 ( 644) hydrogen bonds : angle 3.21809 / 2.34 ( 1305) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: D 88 ARG cc_start: 0.7430 (ttm110) cc_final: 0.6729 (mtm110) REVERT: D 197 ASN cc_start: 0.6447 (t0) cc_final: 0.6127 (t0) REVERT: D 216 LYS cc_start: 0.8682 (tmtt) cc_final: 0.8441 (tttt) REVERT: D 236 MET cc_start: 0.6125 (ppp) cc_final: 0.5694 (ttp) REVERT: D 247 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7625 (tmm-80) REVERT: D 396 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7889 (pttp) outliers start: 12 outliers final: 9 residues processed: 44 average time/residue: 0.1439 time to fit residues: 9.0677 Evaluate side-chains 42 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 396 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 38 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.177527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.134548 restraints weight = 44912.466| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.13 r_work: 0.3092 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16531 Z= 0.215 Angle : 0.622 7.293 25066 Z= 0.313 Chirality : 0.034 0.296 3232 Planarity : 0.005 0.082 1108 Dihedral : 24.053 177.368 8440 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.66 % Favored : 95.81 % Rotamer: Outliers : 4.03 % Allowed : 22.48 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.43), residues: 394 helix: 1.71 (0.32), residues: 272 sheet: -0.73 (0.99), residues: 22 loop : -1.94 (0.58), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 247 TYR 0.022 0.002 TYR D 385 PHE 0.011 0.002 PHE D 145 TRP 0.007 0.001 TRP D 136 HIS 0.003 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.21 (16531) covalent geometry : angle 0.62211 / 0.31 (25066) hydrogen bonds : bond 0.06892 / 4.55 ( 644) hydrogen bonds : angle 3.19763 / 2.32 ( 1305) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.164 Fit side-chains REVERT: D 88 ARG cc_start: 0.7357 (ttm110) cc_final: 0.6649 (mtm110) REVERT: D 197 ASN cc_start: 0.6626 (t0) cc_final: 0.6195 (t0) REVERT: D 216 LYS cc_start: 0.8714 (tmtt) cc_final: 0.8475 (tttt) REVERT: D 236 MET cc_start: 0.6158 (ppp) cc_final: 0.5664 (ttp) REVERT: D 247 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7634 (tmm-80) REVERT: D 396 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.7997 (pttp) outliers start: 10 outliers final: 8 residues processed: 37 average time/residue: 0.1270 time to fit residues: 6.8260 Evaluate side-chains 39 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 396 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 20 optimal weight: 0.8980 chunk 79 optimal weight: 20.0000 chunk 37 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.0770 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.179177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.139061 restraints weight = 59474.345| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.01 r_work: 0.3124 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16531 Z= 0.157 Angle : 0.595 6.946 25066 Z= 0.300 Chirality : 0.033 0.290 3232 Planarity : 0.005 0.082 1108 Dihedral : 24.069 176.730 8440 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.14 % Favored : 96.34 % Rotamer: Outliers : 3.75 % Allowed : 23.34 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.43), residues: 394 helix: 1.84 (0.32), residues: 273 sheet: -0.64 (1.02), residues: 22 loop : -1.81 (0.60), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 247 TYR 0.019 0.002 TYR D 385 PHE 0.010 0.001 PHE D 145 TRP 0.008 0.001 TRP D 136 HIS 0.002 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (16531) covalent geometry : angle 0.59476 / 0.30 (25066) hydrogen bonds : bond 0.06559 / 4.31 ( 644) hydrogen bonds : angle 3.13921 / 2.28 ( 1305) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.209 Fit side-chains REVERT: D 88 ARG cc_start: 0.7394 (ttm110) cc_final: 0.6697 (mtm110) REVERT: D 197 ASN cc_start: 0.6607 (t0) cc_final: 0.6209 (t0) REVERT: D 216 LYS cc_start: 0.8716 (tmtt) cc_final: 0.8473 (tttt) REVERT: D 236 MET cc_start: 0.6194 (ppp) cc_final: 0.5767 (ttp) REVERT: D 247 ARG cc_start: 0.8018 (ttp80) cc_final: 0.7653 (tmm-80) REVERT: D 396 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7948 (pttp) outliers start: 9 outliers final: 7 residues processed: 37 average time/residue: 0.1342 time to fit residues: 7.1497 Evaluate side-chains 38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 396 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 91 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.173605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.128423 restraints weight = 58636.077| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.01 r_work: 0.3006 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 16531 Z= 0.473 Angle : 0.821 8.244 25066 Z= 0.408 Chirality : 0.045 0.317 3232 Planarity : 0.006 0.079 1108 Dihedral : 24.156 177.859 8440 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.45 % Favored : 95.03 % Rotamer: Outliers : 4.32 % Allowed : 22.77 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.41), residues: 394 helix: 1.26 (0.31), residues: 272 sheet: -0.54 (1.01), residues: 22 loop : -2.01 (0.56), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 353 TYR 0.028 0.003 TYR D 385 PHE 0.014 0.003 PHE D 145 TRP 0.008 0.002 TRP D 136 HIS 0.006 0.002 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00910 / 0.47 (16531) covalent geometry : angle 0.82148 / 0.41 (25066) hydrogen bonds : bond 0.09108 / 5.98 ( 644) hydrogen bonds : angle 3.51215 / 2.54 ( 1305) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.197 Fit side-chains REVERT: D 216 LYS cc_start: 0.8677 (tmtt) cc_final: 0.8447 (tttt) REVERT: D 396 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.7976 (pttm) outliers start: 11 outliers final: 10 residues processed: 38 average time/residue: 0.1398 time to fit residues: 7.7021 Evaluate side-chains 40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 399 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 69 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 89 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 80 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.181483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.135419 restraints weight = 44674.768| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.17 r_work: 0.3160 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16531 Z= 0.155 Angle : 0.580 7.231 25066 Z= 0.293 Chirality : 0.032 0.294 3232 Planarity : 0.005 0.082 1108 Dihedral : 23.999 175.642 8440 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.52 % Allowed : 2.62 % Favored : 96.86 % Rotamer: Outliers : 3.75 % Allowed : 22.77 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.42), residues: 394 helix: 1.78 (0.31), residues: 273 sheet: -0.98 (0.96), residues: 22 loop : -1.75 (0.60), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 247 TYR 0.019 0.001 TYR D 385 PHE 0.011 0.001 PHE D 145 TRP 0.007 0.001 TRP D 357 HIS 0.001 0.001 HIS D 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.16 (16531) covalent geometry : angle 0.57960 / 0.29 (25066) hydrogen bonds : bond 0.06172 / 4.06 ( 644) hydrogen bonds : angle 3.13037 / 2.28 ( 1305) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.255 Fit side-chains REVERT: D 88 ARG cc_start: 0.7250 (ttm110) cc_final: 0.6803 (mtp180) REVERT: D 197 ASN cc_start: 0.6465 (t0) cc_final: 0.6101 (t0) REVERT: D 216 LYS cc_start: 0.8754 (tmtt) cc_final: 0.8506 (tttt) REVERT: D 236 MET cc_start: 0.5996 (ppp) cc_final: 0.5456 (ttp) REVERT: D 247 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7676 (tmm-80) REVERT: D 396 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.7949 (pptt) outliers start: 9 outliers final: 6 residues processed: 37 average time/residue: 0.1614 time to fit residues: 8.4316 Evaluate side-chains 37 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 396 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.179698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.135421 restraints weight = 48585.317| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.21 r_work: 0.3125 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16531 Z= 0.186 Angle : 0.595 7.257 25066 Z= 0.300 Chirality : 0.033 0.268 3232 Planarity : 0.005 0.082 1108 Dihedral : 23.929 177.693 8440 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.40 % Favored : 96.07 % Rotamer: Outliers : 4.03 % Allowed : 22.19 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.43), residues: 394 helix: 1.96 (0.31), residues: 272 sheet: -0.77 (0.97), residues: 22 loop : -1.84 (0.59), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 247 TYR 0.021 0.001 TYR D 385 PHE 0.010 0.001 PHE D 145 TRP 0.006 0.001 TRP D 136 HIS 0.002 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.19 (16531) covalent geometry : angle 0.59457 / 0.30 (25066) hydrogen bonds : bond 0.06576 / 4.33 ( 644) hydrogen bonds : angle 3.15612 / 2.30 ( 1305) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.273 Fit side-chains REVERT: D 88 ARG cc_start: 0.7179 (ttm110) cc_final: 0.6605 (mtm110) REVERT: D 197 ASN cc_start: 0.6656 (t0) cc_final: 0.6204 (t0) REVERT: D 216 LYS cc_start: 0.8734 (tmtt) cc_final: 0.8486 (tttt) REVERT: D 236 MET cc_start: 0.5950 (ppp) cc_final: 0.5634 (ttp) REVERT: D 247 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7686 (tmm-80) REVERT: D 338 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7584 (mttp) REVERT: D 396 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8220 (pttm) outliers start: 10 outliers final: 8 residues processed: 37 average time/residue: 0.1594 time to fit residues: 8.3929 Evaluate side-chains 39 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 338 LYS Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 399 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 59 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 80 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.178650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129710 restraints weight = 44558.472| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.52 r_work: 0.3094 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16531 Z= 0.257 Angle : 0.634 7.511 25066 Z= 0.319 Chirality : 0.035 0.265 3232 Planarity : 0.005 0.081 1108 Dihedral : 23.913 177.520 8440 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.45 % Favored : 95.03 % Rotamer: Outliers : 3.75 % Allowed : 22.48 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.43), residues: 394 helix: 1.90 (0.31), residues: 272 sheet: -0.74 (0.97), residues: 22 loop : -1.84 (0.59), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 247 TYR 0.025 0.002 TYR D 385 PHE 0.011 0.002 PHE D 145 TRP 0.006 0.001 TRP D 136 HIS 0.003 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.26 (16531) covalent geometry : angle 0.63408 / 0.32 (25066) hydrogen bonds : bond 0.07033 / 4.63 ( 644) hydrogen bonds : angle 3.21711 / 2.34 ( 1305) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.242 Fit side-chains REVERT: D 88 ARG cc_start: 0.7182 (ttm110) cc_final: 0.6729 (mtp180) REVERT: D 197 ASN cc_start: 0.6603 (t0) cc_final: 0.6135 (t0) REVERT: D 216 LYS cc_start: 0.8694 (tmtt) cc_final: 0.8459 (tttt) REVERT: D 247 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7684 (tmm-80) REVERT: D 396 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8039 (pttp) outliers start: 9 outliers final: 8 residues processed: 37 average time/residue: 0.1401 time to fit residues: 7.4707 Evaluate side-chains 38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 399 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 64 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.179111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.129324 restraints weight = 39909.445| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.56 r_work: 0.3104 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16531 Z= 0.229 Angle : 0.622 7.440 25066 Z= 0.313 Chirality : 0.034 0.260 3232 Planarity : 0.005 0.081 1108 Dihedral : 23.928 177.426 8440 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.45 % Favored : 95.03 % Rotamer: Outliers : 4.03 % Allowed : 22.19 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.43), residues: 394 helix: 1.94 (0.31), residues: 272 sheet: -0.73 (0.97), residues: 22 loop : -1.83 (0.59), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 247 TYR 0.023 0.002 TYR D 385 PHE 0.010 0.002 PHE D 145 TRP 0.006 0.001 TRP D 136 HIS 0.003 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.23 (16531) covalent geometry : angle 0.62220 / 0.31 (25066) hydrogen bonds : bond 0.06959 / 4.57 ( 644) hydrogen bonds : angle 3.20388 / 2.33 ( 1305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3481.08 seconds wall clock time: 60 minutes 21.81 seconds (3621.81 seconds total)