Starting phenix.real_space_refine on Fri Aug 22 14:06:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u47_63833/08_2025/9u47_63833.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u47_63833/08_2025/9u47_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_63833/08_2025/9u47_63833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u47_63833/08_2025/9u47_63833.map" model { file = "/net/cci-nas-00/data/ceres_data/9u47_63833/08_2025/9u47_63833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u47_63833/08_2025/9u47_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-2.0-5787/lib/python3.9/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: 1.23, per 1000 atoms: 0.36 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: 0.31 Conformation dependent library (CDL) restraints added in 97.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.50 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: 0.55 Time building geometry restraints manager: 0.40 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=" 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 bond pdb=" N SER A 347 " pdb=" CA SER A 347 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.85e+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=" CA PRO A 154 " pdb=" N PRO A 154 " pdb=" CD PRO A 154 " ideal model delta sigma weight residual 112.00 106.26 5.74 1.40e+00 5.10e-01 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: 1.850 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: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.860 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5529 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= 0.344 Angle : 0.899 8.306 4964 Z= 0.523 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 aren 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 covalent geometry : bond 0.00640 ( 3531) covalent geometry : angle 0.89868 ( 4964) hydrogen bonds : bond 0.14913 ( 151) hydrogen bonds : angle 7.76636 ( 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 : 0.113 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: 0.0818 time to fit residues: 6.6448 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 : 0.111 ------------------------------------------------------------------------------- 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: 1.9990 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... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 ASN ** 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 = 0.4583 r_free = 0.4583 target = 0.199274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.175885 restraints weight = 5816.479| |-----------------------------------------------------------------------------| r_work (start): 0.4328 rms_B_bonded: 3.19 r_work: 0.4185 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4181 r_free = 0.4181 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4181 r_free = 0.4181 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3531 Z= 0.177 Angle : 0.604 5.416 4964 Z= 0.320 Chirality : 0.040 0.155 580 Planarity : 0.005 0.042 471 Dihedral : 19.574 74.298 971 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.08 % Allowed : 11.47 % Favored : 87.46 % 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 aren not related in a simple way. whole: -1.13 (0.48), residues: 304 helix: 0.06 (0.48), residues: 116 sheet: -0.40 (0.60), residues: 75 loop : -1.75 (0.57), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 146 TYR 0.008 0.002 TYR A 111 PHE 0.010 0.001 PHE A 164 TRP 0.016 0.002 TRP A 222 HIS 0.003 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 3531) covalent geometry : angle 0.60352 ( 4964) hydrogen bonds : bond 0.04682 ( 151) hydrogen bonds : angle 5.89645 ( 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 64 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 163 THR cc_start: 0.5846 (p) cc_final: 0.5243 (m) REVERT: A 250 ILE cc_start: 0.8186 (mt) cc_final: 0.7942 (mt) REVERT: A 252 GLU cc_start: 0.5297 (tt0) cc_final: 0.4962 (tt0) REVERT: A 344 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8227 (pt) outliers start: 3 outliers final: 2 residues processed: 61 average time/residue: 0.0760 time to fit residues: 5.6205 Evaluate side-chains 60 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.072 ------------------------------------------------------------------------------- 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 344 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 0.0370 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.6056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 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 = 0.4564 r_free = 0.4564 target = 0.197763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.175857 restraints weight = 5623.655| |-----------------------------------------------------------------------------| r_work (start): 0.4311 rms_B_bonded: 3.08 r_work: 0.4156 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4164 r_free = 0.4164 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4164 r_free = 0.4164 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3531 Z= 0.179 Angle : 0.577 5.388 4964 Z= 0.308 Chirality : 0.040 0.152 580 Planarity : 0.004 0.040 471 Dihedral : 19.650 74.088 971 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.23 % Allowed : 10.75 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.49), residues: 304 helix: 0.75 (0.50), residues: 114 sheet: -0.62 (0.60), residues: 79 loop : -1.26 (0.59), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 391 TYR 0.028 0.002 TYR A 382 PHE 0.013 0.001 PHE A 164 TRP 0.012 0.002 TRP A 222 HIS 0.003 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 3531) covalent geometry : angle 0.57698 ( 4964) hydrogen bonds : bond 0.04255 ( 151) hydrogen bonds : angle 5.54908 ( 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 70 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.078 Fit side-chains REVERT: A 163 THR cc_start: 0.5819 (p) cc_final: 0.5323 (m) REVERT: A 240 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7708 (mt) REVERT: A 250 ILE cc_start: 0.8231 (mt) cc_final: 0.7988 (mt) REVERT: A 264 CYS cc_start: 0.7611 (p) cc_final: 0.7352 (p) REVERT: A 271 ARG cc_start: 0.7760 (mmt-90) cc_final: 0.7443 (tpp-160) REVERT: A 342 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6608 (mtm-85) REVERT: A 393 LEU cc_start: 0.6300 (mp) cc_final: 0.6088 (mt) outliers start: 9 outliers final: 3 residues processed: 65 average time/residue: 0.0809 time to fit residues: 6.2458 Evaluate side-chains 63 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.101 ------------------------------------------------------------------------------- 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 301 GLU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 342 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 33 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 20 optimal weight: 0.0570 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.199396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.176291 restraints weight = 5564.962| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 3.13 r_work: 0.4187 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4187 ------------------------------------------------------------------------------- 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 = 0.45 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 = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3531 Z= 0.133 Angle : 0.537 6.485 4964 Z= 0.286 Chirality : 0.038 0.151 580 Planarity : 0.004 0.039 471 Dihedral : 19.603 74.010 971 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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 aren not related in a simple way. whole: -0.14 (0.50), residues: 304 helix: 1.15 (0.51), residues: 115 sheet: -0.48 (0.60), residues: 77 loop : -1.02 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 391 TYR 0.029 0.002 TYR A 382 PHE 0.014 0.001 PHE A 164 TRP 0.011 0.002 TRP A 222 HIS 0.002 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3531) covalent geometry : angle 0.53712 ( 4964) hydrogen bonds : bond 0.03746 ( 151) hydrogen bonds : angle 5.39901 ( 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 69 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.089 Fit side-chains REVERT: A 74 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7884 (mm) REVERT: A 163 THR cc_start: 0.5898 (p) cc_final: 0.5353 (m) REVERT: A 250 ILE cc_start: 0.8256 (mt) cc_final: 0.8003 (mt) REVERT: A 271 ARG cc_start: 0.7770 (mmt-90) cc_final: 0.7170 (mmt-90) REVERT: A 342 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6771 (mtm-85) REVERT: A 393 LEU cc_start: 0.6267 (mp) cc_final: 0.5991 (mt) outliers start: 8 outliers final: 6 residues processed: 63 average time/residue: 0.0799 time to fit residues: 5.9724 Evaluate side-chains 69 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE 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 312 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 13 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.200268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.178513 restraints weight = 5562.070| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 2.96 r_work: 0.4180 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4186 r_free = 0.4186 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 = 0.4186 r_free = 0.4186 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3531 Z= 0.143 Angle : 0.559 7.083 4964 Z= 0.297 Chirality : 0.040 0.216 580 Planarity : 0.004 0.041 471 Dihedral : 19.633 74.065 971 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.66 % Allowed : 12.19 % Favored : 83.15 % 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 aren not related in a simple way. whole: -0.06 (0.50), residues: 304 helix: 1.18 (0.51), residues: 116 sheet: -0.29 (0.61), residues: 75 loop : -1.06 (0.59), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 391 TYR 0.035 0.002 TYR A 382 PHE 0.016 0.001 PHE A 164 TRP 0.010 0.002 TRP A 265 HIS 0.002 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 3531) covalent geometry : angle 0.55866 ( 4964) hydrogen bonds : bond 0.03927 ( 151) hydrogen bonds : angle 5.35645 ( 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 73 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.142 Fit side-chains REVERT: A 74 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7885 (mm) REVERT: A 250 ILE cc_start: 0.8259 (mt) cc_final: 0.7998 (mt) REVERT: A 271 ARG cc_start: 0.7802 (mmt-90) cc_final: 0.7289 (mmt-90) REVERT: A 342 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6876 (mtm-85) outliers start: 13 outliers final: 7 residues processed: 64 average time/residue: 0.0727 time to fit residues: 5.6026 Evaluate side-chains 68 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 312 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 HIS A 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.197739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.174346 restraints weight = 5730.144| |-----------------------------------------------------------------------------| r_work (start): 0.4311 rms_B_bonded: 3.24 r_work: 0.4156 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4156 r_free = 0.4156 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4156 r_free = 0.4156 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3531 Z= 0.180 Angle : 0.593 6.327 4964 Z= 0.320 Chirality : 0.041 0.195 580 Planarity : 0.004 0.043 471 Dihedral : 19.773 74.047 971 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.65 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 aren not related in a simple way. whole: -0.18 (0.49), residues: 304 helix: 1.01 (0.50), residues: 116 sheet: -0.26 (0.61), residues: 76 loop : -1.12 (0.56), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 391 TYR 0.038 0.002 TYR A 382 PHE 0.014 0.001 PHE A 164 TRP 0.024 0.002 TRP A 222 HIS 0.002 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 3531) covalent geometry : angle 0.59287 ( 4964) hydrogen bonds : bond 0.04298 ( 151) hydrogen bonds : angle 5.36471 ( 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 67 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: A 163 THR cc_start: 0.5935 (p) cc_final: 0.5505 (m) REVERT: A 247 ASN cc_start: 0.8034 (t0) cc_final: 0.7677 (t0) REVERT: A 250 ILE cc_start: 0.8182 (mt) cc_final: 0.7930 (mt) REVERT: A 271 ARG cc_start: 0.7771 (mmt-90) cc_final: 0.7331 (mmt180) outliers start: 8 outliers final: 7 residues processed: 61 average time/residue: 0.0808 time to fit residues: 5.7854 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 : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 275 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4569 r_free = 0.4569 target = 0.199612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.178310 restraints weight = 5712.530| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 2.98 r_work: 0.4168 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4177 r_free = 0.4177 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 = 0.4177 r_free = 0.4177 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3531 Z= 0.164 Angle : 0.577 5.144 4964 Z= 0.314 Chirality : 0.040 0.178 580 Planarity : 0.005 0.044 471 Dihedral : 19.823 73.989 971 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.87 % Allowed : 13.62 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.49), residues: 304 helix: 0.98 (0.50), residues: 116 sheet: -0.25 (0.61), residues: 76 loop : -0.95 (0.59), residues: 112 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 0.022 0.002 TRP A 222 HIS 0.002 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 3531) covalent geometry : angle 0.57656 ( 4964) hydrogen bonds : bond 0.04046 ( 151) hydrogen bonds : angle 5.43716 ( 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 64 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.070 Fit side-chains revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7874 (mm) REVERT: A 247 ASN cc_start: 0.8014 (t0) cc_final: 0.7650 (t0) REVERT: A 250 ILE cc_start: 0.8242 (mt) cc_final: 0.7989 (mt) REVERT: A 271 ARG cc_start: 0.7745 (mmt-90) cc_final: 0.7315 (mmt180) outliers start: 8 outliers final: 7 residues processed: 57 average time/residue: 0.0563 time to fit residues: 3.9598 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 : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 312 LYS 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: 1.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4551 r_free = 0.4551 target = 0.198164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.174090 restraints weight = 5684.509| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 3.44 r_work: 0.4104 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4113 r_free = 0.4113 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4112 r_free = 0.4112 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3531 Z= 0.167 Angle : 0.580 5.082 4964 Z= 0.314 Chirality : 0.040 0.162 580 Planarity : 0.004 0.044 471 Dihedral : 19.844 74.934 971 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.87 % Allowed : 13.98 % Favored : 83.15 % 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 aren not related in a simple way. whole: 0.01 (0.50), residues: 304 helix: 1.10 (0.50), residues: 115 sheet: -0.36 (0.60), residues: 78 loop : -0.75 (0.60), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 391 TYR 0.031 0.002 TYR A 382 PHE 0.008 0.001 PHE A 164 TRP 0.012 0.002 TRP A 222 HIS 0.002 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 3531) covalent geometry : angle 0.58020 ( 4964) hydrogen bonds : bond 0.04053 ( 151) hydrogen bonds : angle 5.37170 ( 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 66 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7918 (mm) REVERT: A 250 ILE cc_start: 0.8265 (mt) cc_final: 0.8010 (mt) REVERT: A 271 ARG cc_start: 0.7808 (mmt-90) cc_final: 0.7040 (mmt-90) outliers start: 8 outliers final: 7 residues processed: 59 average time/residue: 0.0631 time to fit residues: 4.5451 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 : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 323 LYS 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: 0.2980 chunk 27 optimal weight: 0.5980 chunk 23 optimal weight: 0.0050 chunk 32 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 0.0370 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 overall best weight: 0.2872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4570 r_free = 0.4570 target = 0.200148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.176463 restraints weight = 5606.574| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 3.44 r_work: 0.4134 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4140 r_free = 0.4140 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4140 r_free = 0.4140 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3531 Z= 0.129 Angle : 0.562 7.653 4964 Z= 0.301 Chirality : 0.039 0.182 580 Planarity : 0.004 0.043 471 Dihedral : 19.742 75.776 971 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.87 % Allowed : 14.34 % Favored : 82.80 % 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 aren not related in a simple way. whole: 0.24 (0.50), residues: 304 helix: 1.28 (0.51), residues: 115 sheet: -0.38 (0.60), residues: 80 loop : -0.48 (0.61), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 391 TYR 0.060 0.003 TYR A 382 PHE 0.009 0.001 PHE A 164 TRP 0.026 0.003 TRP A 222 HIS 0.002 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3531) covalent geometry : angle 0.56246 ( 4964) hydrogen bonds : bond 0.03681 ( 151) hydrogen bonds : angle 5.44747 ( 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 62 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7903 (mm) REVERT: A 247 ASN cc_start: 0.7947 (t0) cc_final: 0.7547 (t0) REVERT: A 250 ILE cc_start: 0.8246 (mt) cc_final: 0.7990 (mt) REVERT: A 252 GLU cc_start: 0.5589 (tt0) cc_final: 0.5267 (mt-10) REVERT: A 271 ARG cc_start: 0.7741 (mmt-90) cc_final: 0.7138 (mmt-90) outliers start: 8 outliers final: 6 residues processed: 56 average time/residue: 0.0538 time to fit residues: 3.7290 Evaluate side-chains 58 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 323 LYS 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: 3.9990 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4545 r_free = 0.4545 target = 0.197605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.174323 restraints weight = 5684.587| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 3.43 r_work: 0.4110 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4117 r_free = 0.4117 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4117 r_free = 0.4117 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3531 Z= 0.179 Angle : 0.604 7.363 4964 Z= 0.322 Chirality : 0.041 0.173 580 Planarity : 0.005 0.045 471 Dihedral : 19.806 77.528 971 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.15 % Allowed : 15.41 % 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 aren not related in a simple way. whole: 0.08 (0.49), residues: 304 helix: 1.07 (0.50), residues: 115 sheet: -0.33 (0.60), residues: 80 loop : -0.59 (0.60), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 391 TYR 0.058 0.003 TYR A 382 PHE 0.011 0.001 PHE A 164 TRP 0.018 0.002 TRP A 222 HIS 0.002 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 3531) covalent geometry : angle 0.60423 ( 4964) hydrogen bonds : bond 0.04220 ( 151) hydrogen bonds : angle 5.50738 ( 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 60 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7969 (mm) REVERT: A 250 ILE cc_start: 0.8232 (mt) cc_final: 0.7985 (mt) REVERT: A 252 GLU cc_start: 0.5599 (tt0) cc_final: 0.5387 (mt-10) REVERT: A 271 ARG cc_start: 0.7745 (mmt-90) cc_final: 0.7288 (mmt-90) outliers start: 6 outliers final: 4 residues processed: 56 average time/residue: 0.0685 time to fit residues: 4.7821 Evaluate side-chains 59 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 282 THR 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: 3.9990 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.0270 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4563 r_free = 0.4563 target = 0.199445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.175408 restraints weight = 5670.472| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 3.52 r_work: 0.4111 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4118 r_free = 0.4118 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4118 r_free = 0.4118 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3531 Z= 0.153 Angle : 0.586 7.514 4964 Z= 0.310 Chirality : 0.040 0.182 580 Planarity : 0.005 0.044 471 Dihedral : 19.756 77.982 971 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.79 % Allowed : 15.05 % Favored : 83.15 % 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 aren not related in a simple way. whole: 0.29 (0.50), residues: 304 helix: 1.23 (0.50), residues: 115 sheet: -0.21 (0.62), residues: 80 loop : -0.46 (0.60), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 391 TYR 0.059 0.003 TYR A 382 PHE 0.009 0.001 PHE A 164 TRP 0.033 0.003 TRP A 222 HIS 0.002 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 3531) covalent geometry : angle 0.58559 ( 4964) hydrogen bonds : bond 0.03797 ( 151) hydrogen bonds : angle 5.48629 ( 397) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1016.79 seconds wall clock time: 18 minutes 7.12 seconds (1087.12 seconds total)