Starting phenix.real_space_refine on Tue Feb 3 18:46:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w1q_65554/02_2026/9w1q_65554.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w1q_65554/02_2026/9w1q_65554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w1q_65554/02_2026/9w1q_65554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w1q_65554/02_2026/9w1q_65554.map" model { file = "/net/cci-nas-00/data/ceres_data/9w1q_65554/02_2026/9w1q_65554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w1q_65554/02_2026/9w1q_65554.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4068 2.51 5 N 976 2.21 5 O 1092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6172 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3086 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 15, 'TRANS': 387} Chain breaks: 2 Restraints were copied for chains: B Time building chain proxies: 1.35, per 1000 atoms: 0.22 Number of scatterers: 6172 At special positions: 0 Unit cell: (90.47, 80.51, 69.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1092 8.00 N 976 7.00 C 4068 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: 0.48 Conformation dependent library (CDL) restraints added in 340.2 milliseconds 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1456 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 91.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 6 through 29 Processing helix chain 'A' and resid 29 through 42 Proline residue: A 36 - end of helix Processing helix chain 'A' and resid 45 through 74 removed outlier: 4.059A pdb=" N PHE A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 97 Processing helix chain 'A' and resid 99 through 129 removed outlier: 4.284A pdb=" N TRP A 118 " --> pdb=" O GLN A 114 " (cutoff:3.500A) Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.984A pdb=" N TRP A 137 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 163 Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 164 through 187 Processing helix chain 'A' and resid 216 through 222 Processing helix chain 'A' and resid 223 through 253 removed outlier: 3.805A pdb=" N TRP A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLN A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N PHE A 249 " --> pdb=" O ASP A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 291 Processing helix chain 'A' and resid 301 through 321 removed outlier: 3.822A pdb=" N PHE A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 356 removed outlier: 3.788A pdb=" N GLY A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Proline residue: A 345 - end of helix Processing helix chain 'A' and resid 361 through 391 removed outlier: 3.816A pdb=" N LEU A 382 " --> pdb=" O PHE A 378 " (cutoff:3.500A) Proline residue: A 383 - end of helix Processing helix chain 'A' and resid 392 through 426 removed outlier: 3.534A pdb=" N GLU A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 29 Processing helix chain 'B' and resid 29 through 42 Proline residue: B 36 - end of helix Processing helix chain 'B' and resid 45 through 74 removed outlier: 4.059A pdb=" N PHE B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN B 73 " --> pdb=" O VAL B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 97 Processing helix chain 'B' and resid 99 through 129 removed outlier: 4.285A pdb=" N TRP B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 133 through 143 removed outlier: 3.984A pdb=" N TRP B 137 " --> pdb=" O GLN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 163 Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 164 through 187 Processing helix chain 'B' and resid 216 through 222 Processing helix chain 'B' and resid 223 through 253 removed outlier: 3.806A pdb=" N TRP B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLN B 248 " --> pdb=" O THR B 244 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N PHE B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 291 Processing helix chain 'B' and resid 301 through 321 removed outlier: 3.821A pdb=" N PHE B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 356 removed outlier: 3.789A pdb=" N GLY B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) Proline residue: B 345 - end of helix Processing helix chain 'B' and resid 361 through 391 removed outlier: 3.817A pdb=" N LEU B 382 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Proline residue: B 383 - end of helix Processing helix chain 'B' and resid 392 through 426 removed outlier: 3.534A pdb=" N GLU B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) 562 hydrogen bonds defined for protein. 1686 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.74 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1643 1.34 - 1.45: 1317 1.45 - 1.57: 3326 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6344 Sorted by residual: bond pdb=" CB PRO B 120 " pdb=" CG PRO B 120 " ideal model delta sigma weight residual 1.492 1.384 0.108 5.00e-02 4.00e+02 4.68e+00 bond pdb=" CB PRO A 120 " pdb=" CG PRO A 120 " ideal model delta sigma weight residual 1.492 1.384 0.108 5.00e-02 4.00e+02 4.64e+00 bond pdb=" C MET A 35 " pdb=" N PRO A 36 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.20e-02 6.94e+03 2.49e+00 bond pdb=" C VAL B 100 " pdb=" N PRO B 101 " ideal model delta sigma weight residual 1.336 1.354 -0.019 1.23e-02 6.61e+03 2.30e+00 bond pdb=" C MET B 35 " pdb=" N PRO B 36 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.20e-02 6.94e+03 2.28e+00 ... (remaining 6339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 8201 1.88 - 3.75: 345 3.75 - 5.63: 60 5.63 - 7.51: 20 7.51 - 9.38: 4 Bond angle restraints: 8630 Sorted by residual: angle pdb=" N TRP B 118 " pdb=" CA TRP B 118 " pdb=" C TRP B 118 " ideal model delta sigma weight residual 109.81 119.19 -9.38 2.21e+00 2.05e-01 1.80e+01 angle pdb=" N TRP A 118 " pdb=" CA TRP A 118 " pdb=" C TRP A 118 " ideal model delta sigma weight residual 109.81 119.19 -9.38 2.21e+00 2.05e-01 1.80e+01 angle pdb=" N MET B 35 " pdb=" CA MET B 35 " pdb=" C MET B 35 " ideal model delta sigma weight residual 109.81 117.86 -8.05 2.21e+00 2.05e-01 1.33e+01 angle pdb=" N MET A 35 " pdb=" CA MET A 35 " pdb=" C MET A 35 " ideal model delta sigma weight residual 109.81 117.85 -8.04 2.21e+00 2.05e-01 1.32e+01 angle pdb=" N PRO B 119 " pdb=" CA PRO B 119 " pdb=" C PRO B 119 " ideal model delta sigma weight residual 110.70 115.00 -4.30 1.22e+00 6.72e-01 1.24e+01 ... (remaining 8625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.04: 3397 15.04 - 30.08: 163 30.08 - 45.13: 36 45.13 - 60.17: 0 60.17 - 75.21: 2 Dihedral angle restraints: 3598 sinusoidal: 1310 harmonic: 2288 Sorted by residual: dihedral pdb=" CA THR A 143 " pdb=" C THR A 143 " pdb=" N SER A 144 " pdb=" CA SER A 144 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA THR B 143 " pdb=" C THR B 143 " pdb=" N SER B 144 " pdb=" CA SER B 144 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA TRP B 137 " pdb=" C TRP B 137 " pdb=" N TRP B 138 " pdb=" CA TRP B 138 " ideal model delta harmonic sigma weight residual 180.00 161.86 18.14 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 3595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 691 0.049 - 0.098: 222 0.098 - 0.147: 47 0.147 - 0.196: 6 0.196 - 0.245: 6 Chirality restraints: 972 Sorted by residual: chirality pdb=" CB VAL A 228 " pdb=" CA VAL A 228 " pdb=" CG1 VAL A 228 " pdb=" CG2 VAL A 228 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB VAL B 228 " pdb=" CA VAL B 228 " pdb=" CG1 VAL B 228 " pdb=" CG2 VAL B 228 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CG LEU B 169 " pdb=" CB LEU B 169 " pdb=" CD1 LEU B 169 " pdb=" CD2 LEU B 169 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 969 not shown) Planarity restraints: 1058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 119 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO A 120 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 120 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 120 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 119 " 0.044 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO B 120 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 120 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 120 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 344 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO B 345 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 345 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 345 " 0.028 5.00e-02 4.00e+02 ... (remaining 1055 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 852 2.75 - 3.29: 6260 3.29 - 3.83: 11275 3.83 - 4.36: 12461 4.36 - 4.90: 22252 Nonbonded interactions: 53100 Sorted by model distance: nonbonded pdb=" OD2 ASP B 72 " pdb=" OG1 THR B 364 " model vdw 2.214 3.040 nonbonded pdb=" OD2 ASP A 72 " pdb=" OG1 THR A 364 " model vdw 2.214 3.040 nonbonded pdb=" O PHE B 26 " pdb=" OG1 THR B 30 " model vdw 2.257 3.040 nonbonded pdb=" O PHE A 26 " pdb=" OG1 THR A 30 " model vdw 2.258 3.040 nonbonded pdb=" O LEU A 141 " pdb=" OG SER A 144 " model vdw 2.313 3.040 ... (remaining 53095 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.280 Find NCS groups from input model: 0.030 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 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 : 0.007 0.108 6344 Z= 0.289 Angle : 0.936 9.385 8630 Z= 0.502 Chirality : 0.052 0.245 972 Planarity : 0.009 0.066 1058 Dihedral : 9.529 75.209 2142 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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 are not related in a simple way. whole: -2.83 (0.22), residues: 794 helix: -1.80 (0.14), residues: 702 sheet: None (None), residues: 0 loop : -0.28 (0.61), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 28 TYR 0.022 0.003 TYR A 60 PHE 0.025 0.004 PHE B 411 TRP 0.028 0.003 TRP B 138 HIS 0.005 0.002 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00691 ( 6344) covalent geometry : angle 0.93618 ( 8630) hydrogen bonds : bond 0.10781 ( 562) hydrogen bonds : angle 6.41772 ( 1686) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 37 SER cc_start: 0.7523 (m) cc_final: 0.7259 (p) REVERT: A 132 SER cc_start: 0.8055 (t) cc_final: 0.7796 (m) REVERT: A 133 GLN cc_start: 0.6792 (mt0) cc_final: 0.6558 (tp40) REVERT: B 133 GLN cc_start: 0.6735 (mt0) cc_final: 0.6417 (tp40) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0642 time to fit residues: 6.0205 Evaluate side-chains 44 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 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 = 0.3529 r_free = 0.3529 target = 0.138480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.122521 restraints weight = 7315.805| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.46 r_work: 0.3454 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6344 Z= 0.196 Angle : 0.632 8.580 8630 Z= 0.323 Chirality : 0.040 0.135 972 Planarity : 0.006 0.044 1058 Dihedral : 4.399 16.498 854 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.85 % Allowed : 3.40 % Favored : 94.75 % 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: 0.56 (0.28), residues: 794 helix: 0.47 (0.18), residues: 706 sheet: None (None), residues: 0 loop : 0.60 (0.71), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 300 TYR 0.013 0.002 TYR B 60 PHE 0.017 0.002 PHE B 338 TRP 0.016 0.002 TRP B 138 HIS 0.004 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 6344) covalent geometry : angle 0.63237 ( 8630) hydrogen bonds : bond 0.04727 ( 562) hydrogen bonds : angle 4.50931 ( 1686) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.214 Fit side-chains REVERT: A 9 TYR cc_start: 0.7672 (m-10) cc_final: 0.7266 (m-10) REVERT: A 133 GLN cc_start: 0.7185 (mt0) cc_final: 0.6679 (tp40) REVERT: A 329 LEU cc_start: 0.6804 (tt) cc_final: 0.6290 (pp) REVERT: A 414 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7096 (tt) REVERT: B 9 TYR cc_start: 0.7769 (m-10) cc_final: 0.7308 (m-10) REVERT: B 133 GLN cc_start: 0.7159 (mt0) cc_final: 0.6719 (tp40) REVERT: B 414 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7058 (tt) outliers start: 12 outliers final: 6 residues processed: 65 average time/residue: 0.0787 time to fit residues: 6.8523 Evaluate side-chains 54 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 414 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 6 optimal weight: 0.7980 chunk 72 optimal weight: 0.0870 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 79 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN B 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.139969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.123774 restraints weight = 7254.110| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.45 r_work: 0.3485 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6344 Z= 0.166 Angle : 0.582 7.007 8630 Z= 0.298 Chirality : 0.038 0.121 972 Planarity : 0.005 0.042 1058 Dihedral : 4.233 14.984 854 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.23 % Allowed : 7.10 % Favored : 91.67 % 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: 1.90 (0.29), residues: 794 helix: 1.35 (0.19), residues: 702 sheet: None (None), residues: 0 loop : 1.20 (0.73), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 300 TYR 0.011 0.002 TYR A 24 PHE 0.014 0.002 PHE B 14 TRP 0.014 0.002 TRP B 138 HIS 0.003 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6344) covalent geometry : angle 0.58245 ( 8630) hydrogen bonds : bond 0.04571 ( 562) hydrogen bonds : angle 4.15423 ( 1686) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.209 Fit side-chains REVERT: A 9 TYR cc_start: 0.7614 (m-10) cc_final: 0.7358 (m-80) REVERT: A 133 GLN cc_start: 0.7124 (mt0) cc_final: 0.6682 (tp40) REVERT: A 329 LEU cc_start: 0.6796 (tt) cc_final: 0.6365 (pp) REVERT: A 414 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.6971 (tt) REVERT: B 133 GLN cc_start: 0.7116 (mt0) cc_final: 0.6741 (tp40) REVERT: B 414 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6934 (tt) outliers start: 8 outliers final: 5 residues processed: 58 average time/residue: 0.0424 time to fit residues: 3.8081 Evaluate side-chains 53 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 414 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.132666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.116898 restraints weight = 7330.462| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.42 r_work: 0.3428 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6344 Z= 0.206 Angle : 0.623 7.931 8630 Z= 0.315 Chirality : 0.040 0.125 972 Planarity : 0.005 0.042 1058 Dihedral : 4.210 14.238 854 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.62 % Allowed : 7.87 % Favored : 89.51 % 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 are not related in a simple way. whole: 2.22 (0.29), residues: 794 helix: 1.52 (0.19), residues: 706 sheet: None (None), residues: 0 loop : 1.62 (0.78), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 300 TYR 0.015 0.002 TYR A 6 PHE 0.015 0.002 PHE B 250 TRP 0.015 0.002 TRP A 138 HIS 0.005 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 6344) covalent geometry : angle 0.62346 ( 8630) hydrogen bonds : bond 0.04769 ( 562) hydrogen bonds : angle 4.21529 ( 1686) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.216 Fit side-chains REVERT: A 133 GLN cc_start: 0.7117 (mt0) cc_final: 0.6678 (tp40) REVERT: A 329 LEU cc_start: 0.6884 (tt) cc_final: 0.6456 (pp) REVERT: A 414 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7049 (tt) REVERT: B 133 GLN cc_start: 0.7182 (mt0) cc_final: 0.6750 (tp40) REVERT: B 228 VAL cc_start: 0.8354 (p) cc_final: 0.8055 (t) REVERT: B 332 LEU cc_start: 0.7661 (mt) cc_final: 0.7458 (mt) REVERT: B 372 MET cc_start: 0.7986 (mmt) cc_final: 0.7777 (mmt) REVERT: B 414 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7039 (tt) outliers start: 17 outliers final: 11 residues processed: 81 average time/residue: 0.0438 time to fit residues: 5.6538 Evaluate side-chains 72 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 414 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 29 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 60 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.135299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.119346 restraints weight = 7372.354| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.43 r_work: 0.3427 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6344 Z= 0.169 Angle : 0.581 7.484 8630 Z= 0.295 Chirality : 0.039 0.121 972 Planarity : 0.005 0.043 1058 Dihedral : 4.134 14.161 854 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.93 % Allowed : 9.26 % Favored : 87.81 % 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: 2.63 (0.29), residues: 794 helix: 1.79 (0.19), residues: 704 sheet: None (None), residues: 0 loop : 1.79 (0.78), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 300 TYR 0.011 0.002 TYR A 9 PHE 0.019 0.002 PHE B 250 TRP 0.012 0.001 TRP B 138 HIS 0.004 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 6344) covalent geometry : angle 0.58084 ( 8630) hydrogen bonds : bond 0.04601 ( 562) hydrogen bonds : angle 4.07383 ( 1686) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.169 Fit side-chains REVERT: A 133 GLN cc_start: 0.7097 (mt0) cc_final: 0.6657 (tp40) REVERT: A 329 LEU cc_start: 0.6869 (tt) cc_final: 0.6486 (pp) REVERT: A 414 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6872 (tt) REVERT: B 133 GLN cc_start: 0.7161 (mt0) cc_final: 0.6748 (tp40) REVERT: B 372 MET cc_start: 0.7825 (mmt) cc_final: 0.7292 (mmt) REVERT: B 414 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6860 (tt) outliers start: 19 outliers final: 9 residues processed: 61 average time/residue: 0.0419 time to fit residues: 3.9948 Evaluate side-chains 52 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 414 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 30 optimal weight: 0.0030 chunk 41 optimal weight: 1.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.136235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.120258 restraints weight = 7292.472| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.43 r_work: 0.3288 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6344 Z= 0.160 Angle : 0.569 6.749 8630 Z= 0.292 Chirality : 0.038 0.119 972 Planarity : 0.005 0.042 1058 Dihedral : 4.093 14.341 854 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.01 % Allowed : 10.80 % Favored : 87.19 % 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: 2.92 (0.29), residues: 794 helix: 1.98 (0.19), residues: 702 sheet: None (None), residues: 0 loop : 1.94 (0.78), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 28 TYR 0.010 0.002 TYR A 24 PHE 0.012 0.001 PHE B 14 TRP 0.011 0.001 TRP B 138 HIS 0.004 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 6344) covalent geometry : angle 0.56885 ( 8630) hydrogen bonds : bond 0.04527 ( 562) hydrogen bonds : angle 3.98184 ( 1686) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.131 Fit side-chains REVERT: A 133 GLN cc_start: 0.6929 (mt0) cc_final: 0.6472 (tp40) REVERT: A 329 LEU cc_start: 0.6869 (tt) cc_final: 0.6465 (pp) REVERT: A 372 MET cc_start: 0.7483 (mmm) cc_final: 0.6949 (mmt) REVERT: A 414 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6597 (tt) REVERT: B 133 GLN cc_start: 0.7024 (mt0) cc_final: 0.6579 (tp40) REVERT: B 414 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6601 (tt) outliers start: 13 outliers final: 9 residues processed: 58 average time/residue: 0.0398 time to fit residues: 3.6222 Evaluate side-chains 54 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 414 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 79 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.0070 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 59 optimal weight: 0.0970 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.137449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.121574 restraints weight = 7229.333| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.44 r_work: 0.3466 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6344 Z= 0.146 Angle : 0.564 7.178 8630 Z= 0.286 Chirality : 0.038 0.117 972 Planarity : 0.005 0.040 1058 Dihedral : 4.044 14.170 854 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.47 % Allowed : 10.34 % Favored : 87.19 % 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: 3.19 (0.29), residues: 794 helix: 2.15 (0.19), residues: 702 sheet: None (None), residues: 0 loop : 2.09 (0.79), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 28 TYR 0.010 0.001 TYR A 24 PHE 0.012 0.001 PHE B 14 TRP 0.011 0.001 TRP B 138 HIS 0.003 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6344) covalent geometry : angle 0.56449 ( 8630) hydrogen bonds : bond 0.04399 ( 562) hydrogen bonds : angle 3.87297 ( 1686) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.131 Fit side-chains REVERT: A 133 GLN cc_start: 0.7071 (mt0) cc_final: 0.6696 (tp40) REVERT: A 329 LEU cc_start: 0.6940 (tt) cc_final: 0.6581 (pp) REVERT: A 372 MET cc_start: 0.7483 (mmm) cc_final: 0.6954 (mmt) REVERT: A 414 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6867 (tt) REVERT: B 133 GLN cc_start: 0.7118 (mt0) cc_final: 0.6755 (tp40) REVERT: B 414 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6878 (tt) outliers start: 16 outliers final: 11 residues processed: 58 average time/residue: 0.0469 time to fit residues: 4.2826 Evaluate side-chains 51 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 414 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 73 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.134761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.118638 restraints weight = 7310.255| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.45 r_work: 0.3417 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6344 Z= 0.175 Angle : 0.589 6.941 8630 Z= 0.298 Chirality : 0.039 0.122 972 Planarity : 0.005 0.040 1058 Dihedral : 4.075 14.376 854 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.31 % Allowed : 10.96 % Favored : 86.73 % 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: 3.08 (0.29), residues: 794 helix: 2.07 (0.19), residues: 702 sheet: None (None), residues: 0 loop : 2.16 (0.79), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 28 TYR 0.012 0.002 TYR A 9 PHE 0.014 0.002 PHE B 33 TRP 0.012 0.001 TRP A 138 HIS 0.004 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 6344) covalent geometry : angle 0.58936 ( 8630) hydrogen bonds : bond 0.04556 ( 562) hydrogen bonds : angle 3.95529 ( 1686) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.235 Fit side-chains REVERT: A 133 GLN cc_start: 0.7068 (mt0) cc_final: 0.6672 (tp40) REVERT: A 329 LEU cc_start: 0.6871 (tt) cc_final: 0.6507 (pp) REVERT: A 372 MET cc_start: 0.7585 (mmm) cc_final: 0.7005 (mmt) REVERT: A 414 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6817 (tt) REVERT: B 133 GLN cc_start: 0.7120 (mt0) cc_final: 0.6734 (tp40) REVERT: B 414 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6840 (tt) outliers start: 15 outliers final: 10 residues processed: 56 average time/residue: 0.0641 time to fit residues: 5.3527 Evaluate side-chains 52 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 414 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 30 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3461 r_free = 0.3461 target = 0.132920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.116771 restraints weight = 7356.991| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.44 r_work: 0.3298 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6344 Z= 0.194 Angle : 0.612 7.024 8630 Z= 0.309 Chirality : 0.040 0.121 972 Planarity : 0.005 0.040 1058 Dihedral : 4.135 15.068 854 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.85 % Allowed : 11.42 % Favored : 86.73 % 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: 2.95 (0.29), residues: 794 helix: 1.97 (0.19), residues: 704 sheet: None (None), residues: 0 loop : 2.26 (0.81), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 28 TYR 0.016 0.002 TYR A 9 PHE 0.013 0.002 PHE B 33 TRP 0.013 0.001 TRP A 138 HIS 0.005 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 6344) covalent geometry : angle 0.61164 ( 8630) hydrogen bonds : bond 0.04702 ( 562) hydrogen bonds : angle 4.05637 ( 1686) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.255 Fit side-chains REVERT: A 133 GLN cc_start: 0.7060 (mt0) cc_final: 0.6635 (tp40) REVERT: A 329 LEU cc_start: 0.6895 (tt) cc_final: 0.6513 (pp) REVERT: A 414 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6822 (tt) REVERT: B 133 GLN cc_start: 0.7134 (mt0) cc_final: 0.6709 (tp40) REVERT: B 414 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6844 (tt) outliers start: 12 outliers final: 9 residues processed: 62 average time/residue: 0.0680 time to fit residues: 6.0463 Evaluate side-chains 60 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 414 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 52 optimal weight: 0.2980 chunk 18 optimal weight: 0.0060 chunk 33 optimal weight: 0.6980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.136820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.120610 restraints weight = 7228.192| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.45 r_work: 0.3331 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6344 Z= 0.149 Angle : 0.573 6.836 8630 Z= 0.290 Chirality : 0.038 0.115 972 Planarity : 0.005 0.039 1058 Dihedral : 4.064 15.519 854 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.16 % Allowed : 11.57 % Favored : 86.27 % 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: 3.21 (0.29), residues: 794 helix: 2.15 (0.19), residues: 704 sheet: None (None), residues: 0 loop : 2.30 (0.81), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 300 TYR 0.010 0.001 TYR A 24 PHE 0.012 0.001 PHE B 33 TRP 0.011 0.001 TRP B 138 HIS 0.004 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6344) covalent geometry : angle 0.57260 ( 8630) hydrogen bonds : bond 0.04447 ( 562) hydrogen bonds : angle 3.88801 ( 1686) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.247 Fit side-chains REVERT: A 133 GLN cc_start: 0.6973 (mt0) cc_final: 0.6603 (tp40) REVERT: A 329 LEU cc_start: 0.6841 (tt) cc_final: 0.6516 (pp) REVERT: A 372 MET cc_start: 0.7420 (mmm) cc_final: 0.6880 (mmt) REVERT: A 414 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6780 (tt) REVERT: B 133 GLN cc_start: 0.7081 (mt0) cc_final: 0.6679 (tp40) REVERT: B 414 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6783 (tt) outliers start: 14 outliers final: 11 residues processed: 57 average time/residue: 0.0775 time to fit residues: 6.3234 Evaluate side-chains 52 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 414 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.132905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.116833 restraints weight = 7292.228| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.44 r_work: 0.3316 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6344 Z= 0.193 Angle : 0.612 7.009 8630 Z= 0.308 Chirality : 0.040 0.121 972 Planarity : 0.005 0.041 1058 Dihedral : 4.124 14.214 854 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.01 % Allowed : 12.04 % Favored : 85.96 % 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: 3.00 (0.29), residues: 794 helix: 1.99 (0.19), residues: 704 sheet: None (None), residues: 0 loop : 2.38 (0.82), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 28 TYR 0.015 0.002 TYR A 9 PHE 0.012 0.001 PHE B 14 TRP 0.013 0.001 TRP A 138 HIS 0.005 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 6344) covalent geometry : angle 0.61169 ( 8630) hydrogen bonds : bond 0.04668 ( 562) hydrogen bonds : angle 4.03263 ( 1686) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1300.89 seconds wall clock time: 23 minutes 10.88 seconds (1390.88 seconds total)