Starting phenix.real_space_refine on Wed Jul 1 22:57:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u47_63833/07_2026/9u47_63833.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u47_63833/07_2026/9u47_63833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u47_63833/07_2026/9u47_63833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u47_63833/07_2026/9u47_63833.map" model { file = "/net/cci-nas-00/data/ceres_data/9u47_63833/07_2026/9u47_63833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u47_63833/07_2026/9u47_63833.cif" } resolution = 3.4 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 436 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 42 5.49 5 S 18 5.16 5 C 1976 2.51 5 N 588 2.21 5 O 750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 3374 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 896 Classifications: {'RNA': 42} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna2p': 5, 'rna3p': 36} Chain: "A" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2478 Classifications: {'peptide': 308} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 296} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P U B 82 " occ=0.50 ... (18 atoms not shown) pdb=" C6 U B 82 " occ=0.50 Time building chain proxies: 0.88, per 1000 atoms: 0.26 Number of scatterers: 3374 At special positions: 0 Unit cell: (66.4, 82.17, 88.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 42 15.00 O 750 8.00 N 588 7.00 C 1976 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: 0.24 Conformation dependent library (CDL) restraints added in 122.9 milliseconds 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 582 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 2 sheets defined 40.3% alpha, 21.4% beta 13 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 63 through 80 Processing helix chain 'A' and resid 101 through 112 removed outlier: 4.040A pdb=" N LEU A 105 " --> pdb=" O CYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 202 through 215 removed outlier: 3.599A pdb=" N LYS A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 241 removed outlier: 4.581A pdb=" N ALA A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.664A pdb=" N ILE A 277 " --> pdb=" O HIS A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.172A pdb=" N LEU A 284 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 316 removed outlier: 5.320A pdb=" N ASP A 307 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASP A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 346 Processing helix chain 'A' and resid 378 through 395 removed outlier: 4.351A pdb=" N TYR A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 141 through 145 removed outlier: 6.564A pdb=" N GLY A 92 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR A 118 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP A 94 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A 91 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N MET A 166 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU A 93 " --> pdb=" O MET A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 296 removed outlier: 6.343A pdb=" N LYS A 359 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLY A 356 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 334 " --> pdb=" O GLY A 356 " (cutoff:3.500A) 119 hydrogen bonds defined for protein. 345 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 0.35 Time building geometry restraints manager: 0.29 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: 466 1.32 - 1.44: 1190 1.44 - 1.57: 1766 1.57 - 1.70: 83 1.70 - 1.83: 26 Bond restraints: 3531 Sorted by residual: bond pdb=" N PRO A 154 " pdb=" CA PRO A 154 " ideal model delta sigma weight residual 1.465 1.426 0.039 1.10e-02 8.26e+03 1.24e+01 bond pdb=" C PRO A 154 " pdb=" O PRO A 154 " ideal model delta sigma weight residual 1.232 1.187 0.044 1.31e-02 5.83e+03 1.13e+01 bond pdb=" C LEU A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 1.328 1.367 -0.038 1.26e-02 6.30e+03 9.34e+00 bond pdb=" N7 A B 64 " pdb=" C5 A B 64 " ideal model delta sigma weight residual 1.388 1.371 0.017 6.00e-03 2.78e+04 8.50e+00 bond pdb=" C THR A 336 " pdb=" N TRP A 337 " ideal model delta sigma weight residual 1.330 1.366 -0.036 1.28e-02 6.10e+03 8.09e+00 ... (remaining 3526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 4662 1.66 - 3.32: 240 3.32 - 4.98: 49 4.98 - 6.64: 10 6.64 - 8.31: 3 Bond angle restraints: 4964 Sorted by residual: angle pdb=" CA TRP A 337 " pdb=" C TRP A 337 " pdb=" O TRP A 337 " ideal model delta sigma weight residual 121.78 116.43 5.35 1.12e+00 7.97e-01 2.28e+01 angle pdb=" N PRO A 154 " pdb=" CA PRO A 154 " pdb=" CB PRO A 154 " ideal model delta sigma weight residual 103.15 109.21 -6.06 1.29e+00 6.01e-01 2.20e+01 angle pdb=" C ALA A 341 " pdb=" N ARG A 342 " pdb=" CA ARG A 342 " ideal model delta sigma weight residual 120.63 114.91 5.72 1.36e+00 5.41e-01 1.77e+01 angle pdb=" N TRP A 337 " pdb=" CA TRP A 337 " pdb=" C TRP A 337 " ideal model delta sigma weight residual 110.06 116.00 -5.94 1.43e+00 4.89e-01 1.73e+01 angle pdb=" N1 C B 76 " pdb=" C6 C B 76 " pdb=" C5 C B 76 " ideal model delta sigma weight residual 121.00 123.05 -2.05 5.00e-01 4.00e+00 1.68e+01 ... (remaining 4959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 1943 14.97 - 29.93: 109 29.93 - 44.90: 54 44.90 - 59.87: 41 59.87 - 74.83: 35 Dihedral angle restraints: 2182 sinusoidal: 1282 harmonic: 900 Sorted by residual: dihedral pdb=" CA LEU A 354 " pdb=" C LEU A 354 " pdb=" N GLU A 355 " pdb=" CA GLU A 355 " ideal model delta harmonic sigma weight residual -180.00 -156.74 -23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA GLN A 268 " pdb=" C GLN A 268 " pdb=" N ALA A 269 " pdb=" CA ALA A 269 " ideal model delta harmonic sigma weight residual -180.00 -158.43 -21.57 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" N PRO A 154 " pdb=" C PRO A 154 " pdb=" CA PRO A 154 " pdb=" CB PRO A 154 " ideal model delta harmonic sigma weight residual 115.10 125.83 -10.73 0 2.50e+00 1.60e-01 1.84e+01 ... (remaining 2179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 533 0.095 - 0.190: 46 0.190 - 0.285: 0 0.285 - 0.380: 0 0.380 - 0.475: 1 Chirality restraints: 580 Sorted by residual: chirality pdb=" CA PRO A 154 " pdb=" N PRO A 154 " pdb=" C PRO A 154 " pdb=" CB PRO A 154 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.47 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" C2' A B 70 " pdb=" C3' A B 70 " pdb=" O2' A B 70 " pdb=" C1' A B 70 " both_signs ideal model delta sigma weight residual False -2.75 -2.58 -0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" C4' U B 58 " pdb=" C5' U B 58 " pdb=" O4' U B 58 " pdb=" C3' U B 58 " both_signs ideal model delta sigma weight residual False -2.50 -2.33 -0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 577 not shown) Planarity restraints: 471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 373 " -0.016 2.00e-02 2.50e+03 1.81e-02 8.23e+00 pdb=" CG TRP A 373 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP A 373 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 373 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 373 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 373 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 373 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 373 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 373 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 373 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 299 " 0.040 5.00e-02 4.00e+02 5.98e-02 5.71e+00 pdb=" N PRO A 300 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 300 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 300 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 277 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.57e+00 pdb=" C ILE A 277 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE A 277 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG A 278 " 0.014 2.00e-02 2.50e+03 ... (remaining 468 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 722 2.79 - 3.31: 2850 3.31 - 3.84: 5961 3.84 - 4.37: 6987 4.37 - 4.90: 10382 Nonbonded interactions: 26902 Sorted by model distance: nonbonded pdb=" OE2 GLU A 203 " pdb=" OG SER A 232 " model vdw 2.256 3.040 nonbonded pdb=" O2' C B 55 " pdb=" NE ARG A 391 " model vdw 2.261 3.120 nonbonded pdb=" O2' C B 79 " pdb=" O4' A B 80 " model vdw 2.270 3.040 nonbonded pdb=" O LEU A 77 " pdb=" OG1 THR A 81 " model vdw 2.316 3.040 nonbonded pdb=" OH TYR A 70 " pdb=" OG1 THR A 224 " model vdw 2.332 3.040 ... (remaining 26897 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=0.50 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.480 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5711 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 0.063 3531 Z= 0.385 Angle : 0.899 8.306 4964 Z= 0.635 Chirality : 0.054 0.475 580 Planarity : 0.006 0.060 471 Dihedral : 16.671 74.832 1600 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.34 % 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: -2.80 (0.43), residues: 304 helix: -1.72 (0.42), residues: 108 sheet: -0.93 (0.60), residues: 77 loop : -2.48 (0.50), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 271 TYR 0.020 0.004 TYR A 382 PHE 0.021 0.003 PHE A 164 TRP 0.049 0.005 TRP A 373 HIS 0.001 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.39 ( 3531) covalent geometry : angle 0.89875 / 0.63 ( 4964) hydrogen bonds : bond 0.14913 / 16.05 ( 151) hydrogen bonds : angle 7.76636 / 9.07 ( 397) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: A 77 LEU cc_start: 0.7823 (tp) cc_final: 0.7468 (tp) REVERT: A 248 TYR cc_start: 0.7545 (p90) cc_final: 0.6876 (p90) REVERT: A 250 ILE cc_start: 0.8093 (mt) cc_final: 0.7828 (tt) REVERT: A 264 CYS cc_start: 0.6421 (p) cc_final: 0.5430 (p) REVERT: A 358 MET cc_start: 0.6750 (ttp) cc_final: 0.6493 (ttt) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0521 time to fit residues: 4.3397 Evaluate side-chains 58 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 ASN A 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.200708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.176950 restraints weight = 5850.496| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 3.25 r_work: 0.4201 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4200 r_free = 0.4200 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4200 r_free = 0.4200 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6232 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3531 Z= 0.186 Angle : 0.615 5.803 4964 Z= 0.346 Chirality : 0.041 0.156 580 Planarity : 0.005 0.045 471 Dihedral : 19.641 74.599 971 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.43 % Allowed : 9.68 % Favored : 88.89 % 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: -1.42 (0.47), residues: 304 helix: -0.19 (0.47), residues: 116 sheet: -0.76 (0.57), residues: 77 loop : -1.74 (0.59), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 343 TYR 0.012 0.002 TYR A 111 PHE 0.016 0.002 PHE A 164 TRP 0.027 0.003 TRP A 222 HIS 0.003 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 ( 3531) covalent geometry : angle 0.61451 / 0.35 ( 4964) hydrogen bonds : bond 0.05578 / 4.98 ( 151) hydrogen bonds : angle 6.11109 / 7.09 ( 397) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.058 Fit side-chains REVERT: A 163 THR cc_start: 0.5925 (p) cc_final: 0.5325 (m) REVERT: A 224 THR cc_start: 0.7497 (p) cc_final: 0.7231 (p) REVERT: A 250 ILE cc_start: 0.8183 (mt) cc_final: 0.7940 (mt) REVERT: A 252 GLU cc_start: 0.5325 (tt0) cc_final: 0.4980 (tt0) outliers start: 4 outliers final: 2 residues processed: 61 average time/residue: 0.0490 time to fit residues: 3.5885 Evaluate side-chains 59 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 GLN ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.199295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.176125 restraints weight = 5771.462| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 3.14 r_work: 0.4181 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4179 r_free = 0.4179 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4179 r_free = 0.4179 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.4179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3531 Z= 0.184 Angle : 0.574 6.008 4964 Z= 0.321 Chirality : 0.040 0.145 580 Planarity : 0.006 0.056 471 Dihedral : 19.598 74.126 971 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.87 % Allowed : 8.60 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.48), residues: 304 helix: 0.37 (0.48), residues: 116 sheet: -0.67 (0.57), residues: 76 loop : -1.43 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 260 TYR 0.030 0.002 TYR A 382 PHE 0.014 0.002 PHE A 164 TRP 0.012 0.002 TRP A 222 HIS 0.002 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 ( 3531) covalent geometry : angle 0.57378 / 0.32 ( 4964) hydrogen bonds : bond 0.05015 / 4.73 ( 151) hydrogen bonds : angle 5.91386 / 7.00 ( 397) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: A 159 MET cc_start: 0.6266 (mpp) cc_final: 0.6004 (mpp) REVERT: A 163 THR cc_start: 0.5957 (p) cc_final: 0.5355 (m) REVERT: A 224 THR cc_start: 0.7471 (p) cc_final: 0.7248 (p) REVERT: A 250 ILE cc_start: 0.8212 (mt) cc_final: 0.7962 (mt) REVERT: A 342 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.6431 (mtm-85) outliers start: 8 outliers final: 3 residues processed: 61 average time/residue: 0.0599 time to fit residues: 4.4141 Evaluate side-chains 60 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 33 optimal weight: 0.6980 chunk 29 optimal weight: 0.0020 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.198906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.176058 restraints weight = 5676.870| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 3.10 r_work: 0.4177 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4176 r_free = 0.4176 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4176 r_free = 0.4176 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3531 Z= 0.165 Angle : 0.546 5.274 4964 Z= 0.306 Chirality : 0.040 0.148 580 Planarity : 0.005 0.044 471 Dihedral : 19.642 74.149 971 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.87 % Allowed : 10.39 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.49), residues: 304 helix: 0.68 (0.50), residues: 116 sheet: -0.53 (0.59), residues: 76 loop : -1.16 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 260 TYR 0.036 0.002 TYR A 382 PHE 0.018 0.002 PHE A 164 TRP 0.011 0.002 TRP A 265 HIS 0.003 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 ( 3531) covalent geometry : angle 0.54641 / 0.31 ( 4964) hydrogen bonds : bond 0.04500 / 4.37 ( 151) hydrogen bonds : angle 5.82444 / 6.90 ( 397) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.056 Fit side-chains revert: symmetry clash REVERT: A 159 MET cc_start: 0.6439 (mpp) cc_final: 0.5758 (mpp) REVERT: A 163 THR cc_start: 0.6186 (p) cc_final: 0.5615 (m) REVERT: A 250 ILE cc_start: 0.8268 (mt) cc_final: 0.8026 (mt) REVERT: A 252 GLU cc_start: 0.5576 (tt0) cc_final: 0.5372 (tt0) REVERT: A 342 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6548 (mtm-85) outliers start: 8 outliers final: 4 residues processed: 61 average time/residue: 0.0495 time to fit residues: 3.6427 Evaluate side-chains 62 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 386 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 20 optimal weight: 0.0770 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.0570 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 14 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN A 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.201717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.179080 restraints weight = 5658.572| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 3.15 r_work: 0.4188 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4188 r_free = 0.4188 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4188 r_free = 0.4188 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3531 Z= 0.129 Angle : 0.524 5.272 4964 Z= 0.295 Chirality : 0.040 0.282 580 Planarity : 0.005 0.043 471 Dihedral : 19.578 74.103 971 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.51 % Allowed : 12.54 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.50), residues: 304 helix: 1.02 (0.51), residues: 116 sheet: -0.53 (0.60), residues: 78 loop : -0.89 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 260 TYR 0.035 0.002 TYR A 382 PHE 0.016 0.001 PHE A 164 TRP 0.012 0.001 TRP A 265 HIS 0.002 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 3531) covalent geometry : angle 0.52355 / 0.29 ( 4964) hydrogen bonds : bond 0.03971 / 3.90 ( 151) hydrogen bonds : angle 5.73669 / 6.89 ( 397) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: A 159 MET cc_start: 0.6323 (mpp) cc_final: 0.5657 (mpp) REVERT: A 240 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7738 (mt) REVERT: A 250 ILE cc_start: 0.8275 (mt) cc_final: 0.8032 (mt) REVERT: A 342 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6550 (mtm-85) outliers start: 7 outliers final: 4 residues processed: 62 average time/residue: 0.0450 time to fit residues: 3.3915 Evaluate side-chains 62 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 386 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 0.0070 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 0.0270 chunk 2 optimal weight: 3.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.200630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.177997 restraints weight = 5703.078| |-----------------------------------------------------------------------------| r_work (start): 0.4329 rms_B_bonded: 3.15 r_work: 0.4182 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4195 r_free = 0.4195 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4195 r_free = 0.4195 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3531 Z= 0.152 Angle : 0.565 5.324 4964 Z= 0.318 Chirality : 0.040 0.211 580 Planarity : 0.005 0.047 471 Dihedral : 19.585 74.113 971 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.51 % Allowed : 11.83 % Favored : 85.66 % 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 (0.49), residues: 304 helix: 1.06 (0.51), residues: 115 sheet: -0.41 (0.62), residues: 76 loop : -0.94 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 271 TYR 0.038 0.002 TYR A 382 PHE 0.014 0.001 PHE A 164 TRP 0.010 0.001 TRP A 265 HIS 0.002 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 3531) covalent geometry : angle 0.56487 / 0.32 ( 4964) hydrogen bonds : bond 0.04227 / 4.11 ( 151) hydrogen bonds : angle 5.67610 / 6.87 ( 397) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6387 (mpp) cc_final: 0.5730 (mpp) REVERT: A 240 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7740 (mt) REVERT: A 250 ILE cc_start: 0.8251 (mt) cc_final: 0.8018 (mt) REVERT: A 342 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6609 (mtm-85) outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 0.0600 time to fit residues: 4.3094 Evaluate side-chains 63 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 386 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.198301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.175863 restraints weight = 5748.870| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 3.12 r_work: 0.4148 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4154 r_free = 0.4154 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4154 r_free = 0.4154 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3531 Z= 0.190 Angle : 0.596 5.998 4964 Z= 0.337 Chirality : 0.042 0.176 580 Planarity : 0.005 0.047 471 Dihedral : 19.691 74.123 971 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.87 % Allowed : 12.19 % Favored : 84.95 % 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 (0.49), residues: 304 helix: 1.03 (0.50), residues: 114 sheet: -0.69 (0.61), residues: 80 loop : -0.88 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 271 TYR 0.052 0.003 TYR A 382 PHE 0.013 0.002 PHE A 164 TRP 0.007 0.002 TRP A 337 HIS 0.006 0.002 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 ( 3531) covalent geometry : angle 0.59558 / 0.34 ( 4964) hydrogen bonds : bond 0.04556 / 4.45 ( 151) hydrogen bonds : angle 5.67047 / 6.86 ( 397) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.092 Fit side-chains REVERT: A 159 MET cc_start: 0.6408 (mpp) cc_final: 0.5717 (mpp) REVERT: A 163 THR cc_start: 0.5985 (p) cc_final: 0.5617 (m) REVERT: A 240 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7673 (mt) REVERT: A 250 ILE cc_start: 0.8276 (mt) cc_final: 0.8049 (mt) REVERT: A 332 THR cc_start: 0.8103 (t) cc_final: 0.7297 (m) REVERT: A 342 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6711 (mtm-85) outliers start: 8 outliers final: 5 residues processed: 60 average time/residue: 0.0608 time to fit residues: 4.4061 Evaluate side-chains 64 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 386 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 10 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.198774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.176852 restraints weight = 5805.858| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 3.02 r_work: 0.4167 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4177 r_free = 0.4177 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4177 r_free = 0.4177 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3531 Z= 0.167 Angle : 0.575 5.555 4964 Z= 0.323 Chirality : 0.041 0.160 580 Planarity : 0.005 0.047 471 Dihedral : 19.756 74.102 971 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.87 % Allowed : 12.90 % Favored : 84.23 % 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: -0.19 (0.49), residues: 304 helix: 0.91 (0.49), residues: 116 sheet: -0.54 (0.61), residues: 78 loop : -0.77 (0.61), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 391 TYR 0.051 0.002 TYR A 382 PHE 0.010 0.001 PHE A 164 TRP 0.011 0.001 TRP A 265 HIS 0.003 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 ( 3531) covalent geometry : angle 0.57493 / 0.32 ( 4964) hydrogen bonds : bond 0.04300 / 4.22 ( 151) hydrogen bonds : angle 5.59672 / 6.72 ( 397) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.100 Fit side-chains REVERT: A 159 MET cc_start: 0.6311 (mpp) cc_final: 0.5652 (mpp) REVERT: A 163 THR cc_start: 0.5804 (p) cc_final: 0.5422 (m) REVERT: A 240 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7652 (mt) REVERT: A 250 ILE cc_start: 0.8259 (mt) cc_final: 0.8043 (mt) REVERT: A 332 THR cc_start: 0.8118 (t) cc_final: 0.7306 (m) REVERT: A 342 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6704 (mtm-85) outliers start: 8 outliers final: 5 residues processed: 59 average time/residue: 0.0610 time to fit residues: 4.3973 Evaluate side-chains 63 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 386 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 0.0670 chunk 12 optimal weight: 0.2980 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.200745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.179253 restraints weight = 5750.212| |-----------------------------------------------------------------------------| r_work (start): 0.4343 rms_B_bonded: 3.01 r_work: 0.4188 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4193 r_free = 0.4193 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4193 r_free = 0.4193 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3531 Z= 0.133 Angle : 0.553 5.330 4964 Z= 0.312 Chirality : 0.040 0.173 580 Planarity : 0.005 0.057 471 Dihedral : 19.745 74.094 971 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.87 % Allowed : 12.90 % Favored : 84.23 % 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 (0.49), residues: 304 helix: 1.03 (0.49), residues: 115 sheet: -0.62 (0.60), residues: 78 loop : -0.71 (0.60), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 391 TYR 0.041 0.002 TYR A 382 PHE 0.023 0.002 PHE A 125 TRP 0.014 0.002 TRP A 265 HIS 0.002 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 3531) covalent geometry : angle 0.55293 / 0.31 ( 4964) hydrogen bonds : bond 0.04044 / 3.97 ( 151) hydrogen bonds : angle 5.56307 / 6.63 ( 397) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 159 MET cc_start: 0.6281 (mpp) cc_final: 0.5653 (mpp) REVERT: A 240 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7609 (mt) REVERT: A 250 ILE cc_start: 0.8297 (mt) cc_final: 0.8064 (mt) outliers start: 8 outliers final: 6 residues processed: 60 average time/residue: 0.0636 time to fit residues: 4.6300 Evaluate side-chains 64 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 386 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 0.0980 chunk 3 optimal weight: 4.9990 chunk 33 optimal weight: 0.0770 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 10 optimal weight: 0.0980 chunk 8 optimal weight: 0.8980 chunk 20 optimal weight: 0.0570 chunk 24 optimal weight: 0.6980 overall best weight: 0.1656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.203200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.181384 restraints weight = 5772.813| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 3.05 r_work: 0.4213 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4219 r_free = 0.4219 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4219 r_free = 0.4219 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3531 Z= 0.118 Angle : 0.542 5.897 4964 Z= 0.305 Chirality : 0.039 0.187 580 Planarity : 0.006 0.055 471 Dihedral : 19.665 74.058 971 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.51 % Allowed : 13.62 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.50), residues: 304 helix: 1.12 (0.51), residues: 115 sheet: -0.24 (0.61), residues: 76 loop : -0.77 (0.60), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 271 TYR 0.039 0.002 TYR A 382 PHE 0.014 0.001 PHE A 125 TRP 0.019 0.002 TRP A 265 HIS 0.001 0.000 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 3531) covalent geometry : angle 0.54199 / 0.31 ( 4964) hydrogen bonds : bond 0.03612 / 3.49 ( 151) hydrogen bonds : angle 5.49681 / 6.51 ( 397) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 159 MET cc_start: 0.6180 (mpp) cc_final: 0.5587 (mpp) REVERT: A 240 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7586 (mt) REVERT: A 250 ILE cc_start: 0.8236 (mt) cc_final: 0.8000 (mt) REVERT: A 271 ARG cc_start: 0.7758 (mmt-90) cc_final: 0.7474 (mmt-90) outliers start: 7 outliers final: 5 residues processed: 61 average time/residue: 0.0652 time to fit residues: 4.8882 Evaluate side-chains 65 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 386 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 0.0770 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.0980 chunk 30 optimal weight: 0.1980 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.201963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.180004 restraints weight = 5741.836| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 3.05 r_work: 0.4205 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4208 r_free = 0.4208 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4208 r_free = 0.4208 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3531 Z= 0.134 Angle : 0.549 7.780 4964 Z= 0.307 Chirality : 0.039 0.172 580 Planarity : 0.005 0.046 471 Dihedral : 19.634 74.043 971 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.87 % Allowed : 14.70 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.14 (0.50), residues: 304 helix: 1.15 (0.51), residues: 115 sheet: -0.28 (0.62), residues: 78 loop : -0.61 (0.60), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 271 TYR 0.036 0.002 TYR A 382 PHE 0.008 0.001 PHE A 164 TRP 0.009 0.002 TRP A 265 HIS 0.001 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 3531) covalent geometry : angle 0.54947 / 0.31 ( 4964) hydrogen bonds : bond 0.03806 / 3.77 ( 151) hydrogen bonds : angle 5.46137 / 6.38 ( 397) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 843.48 seconds wall clock time: 15 minutes 9.23 seconds (909.23 seconds total)