Starting phenix.real_space_refine on Fri Aug 22 13:06:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tte_41605/08_2025/8tte_41605.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tte_41605/08_2025/8tte_41605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tte_41605/08_2025/8tte_41605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tte_41605/08_2025/8tte_41605.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tte_41605/08_2025/8tte_41605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tte_41605/08_2025/8tte_41605.map" } resolution = 3.26 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= 0.059 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 18 5.16 5 C 2015 2.51 5 N 454 2.21 5 O 504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2991 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2842 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Chain: "C" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 149 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 13} Time building chain proxies: 1.24, per 1000 atoms: 0.41 Number of scatterers: 2991 At special positions: 0 Unit cell: (55.704, 73.428, 75.116, 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 18 16.00 O 504 8.00 N 454 7.00 C 2015 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: 0.32 Conformation dependent library (CDL) restraints added in 162.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 694 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 1 sheets defined 88.8% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 2 through 21 removed outlier: 3.549A pdb=" N ILE A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.748A pdb=" N LEU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 66 removed outlier: 3.576A pdb=" N LEU A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Proline residue: A 56 - end of helix Processing helix chain 'A' and resid 67 through 86 removed outlier: 3.631A pdb=" N ALA A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 120 removed outlier: 3.705A pdb=" N LEU A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 121 through 125 removed outlier: 4.070A pdb=" N LYS A 125 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 148 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 157 through 177 Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.994A pdb=" N LYS A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 199' Processing helix chain 'A' and resid 204 through 233 removed outlier: 4.006A pdb=" N SER A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 264 removed outlier: 5.726A pdb=" N ASP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LYS A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 289 Processing helix chain 'A' and resid 291 through 308 removed outlier: 3.732A pdb=" N SER A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE A 300 " --> pdb=" O MET A 296 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 322 removed outlier: 3.844A pdb=" N ALA A 312 " --> pdb=" O MET A 308 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 354 removed outlier: 3.804A pdb=" N ALA A 328 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) Proline residue: A 344 - end of helix removed outlier: 3.736A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 382 Processing sheet with id=AA1, first strand: chain 'C' and resid 129 through 132 245 hydrogen bonds defined for protein. 723 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: 0.56 Time building geometry restraints manager: 0.44 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: 858 1.34 - 1.46: 650 1.46 - 1.58: 1530 1.58 - 1.70: 0 1.70 - 1.82: 35 Bond restraints: 3073 Sorted by residual: bond pdb=" CE1 HIS A 123 " pdb=" NE2 HIS A 123 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.71e+01 bond pdb=" N VAL A 365 " pdb=" CA VAL A 365 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.13e+00 bond pdb=" N VAL A 108 " pdb=" CA VAL A 108 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.20e-02 6.94e+03 7.98e+00 bond pdb=" N VAL A 302 " pdb=" CA VAL A 302 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 7.95e+00 bond pdb=" N ILE A 199 " pdb=" CA ILE A 199 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.24e-02 6.50e+03 7.89e+00 ... (remaining 3068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 3918 1.90 - 3.81: 223 3.81 - 5.71: 21 5.71 - 7.61: 2 7.61 - 9.51: 3 Bond angle restraints: 4167 Sorted by residual: angle pdb=" N LEU A 17 " pdb=" CA LEU A 17 " pdb=" C LEU A 17 " ideal model delta sigma weight residual 111.69 105.40 6.29 1.23e+00 6.61e-01 2.62e+01 angle pdb=" CB MET A 361 " pdb=" CG MET A 361 " pdb=" SD MET A 361 " ideal model delta sigma weight residual 112.70 122.21 -9.51 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CB MET A 263 " pdb=" CG MET A 263 " pdb=" SD MET A 263 " ideal model delta sigma weight residual 112.70 103.36 9.34 3.00e+00 1.11e-01 9.69e+00 angle pdb=" N MET A 157 " pdb=" CA MET A 157 " pdb=" C MET A 157 " ideal model delta sigma weight residual 109.81 116.65 -6.84 2.21e+00 2.05e-01 9.57e+00 angle pdb=" N PHE A 262 " pdb=" CA PHE A 262 " pdb=" CB PHE A 262 " ideal model delta sigma weight residual 110.30 114.90 -4.60 1.54e+00 4.22e-01 8.94e+00 ... (remaining 4162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 1476 16.16 - 32.32: 202 32.32 - 48.48: 59 48.48 - 64.64: 12 64.64 - 80.80: 2 Dihedral angle restraints: 1751 sinusoidal: 658 harmonic: 1093 Sorted by residual: dihedral pdb=" CA TRP C 131 " pdb=" C TRP C 131 " pdb=" N TYR C 132 " pdb=" CA TYR C 132 " ideal model delta harmonic sigma weight residual 180.00 159.71 20.29 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ARG A 156 " pdb=" C ARG A 156 " pdb=" N MET A 157 " pdb=" CA MET A 157 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TYR A 235 " pdb=" C TYR A 235 " pdb=" N SER A 236 " pdb=" CA SER A 236 " ideal model delta harmonic sigma weight residual 180.00 162.06 17.94 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 1748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 321 0.047 - 0.095: 100 0.095 - 0.142: 42 0.142 - 0.189: 12 0.189 - 0.237: 4 Chirality restraints: 479 Sorted by residual: chirality pdb=" CA LEU A 17 " pdb=" N LEU A 17 " pdb=" C LEU A 17 " pdb=" CB LEU A 17 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE A 12 " pdb=" N ILE A 12 " pdb=" C ILE A 12 " pdb=" CB ILE A 12 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ILE A 53 " pdb=" N ILE A 53 " pdb=" C ILE A 53 " pdb=" CB ILE A 53 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 476 not shown) Planarity restraints: 506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 262 " 0.021 2.00e-02 2.50e+03 2.30e-02 9.29e+00 pdb=" CG PHE A 262 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 262 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 262 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE A 262 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 262 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 262 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 157 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.92e+00 pdb=" C MET A 157 " -0.052 2.00e-02 2.50e+03 pdb=" O MET A 157 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO A 158 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 233 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C VAL A 233 " -0.024 2.00e-02 2.50e+03 pdb=" O VAL A 233 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN A 234 " 0.008 2.00e-02 2.50e+03 ... (remaining 503 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 891 2.82 - 3.34: 3284 3.34 - 3.86: 5129 3.86 - 4.38: 5547 4.38 - 4.90: 9715 Nonbonded interactions: 24566 Sorted by model distance: nonbonded pdb=" OG SER A 236 " pdb=" OD1 ASP A 239 " model vdw 2.301 3.040 nonbonded pdb=" NZ LYS A 68 " pdb=" O ILE A 177 " model vdw 2.365 3.120 nonbonded pdb=" OG1 THR A 36 " pdb=" OD1 ASP A 352 " model vdw 2.396 3.040 nonbonded pdb=" N SER A 38 " pdb=" OD2 ASP A 352 " model vdw 2.404 3.120 nonbonded pdb=" O LEU A 276 " pdb=" OG SER A 279 " model vdw 2.476 3.040 ... (remaining 24561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.330 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 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 0.041 3073 Z= 0.414 Angle : 0.915 9.513 4167 Z= 0.632 Chirality : 0.059 0.237 479 Planarity : 0.004 0.030 506 Dihedral : 16.553 80.796 1057 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.94 % Allowed : 28.53 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.44), residues: 379 helix: 1.04 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -2.71 (0.73), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 98 TYR 0.019 0.001 TYR A 278 PHE 0.053 0.002 PHE A 262 TRP 0.008 0.001 TRP A 201 HIS 0.005 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 3073) covalent geometry : angle 0.91517 ( 4167) hydrogen bonds : bond 0.10991 ( 245) hydrogen bonds : angle 5.59027 ( 723) *********************** 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 73 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.123 Fit side-chains REVERT: A 156 ARG cc_start: 0.6732 (mtm180) cc_final: 0.5692 (mtp85) outliers start: 3 outliers final: 1 residues processed: 71 average time/residue: 0.0690 time to fit residues: 5.8975 Evaluate side-chains 66 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.162866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142367 restraints weight = 3909.686| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.92 r_work: 0.3571 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3073 Z= 0.149 Angle : 0.666 7.056 4167 Z= 0.345 Chirality : 0.041 0.173 479 Planarity : 0.004 0.027 506 Dihedral : 4.658 18.753 407 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.76 % Allowed : 29.47 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.46), residues: 379 helix: 1.84 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -2.42 (0.85), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 380 TYR 0.016 0.001 TYR A 278 PHE 0.039 0.002 PHE A 262 TRP 0.011 0.001 TRP A 201 HIS 0.005 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 3073) covalent geometry : angle 0.66552 ( 4167) hydrogen bonds : bond 0.04366 ( 245) hydrogen bonds : angle 4.31792 ( 723) *********************** 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 81 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.121 Fit side-chains REVERT: A 5 ILE cc_start: 0.7348 (OUTLIER) cc_final: 0.7088 (tp) REVERT: A 235 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.6992 (m-10) REVERT: A 376 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7916 (tm-30) outliers start: 12 outliers final: 5 residues processed: 76 average time/residue: 0.0568 time to fit residues: 5.3773 Evaluate side-chains 69 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.163144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.142488 restraints weight = 3877.902| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.92 r_work: 0.3575 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3073 Z= 0.146 Angle : 0.672 7.720 4167 Z= 0.342 Chirality : 0.041 0.163 479 Planarity : 0.004 0.026 506 Dihedral : 4.539 18.905 405 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 5.02 % Allowed : 29.47 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.46), residues: 379 helix: 2.04 (0.30), residues: 309 sheet: None (None), residues: 0 loop : -2.42 (0.82), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 380 TYR 0.015 0.001 TYR A 278 PHE 0.012 0.001 PHE A 16 TRP 0.008 0.001 TRP A 201 HIS 0.005 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 3073) covalent geometry : angle 0.67187 ( 4167) hydrogen bonds : bond 0.04144 ( 245) hydrogen bonds : angle 4.28630 ( 723) *********************** 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 84 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.110 Fit side-chains REVERT: A 51 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7184 (tp40) REVERT: A 76 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8507 (mm) REVERT: A 150 MET cc_start: 0.7328 (pmm) cc_final: 0.6886 (pmm) REVERT: A 235 TYR cc_start: 0.7877 (OUTLIER) cc_final: 0.7146 (m-10) outliers start: 16 outliers final: 9 residues processed: 79 average time/residue: 0.0594 time to fit residues: 5.7974 Evaluate side-chains 77 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.164053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.143640 restraints weight = 3856.731| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.96 r_work: 0.3653 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3073 Z= 0.156 Angle : 0.687 6.842 4167 Z= 0.350 Chirality : 0.042 0.165 479 Planarity : 0.004 0.027 506 Dihedral : 4.488 18.813 405 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.33 % Allowed : 28.84 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.46), residues: 379 helix: 2.00 (0.30), residues: 309 sheet: None (None), residues: 0 loop : -2.36 (0.84), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 380 TYR 0.014 0.001 TYR A 278 PHE 0.050 0.002 PHE A 262 TRP 0.006 0.001 TRP A 201 HIS 0.006 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 3073) covalent geometry : angle 0.68717 ( 4167) hydrogen bonds : bond 0.04233 ( 245) hydrogen bonds : angle 4.26458 ( 723) *********************** 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 84 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.110 Fit side-chains REVERT: A 51 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7264 (tp40) REVERT: A 150 MET cc_start: 0.7044 (pmm) cc_final: 0.6683 (pmm) REVERT: A 235 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.7358 (m-10) outliers start: 17 outliers final: 11 residues processed: 77 average time/residue: 0.0567 time to fit residues: 5.4475 Evaluate side-chains 77 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 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 = 0.3948 r_free = 0.3948 target = 0.168981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.148664 restraints weight = 3877.578| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.99 r_work: 0.3593 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3073 Z= 0.162 Angle : 0.693 6.883 4167 Z= 0.354 Chirality : 0.043 0.166 479 Planarity : 0.004 0.029 506 Dihedral : 4.520 18.762 405 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 6.90 % Allowed : 28.21 % Favored : 64.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.46), residues: 379 helix: 1.87 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -2.03 (0.94), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 380 TYR 0.013 0.001 TYR A 278 PHE 0.013 0.002 PHE A 16 TRP 0.005 0.001 TRP A 201 HIS 0.007 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 3073) covalent geometry : angle 0.69252 ( 4167) hydrogen bonds : bond 0.04348 ( 245) hydrogen bonds : angle 4.24659 ( 723) *********************** 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 91 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.114 Fit side-chains REVERT: A 51 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7304 (tp40) REVERT: A 61 LEU cc_start: 0.7850 (tt) cc_final: 0.6580 (mp) REVERT: A 76 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8541 (mm) REVERT: A 235 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.7596 (m-10) outliers start: 22 outliers final: 13 residues processed: 81 average time/residue: 0.0609 time to fit residues: 6.0577 Evaluate side-chains 83 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 30 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 = 0.3870 r_free = 0.3870 target = 0.161650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.141406 restraints weight = 3870.602| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.90 r_work: 0.3656 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3073 Z= 0.155 Angle : 0.701 8.486 4167 Z= 0.353 Chirality : 0.042 0.167 479 Planarity : 0.005 0.049 506 Dihedral : 4.524 18.792 405 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 6.27 % Allowed : 28.53 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.46), residues: 379 helix: 1.90 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -2.06 (0.94), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 380 TYR 0.013 0.001 TYR A 278 PHE 0.052 0.002 PHE A 262 TRP 0.015 0.001 TRP A 201 HIS 0.006 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3073) covalent geometry : angle 0.70089 ( 4167) hydrogen bonds : bond 0.04187 ( 245) hydrogen bonds : angle 4.21145 ( 723) *********************** 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 88 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.112 Fit side-chains REVERT: A 51 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7315 (tp40) REVERT: A 61 LEU cc_start: 0.7715 (tt) cc_final: 0.6590 (mp) REVERT: A 76 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8529 (mm) REVERT: A 235 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7616 (m-10) outliers start: 20 outliers final: 16 residues processed: 80 average time/residue: 0.0569 time to fit residues: 5.6429 Evaluate side-chains 85 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 5 optimal weight: 0.0970 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 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 = 0.3976 r_free = 0.3976 target = 0.170902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.150396 restraints weight = 3867.397| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.95 r_work: 0.3676 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3073 Z= 0.141 Angle : 0.691 8.473 4167 Z= 0.350 Chirality : 0.042 0.165 479 Planarity : 0.004 0.032 506 Dihedral : 4.455 18.694 405 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.33 % Allowed : 30.09 % Favored : 64.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.46), residues: 379 helix: 1.99 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -2.15 (0.92), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 380 TYR 0.013 0.001 TYR A 278 PHE 0.012 0.001 PHE A 16 TRP 0.012 0.001 TRP A 201 HIS 0.005 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3073) covalent geometry : angle 0.69094 ( 4167) hydrogen bonds : bond 0.03949 ( 245) hydrogen bonds : angle 4.17266 ( 723) *********************** 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 83 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.179 Fit side-chains REVERT: A 51 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7258 (tp40) REVERT: A 61 LEU cc_start: 0.7720 (tt) cc_final: 0.6628 (mp) REVERT: A 76 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8510 (mm) REVERT: A 235 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.7647 (m-10) outliers start: 17 outliers final: 13 residues processed: 74 average time/residue: 0.0574 time to fit residues: 5.2973 Evaluate side-chains 81 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 12 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 36 optimal weight: 0.0980 chunk 31 optimal weight: 0.0570 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 0.0870 overall best weight: 0.1876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 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 = 0.4026 r_free = 0.4026 target = 0.176040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.155281 restraints weight = 3851.424| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.96 r_work: 0.3722 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3073 Z= 0.126 Angle : 0.661 9.364 4167 Z= 0.334 Chirality : 0.041 0.160 479 Planarity : 0.004 0.032 506 Dihedral : 4.250 19.681 405 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.39 % Allowed : 30.09 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.47), residues: 379 helix: 2.11 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -2.06 (0.91), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 380 TYR 0.013 0.001 TYR A 278 PHE 0.012 0.001 PHE A 16 TRP 0.013 0.001 TRP A 201 HIS 0.003 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3073) covalent geometry : angle 0.66124 ( 4167) hydrogen bonds : bond 0.03418 ( 245) hydrogen bonds : angle 4.03287 ( 723) *********************** 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 86 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.062 Fit side-chains REVERT: A 51 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7156 (tp40) REVERT: A 61 LEU cc_start: 0.7561 (tt) cc_final: 0.6534 (mp) REVERT: A 76 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8433 (mm) REVERT: A 235 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.7638 (m-10) outliers start: 14 outliers final: 10 residues processed: 79 average time/residue: 0.0495 time to fit residues: 4.8527 Evaluate side-chains 79 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 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 = 0.3972 r_free = 0.3972 target = 0.170674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.151241 restraints weight = 3966.328| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.90 r_work: 0.3674 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3073 Z= 0.150 Angle : 0.695 9.192 4167 Z= 0.351 Chirality : 0.042 0.161 479 Planarity : 0.005 0.046 506 Dihedral : 4.305 19.057 405 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.39 % Allowed : 31.66 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.47), residues: 379 helix: 2.06 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -2.01 (0.92), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 380 TYR 0.012 0.001 TYR A 278 PHE 0.013 0.002 PHE A 159 TRP 0.008 0.001 TRP A 201 HIS 0.006 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 3073) covalent geometry : angle 0.69549 ( 4167) hydrogen bonds : bond 0.03989 ( 245) hydrogen bonds : angle 4.10675 ( 723) *********************** 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 81 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.097 Fit side-chains REVERT: A 51 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7333 (tp40) REVERT: A 61 LEU cc_start: 0.7773 (tt) cc_final: 0.6702 (mp) REVERT: A 76 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8484 (mm) outliers start: 14 outliers final: 10 residues processed: 75 average time/residue: 0.0601 time to fit residues: 5.5311 Evaluate side-chains 78 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 22 optimal weight: 0.0570 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 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 = 0.3983 r_free = 0.3983 target = 0.171894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.152336 restraints weight = 3902.443| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.88 r_work: 0.3601 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3073 Z= 0.145 Angle : 0.701 9.751 4167 Z= 0.357 Chirality : 0.042 0.165 479 Planarity : 0.005 0.047 506 Dihedral : 4.327 18.682 405 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.70 % Allowed : 31.66 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.46), residues: 379 helix: 2.04 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -2.19 (0.88), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 380 TYR 0.024 0.001 TYR A 235 PHE 0.019 0.001 PHE A 149 TRP 0.009 0.001 TRP A 201 HIS 0.005 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3073) covalent geometry : angle 0.70113 ( 4167) hydrogen bonds : bond 0.03897 ( 245) hydrogen bonds : angle 4.09604 ( 723) ********************** 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 81 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.106 Fit side-chains REVERT: A 51 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7265 (tp40) REVERT: A 61 LEU cc_start: 0.7599 (tt) cc_final: 0.6532 (mp) REVERT: A 76 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8432 (mm) REVERT: A 235 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.7686 (m-10) outliers start: 15 outliers final: 11 residues processed: 74 average time/residue: 0.0645 time to fit residues: 5.7540 Evaluate side-chains 80 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 25 optimal weight: 0.0970 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 0.0770 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 0.0980 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 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 = 0.3995 r_free = 0.3995 target = 0.173106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.153644 restraints weight = 3906.946| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.87 r_work: 0.3616 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3073 Z= 0.137 Angle : 0.689 9.431 4167 Z= 0.350 Chirality : 0.042 0.165 479 Planarity : 0.004 0.040 506 Dihedral : 4.278 19.054 405 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.70 % Allowed : 31.66 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.47), residues: 379 helix: 2.09 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -2.22 (0.87), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 380 TYR 0.019 0.001 TYR A 235 PHE 0.021 0.001 PHE A 149 TRP 0.010 0.001 TRP A 201 HIS 0.004 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3073) covalent geometry : angle 0.68899 ( 4167) hydrogen bonds : bond 0.03723 ( 245) hydrogen bonds : angle 4.05588 ( 723) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 876.19 seconds wall clock time: 15 minutes 46.70 seconds (946.70 seconds total)