Starting phenix.real_space_refine on Wed Sep 17 03:25:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jri_61756/09_2025/9jri_61756_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jri_61756/09_2025/9jri_61756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jri_61756/09_2025/9jri_61756_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jri_61756/09_2025/9jri_61756_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jri_61756/09_2025/9jri_61756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jri_61756/09_2025/9jri_61756.map" } resolution = 3.43 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= 0.066 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 10 5.16 5 C 2093 2.51 5 N 515 2.21 5 O 514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3132 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3099 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 12, 'TRANS': 372} Chain breaks: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'C2F': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.09, per 1000 atoms: 0.35 Number of scatterers: 3132 At special positions: 0 Unit cell: (66, 64, 78, 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 10 16.00 O 514 8.00 N 515 7.00 C 2093 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: 0.36 Conformation dependent library (CDL) restraints added in 129.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB C2F A 701 " Number of C-beta restraints generated: 728 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 83.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 29 through 40 removed outlier: 3.716A pdb=" N GLN A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 68 through 88 removed outlier: 3.944A pdb=" N LEU A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 4.715A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 112 removed outlier: 3.516A pdb=" N LEU A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 144 removed outlier: 3.608A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 177 removed outlier: 3.628A pdb=" N TYR A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 202 removed outlier: 3.940A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 264 through 294 removed outlier: 3.816A pdb=" N SER A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 327 Processing helix chain 'A' and resid 335 through 355 removed outlier: 3.746A pdb=" N HIS A 355 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 389 removed outlier: 3.767A pdb=" N LEU A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A 377 " --> pdb=" O ARG A 373 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) Proline residue: A 381 - end of helix removed outlier: 3.733A pdb=" N PHE A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 419 removed outlier: 3.695A pdb=" N PHE A 400 " --> pdb=" O CYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 453 234 hydrogen bonds defined for protein. 702 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: 0.50 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 436 1.30 - 1.43: 977 1.43 - 1.56: 1792 1.56 - 1.69: 0 1.69 - 1.82: 16 Bond restraints: 3221 Sorted by residual: bond pdb=" C8A C2F A 701 " pdb=" N8 C2F A 701 " ideal model delta sigma weight residual 1.344 1.504 -0.160 2.00e-02 2.50e+03 6.38e+01 bond pdb=" C2 C2F A 701 " pdb=" NA2 C2F A 701 " ideal model delta sigma weight residual 1.345 1.444 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" N C2F A 701 " pdb=" C C2F A 701 " ideal model delta sigma weight residual 1.343 1.427 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C4 C2F A 701 " pdb=" C4A C2F A 701 " ideal model delta sigma weight residual 1.415 1.335 0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C6 C2F A 701 " pdb=" N5 C2F A 701 " ideal model delta sigma weight residual 1.452 1.373 0.079 2.00e-02 2.50e+03 1.56e+01 ... (remaining 3216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 4322 3.08 - 6.16: 51 6.16 - 9.24: 15 9.24 - 12.32: 1 12.32 - 15.40: 1 Bond angle restraints: 4390 Sorted by residual: angle pdb=" C15 C2F A 701 " pdb=" N10 C2F A 701 " pdb=" C9 C2F A 701 " ideal model delta sigma weight residual 122.08 106.68 15.40 3.00e+00 1.11e-01 2.63e+01 angle pdb=" C6 C2F A 701 " pdb=" C9 C2F A 701 " pdb=" N10 C2F A 701 " ideal model delta sigma weight residual 109.12 97.21 11.91 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CA PRO A 427 " pdb=" N PRO A 427 " pdb=" CD PRO A 427 " ideal model delta sigma weight residual 112.00 107.99 4.01 1.40e+00 5.10e-01 8.20e+00 angle pdb=" N LEU A 77 " pdb=" CA LEU A 77 " pdb=" C LEU A 77 " ideal model delta sigma weight residual 112.72 109.02 3.70 1.36e+00 5.41e-01 7.42e+00 angle pdb=" CA TYR A 74 " pdb=" CB TYR A 74 " pdb=" CG TYR A 74 " ideal model delta sigma weight residual 113.90 118.71 -4.81 1.80e+00 3.09e-01 7.15e+00 ... (remaining 4385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.07: 1688 26.07 - 52.15: 139 52.15 - 78.22: 12 78.22 - 104.29: 1 104.29 - 130.36: 6 Dihedral angle restraints: 1846 sinusoidal: 713 harmonic: 1133 Sorted by residual: dihedral pdb=" C11 C2F A 701 " pdb=" C6 C2F A 701 " pdb=" N5 C2F A 701 " pdb=" C9 C2F A 701 " ideal model delta sinusoidal sigma weight residual 202.19 71.83 130.36 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" C11 C2F A 701 " pdb=" C6 C2F A 701 " pdb=" N5 C2F A 701 " pdb=" C7 C2F A 701 " ideal model delta sinusoidal sigma weight residual 78.30 -48.05 126.35 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" N5 C2F A 701 " pdb=" C6 C2F A 701 " pdb=" C7 C2F A 701 " pdb=" N8 C2F A 701 " ideal model delta sinusoidal sigma weight residual -52.13 73.03 -125.16 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 1843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 320 0.032 - 0.064: 134 0.064 - 0.097: 39 0.097 - 0.129: 14 0.129 - 0.161: 2 Chirality restraints: 509 Sorted by residual: chirality pdb=" CA LEU A 258 " pdb=" N LEU A 258 " pdb=" C LEU A 258 " pdb=" CB LEU A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CA LEU A 112 " pdb=" N LEU A 112 " pdb=" C LEU A 112 " pdb=" CB LEU A 112 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA THR A 69 " pdb=" N THR A 69 " pdb=" C THR A 69 " pdb=" CB THR A 69 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 506 not shown) Planarity restraints: 523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 426 " -0.069 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO A 427 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 427 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 427 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 145 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO A 146 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C C2F A 701 " 0.008 2.00e-02 2.50e+03 8.38e-03 1.40e+00 pdb=" C12 C2F A 701 " -0.009 2.00e-02 2.50e+03 pdb=" C13 C2F A 701 " 0.005 2.00e-02 2.50e+03 pdb=" C14 C2F A 701 " -0.003 2.00e-02 2.50e+03 pdb=" C15 C2F A 701 " -0.015 2.00e-02 2.50e+03 pdb=" C16 C2F A 701 " 0.000 2.00e-02 2.50e+03 pdb=" C17 C2F A 701 " 0.000 2.00e-02 2.50e+03 pdb=" N10 C2F A 701 " 0.013 2.00e-02 2.50e+03 ... (remaining 520 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 47 2.67 - 3.23: 3139 3.23 - 3.79: 5379 3.79 - 4.34: 6550 4.34 - 4.90: 10905 Nonbonded interactions: 26020 Sorted by model distance: nonbonded pdb=" OE1 GLU A 123 " pdb=" O4 C2F A 701 " model vdw 2.119 3.040 nonbonded pdb=" OH TYR A 31 " pdb=" O LEU A 199 " model vdw 2.239 3.040 nonbonded pdb=" OE2 GLU A 123 " pdb=" O4 C2F A 701 " model vdw 2.320 3.040 nonbonded pdb=" OG SER A 271 " pdb=" OD1 ASN A 403 " model vdw 2.340 3.040 nonbonded pdb=" OG SER A 321 " pdb=" O GLN A 377 " model vdw 2.342 3.040 ... (remaining 26015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=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: 1.130 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.580 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 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 0.160 3221 Z= 0.326 Angle : 0.870 15.395 4390 Z= 0.392 Chirality : 0.040 0.161 509 Planarity : 0.006 0.102 523 Dihedral : 19.715 130.361 1118 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.30 % Allowed : 31.42 % Favored : 68.28 % Cbeta Deviations : 0.27 % 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: 1.04 (0.43), residues: 379 helix: 1.15 (0.29), residues: 311 sheet: None (None), residues: 0 loop : -1.27 (0.85), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 61 TYR 0.017 0.001 TYR A 438 PHE 0.017 0.001 PHE A 84 TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00648 ( 3221) covalent geometry : angle 0.87023 ( 4390) hydrogen bonds : bond 0.11713 ( 234) hydrogen bonds : angle 5.76268 ( 702) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.118 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.0798 time to fit residues: 4.4551 Evaluate side-chains 45 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 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 = 0.3873 r_free = 0.3873 target = 0.161783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.136900 restraints weight = 3978.307| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.92 r_work: 0.3495 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.0675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3221 Z= 0.163 Angle : 0.614 8.002 4390 Z= 0.302 Chirality : 0.039 0.125 509 Planarity : 0.005 0.070 523 Dihedral : 15.578 150.692 452 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.63 % Allowed : 28.70 % Favored : 67.67 % Cbeta Deviations : 0.27 % 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: 1.35 (0.44), residues: 379 helix: 1.41 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.44 (0.87), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 61 TYR 0.019 0.001 TYR A 438 PHE 0.016 0.001 PHE A 84 TRP 0.011 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 3221) covalent geometry : angle 0.61358 ( 4390) hydrogen bonds : bond 0.04692 ( 234) hydrogen bonds : angle 4.56847 ( 702) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.112 Fit side-chains REVERT: A 45 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8464 (tt0) REVERT: A 377 GLN cc_start: 0.9328 (mm-40) cc_final: 0.8906 (mm-40) outliers start: 12 outliers final: 7 residues processed: 53 average time/residue: 0.0802 time to fit residues: 5.1186 Evaluate side-chains 50 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 426 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 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 = 0.3860 r_free = 0.3860 target = 0.160658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.135508 restraints weight = 4050.061| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.99 r_work: 0.3429 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3221 Z= 0.175 Angle : 0.606 8.592 4390 Z= 0.301 Chirality : 0.040 0.127 509 Planarity : 0.004 0.061 523 Dihedral : 15.389 163.370 452 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 6.04 % Allowed : 25.68 % Favored : 68.28 % Cbeta Deviations : 0.27 % 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: 1.32 (0.43), residues: 379 helix: 1.38 (0.28), residues: 314 sheet: None (None), residues: 0 loop : -1.51 (0.87), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.021 0.002 TYR A 438 PHE 0.018 0.001 PHE A 84 TRP 0.011 0.002 TRP A 107 HIS 0.008 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 3221) covalent geometry : angle 0.60621 ( 4390) hydrogen bonds : bond 0.04633 ( 234) hydrogen bonds : angle 4.34668 ( 702) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.071 Fit side-chains REVERT: A 127 SER cc_start: 0.8937 (OUTLIER) cc_final: 0.8723 (t) REVERT: A 162 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7803 (mp) REVERT: A 282 TYR cc_start: 0.8116 (m-10) cc_final: 0.7839 (m-10) REVERT: A 371 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7687 (mp) outliers start: 20 outliers final: 12 residues processed: 64 average time/residue: 0.0707 time to fit residues: 5.4662 Evaluate side-chains 60 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 426 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 2 optimal weight: 0.0980 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.162757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.137486 restraints weight = 3986.899| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.00 r_work: 0.3480 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3221 Z= 0.144 Angle : 0.584 8.115 4390 Z= 0.288 Chirality : 0.039 0.158 509 Planarity : 0.004 0.056 523 Dihedral : 15.271 170.157 452 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 6.04 % Allowed : 25.68 % Favored : 68.28 % Cbeta Deviations : 0.27 % 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: 1.36 (0.43), residues: 379 helix: 1.42 (0.28), residues: 313 sheet: None (None), residues: 0 loop : -1.49 (0.88), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.017 0.001 TYR A 438 PHE 0.014 0.001 PHE A 84 TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3221) covalent geometry : angle 0.58405 ( 4390) hydrogen bonds : bond 0.04282 ( 234) hydrogen bonds : angle 4.19904 ( 702) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.083 Fit side-chains REVERT: A 45 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: A 127 SER cc_start: 0.8924 (OUTLIER) cc_final: 0.8700 (t) REVERT: A 162 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7662 (mp) REVERT: A 255 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6523 (mm) REVERT: A 327 VAL cc_start: 0.7505 (OUTLIER) cc_final: 0.7225 (t) REVERT: A 371 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7708 (mp) outliers start: 20 outliers final: 9 residues processed: 63 average time/residue: 0.0606 time to fit residues: 4.7101 Evaluate side-chains 60 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 375 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 5 optimal weight: 0.0980 chunk 12 optimal weight: 0.0770 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 overall best weight: 0.3738 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.164576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.139598 restraints weight = 3961.706| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.99 r_work: 0.3505 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3221 Z= 0.128 Angle : 0.564 7.836 4390 Z= 0.277 Chirality : 0.039 0.135 509 Planarity : 0.004 0.054 523 Dihedral : 15.146 173.403 452 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.74 % Allowed : 26.28 % Favored : 67.98 % Cbeta Deviations : 0.27 % 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: 1.52 (0.43), residues: 379 helix: 1.52 (0.28), residues: 315 sheet: None (None), residues: 0 loop : -1.49 (0.88), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.020 0.001 TYR A 366 PHE 0.013 0.001 PHE A 84 TRP 0.012 0.001 TRP A 107 HIS 0.008 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 3221) covalent geometry : angle 0.56409 ( 4390) hydrogen bonds : bond 0.04037 ( 234) hydrogen bonds : angle 4.04134 ( 702) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.106 Fit side-chains REVERT: A 45 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8421 (tt0) REVERT: A 127 SER cc_start: 0.8888 (OUTLIER) cc_final: 0.8658 (t) REVERT: A 139 TYR cc_start: 0.8920 (t80) cc_final: 0.8710 (t80) REVERT: A 151 ARG cc_start: 0.8744 (mtp-110) cc_final: 0.8539 (mmm160) REVERT: A 162 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7575 (mp) REVERT: A 255 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6467 (mm) REVERT: A 327 VAL cc_start: 0.7440 (OUTLIER) cc_final: 0.7150 (t) REVERT: A 371 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7747 (mp) outliers start: 19 outliers final: 11 residues processed: 68 average time/residue: 0.0845 time to fit residues: 6.7542 Evaluate side-chains 65 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 398 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 7 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 chunk 4 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.165195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139754 restraints weight = 3980.880| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.02 r_work: 0.3487 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3221 Z= 0.132 Angle : 0.562 7.932 4390 Z= 0.277 Chirality : 0.038 0.136 509 Planarity : 0.004 0.053 523 Dihedral : 15.154 173.201 452 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.74 % Allowed : 27.19 % Favored : 67.07 % Cbeta Deviations : 0.27 % 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: 1.54 (0.43), residues: 379 helix: 1.56 (0.28), residues: 314 sheet: None (None), residues: 0 loop : -1.61 (0.87), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 61 TYR 0.021 0.002 TYR A 149 PHE 0.033 0.001 PHE A 372 TRP 0.011 0.001 TRP A 107 HIS 0.002 0.000 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 3221) covalent geometry : angle 0.56215 ( 4390) hydrogen bonds : bond 0.03987 ( 234) hydrogen bonds : angle 3.99932 ( 702) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.109 Fit side-chains REVERT: A 45 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8396 (tt0) REVERT: A 127 SER cc_start: 0.8907 (OUTLIER) cc_final: 0.8678 (t) REVERT: A 139 TYR cc_start: 0.8924 (t80) cc_final: 0.8699 (t80) REVERT: A 162 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7631 (mp) REVERT: A 255 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6357 (mm) REVERT: A 327 VAL cc_start: 0.7415 (OUTLIER) cc_final: 0.7135 (t) REVERT: A 371 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7725 (mp) REVERT: A 377 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8731 (mm-40) outliers start: 19 outliers final: 11 residues processed: 67 average time/residue: 0.0721 time to fit residues: 5.8146 Evaluate side-chains 63 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.0070 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.162134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137447 restraints weight = 4045.441| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.94 r_work: 0.3505 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3221 Z= 0.134 Angle : 0.567 8.040 4390 Z= 0.280 Chirality : 0.039 0.137 509 Planarity : 0.004 0.052 523 Dihedral : 15.126 172.880 452 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 6.34 % Allowed : 26.59 % Favored : 67.07 % Cbeta Deviations : 0.27 % 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: 1.66 (0.43), residues: 379 helix: 1.61 (0.28), residues: 315 sheet: None (None), residues: 0 loop : -1.40 (0.88), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 61 TYR 0.016 0.001 TYR A 149 PHE 0.027 0.001 PHE A 372 TRP 0.011 0.001 TRP A 107 HIS 0.011 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3221) covalent geometry : angle 0.56718 ( 4390) hydrogen bonds : bond 0.04004 ( 234) hydrogen bonds : angle 3.97716 ( 702) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.070 Fit side-chains REVERT: A 45 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8396 (tt0) REVERT: A 127 SER cc_start: 0.8913 (OUTLIER) cc_final: 0.8690 (t) REVERT: A 139 TYR cc_start: 0.8929 (t80) cc_final: 0.8703 (t80) REVERT: A 162 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7598 (mp) REVERT: A 255 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6383 (mm) REVERT: A 327 VAL cc_start: 0.7467 (OUTLIER) cc_final: 0.7171 (t) REVERT: A 371 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7740 (mp) REVERT: A 377 GLN cc_start: 0.9229 (mm-40) cc_final: 0.8731 (mm-40) outliers start: 21 outliers final: 14 residues processed: 67 average time/residue: 0.0621 time to fit residues: 5.1186 Evaluate side-chains 67 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 28 optimal weight: 0.0470 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.161848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136385 restraints weight = 4096.261| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.99 r_work: 0.3479 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3221 Z= 0.153 Angle : 0.585 8.249 4390 Z= 0.288 Chirality : 0.039 0.137 509 Planarity : 0.004 0.053 523 Dihedral : 15.165 172.053 452 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 6.65 % Allowed : 26.59 % Favored : 66.77 % Cbeta Deviations : 0.27 % 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: 1.57 (0.43), residues: 379 helix: 1.57 (0.28), residues: 314 sheet: None (None), residues: 0 loop : -1.50 (0.87), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 61 TYR 0.017 0.002 TYR A 438 PHE 0.026 0.001 PHE A 372 TRP 0.011 0.001 TRP A 107 HIS 0.004 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 3221) covalent geometry : angle 0.58507 ( 4390) hydrogen bonds : bond 0.04168 ( 234) hydrogen bonds : angle 4.02153 ( 702) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.079 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8413 (tt0) REVERT: A 127 SER cc_start: 0.8975 (OUTLIER) cc_final: 0.8751 (t) REVERT: A 139 TYR cc_start: 0.8933 (t80) cc_final: 0.8706 (t80) REVERT: A 162 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7700 (mp) REVERT: A 255 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6390 (mm) REVERT: A 327 VAL cc_start: 0.7559 (OUTLIER) cc_final: 0.7262 (t) REVERT: A 371 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7750 (mp) outliers start: 22 outliers final: 14 residues processed: 69 average time/residue: 0.0710 time to fit residues: 5.8573 Evaluate side-chains 67 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.159259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.134327 restraints weight = 4048.464| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.95 r_work: 0.3465 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3221 Z= 0.176 Angle : 0.622 8.565 4390 Z= 0.306 Chirality : 0.040 0.131 509 Planarity : 0.004 0.054 523 Dihedral : 15.179 170.420 452 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 6.65 % Allowed : 26.89 % Favored : 66.47 % Cbeta Deviations : 0.27 % 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: 1.48 (0.43), residues: 379 helix: 1.49 (0.28), residues: 314 sheet: None (None), residues: 0 loop : -1.44 (0.88), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 61 TYR 0.020 0.002 TYR A 438 PHE 0.025 0.002 PHE A 372 TRP 0.012 0.001 TRP A 25 HIS 0.013 0.002 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 3221) covalent geometry : angle 0.62161 ( 4390) hydrogen bonds : bond 0.04407 ( 234) hydrogen bonds : angle 4.08257 ( 702) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: A 127 SER cc_start: 0.9010 (OUTLIER) cc_final: 0.8799 (t) REVERT: A 139 TYR cc_start: 0.8931 (t80) cc_final: 0.8525 (t80) REVERT: A 162 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7747 (mp) REVERT: A 255 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6658 (mm) REVERT: A 282 TYR cc_start: 0.8309 (m-10) cc_final: 0.7999 (m-10) REVERT: A 327 VAL cc_start: 0.7553 (OUTLIER) cc_final: 0.7264 (t) REVERT: A 371 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7789 (mp) outliers start: 22 outliers final: 15 residues processed: 69 average time/residue: 0.0767 time to fit residues: 6.3166 Evaluate side-chains 70 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.0270 chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 6 optimal weight: 0.0040 overall best weight: 0.3650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.163445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138700 restraints weight = 3961.896| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.94 r_work: 0.3451 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3221 Z= 0.128 Angle : 0.596 8.349 4390 Z= 0.287 Chirality : 0.039 0.142 509 Planarity : 0.004 0.053 523 Dihedral : 15.095 171.080 452 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 6.95 % Allowed : 27.19 % Favored : 65.86 % Cbeta Deviations : 0.27 % 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: 1.75 (0.43), residues: 379 helix: 1.68 (0.28), residues: 315 sheet: None (None), residues: 0 loop : -1.42 (0.88), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 61 TYR 0.014 0.001 TYR A 438 PHE 0.025 0.001 PHE A 372 TRP 0.012 0.001 TRP A 107 HIS 0.015 0.002 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 3221) covalent geometry : angle 0.59571 ( 4390) hydrogen bonds : bond 0.04007 ( 234) hydrogen bonds : angle 3.95881 ( 702) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.123 Fit side-chains REVERT: A 45 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8364 (tt0) REVERT: A 127 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.8708 (t) REVERT: A 162 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7544 (mp) REVERT: A 255 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6506 (mm) REVERT: A 327 VAL cc_start: 0.7454 (OUTLIER) cc_final: 0.7173 (t) REVERT: A 371 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7676 (mp) outliers start: 23 outliers final: 16 residues processed: 68 average time/residue: 0.0723 time to fit residues: 5.9262 Evaluate side-chains 70 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.160862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.135014 restraints weight = 4040.565| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.97 r_work: 0.3488 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3221 Z= 0.160 Angle : 0.620 8.399 4390 Z= 0.301 Chirality : 0.040 0.132 509 Planarity : 0.004 0.053 523 Dihedral : 15.157 170.399 452 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 7.25 % Allowed : 26.59 % Favored : 66.16 % Cbeta Deviations : 0.27 % 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: 1.56 (0.43), residues: 379 helix: 1.57 (0.28), residues: 314 sheet: None (None), residues: 0 loop : -1.52 (0.87), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 61 TYR 0.037 0.002 TYR A 139 PHE 0.024 0.001 PHE A 372 TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 3221) covalent geometry : angle 0.62031 ( 4390) hydrogen bonds : bond 0.04222 ( 234) hydrogen bonds : angle 4.03909 ( 702) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1080.47 seconds wall clock time: 19 minutes 14.12 seconds (1154.12 seconds total)