Starting phenix.real_space_refine on Wed Jul 23 08:27:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k5b_36900/07_2025/8k5b_36900.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k5b_36900/07_2025/8k5b_36900.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k5b_36900/07_2025/8k5b_36900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k5b_36900/07_2025/8k5b_36900.map" model { file = "/net/cci-nas-00/data/ceres_data/8k5b_36900/07_2025/8k5b_36900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k5b_36900/07_2025/8k5b_36900.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 1587 2.51 5 N 399 2.21 5 O 371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 2374 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2365 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 280} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.24, per 1000 atoms: 0.94 Number of scatterers: 2374 At special positions: 0 Unit cell: (59.76, 72.21, 73.455, 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 17 16.00 O 371 8.00 N 399 7.00 C 1587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 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: 0.69 Conformation dependent library (CDL) restraints added in 256.9 milliseconds 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 558 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 1 sheets defined 74.6% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 29 through 54 removed outlier: 4.099A pdb=" N ILE A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 89 removed outlier: 4.013A pdb=" N ARG A 63 " --> pdb=" O TRP A 59 " (cutoff:3.500A) Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 97 through 131 Processing helix chain 'A' and resid 140 through 158 removed outlier: 3.567A pdb=" N LEU A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.604A pdb=" N LYS A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 165 " --> pdb=" O HIS A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 165' Processing helix chain 'A' and resid 187 through 218 Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 225 through 261 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 265 through 268 removed outlier: 4.202A pdb=" N VAL A 268 " --> pdb=" O ASN A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 269 through 295 removed outlier: 4.060A pdb=" N PHE A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 169 through 171 161 hydrogen bonds defined for protein. 477 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: 0.58 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 713 1.34 - 1.46: 611 1.46 - 1.58: 1096 1.58 - 1.70: 0 1.70 - 1.81: 24 Bond restraints: 2444 Sorted by residual: bond pdb=" C2 NIO A 401 " pdb=" C3 NIO A 401 " ideal model delta sigma weight residual 1.390 1.351 0.039 2.00e-02 2.50e+03 3.86e+00 bond pdb=" C3 NIO A 401 " pdb=" C4 NIO A 401 " ideal model delta sigma weight residual 1.386 1.353 0.033 2.00e-02 2.50e+03 2.74e+00 bond pdb=" C ILE A 98 " pdb=" N PRO A 99 " ideal model delta sigma weight residual 1.335 1.357 -0.021 1.36e-02 5.41e+03 2.41e+00 bond pdb=" N NIO A 401 " pdb=" C1 NIO A 401 " ideal model delta sigma weight residual 1.329 1.350 -0.021 2.00e-02 2.50e+03 1.14e+00 bond pdb=" N NIO A 401 " pdb=" C5 NIO A 401 " ideal model delta sigma weight residual 1.329 1.349 -0.020 2.00e-02 2.50e+03 1.04e+00 ... (remaining 2439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 3235 1.95 - 3.89: 62 3.89 - 5.84: 13 5.84 - 7.78: 6 7.78 - 9.73: 1 Bond angle restraints: 3317 Sorted by residual: angle pdb=" C ASP A 97 " pdb=" N ILE A 98 " pdb=" CA ILE A 98 " ideal model delta sigma weight residual 120.24 122.59 -2.35 6.30e-01 2.52e+00 1.39e+01 angle pdb=" C ILE A 98 " pdb=" CA ILE A 98 " pdb=" CB ILE A 98 " ideal model delta sigma weight residual 114.35 110.93 3.42 1.06e+00 8.90e-01 1.04e+01 angle pdb=" CA TRP A 256 " pdb=" CB TRP A 256 " pdb=" CG TRP A 256 " ideal model delta sigma weight residual 113.60 119.65 -6.05 1.90e+00 2.77e-01 1.01e+01 angle pdb=" CA LEU A 195 " pdb=" CB LEU A 195 " pdb=" CG LEU A 195 " ideal model delta sigma weight residual 116.30 126.03 -9.73 3.50e+00 8.16e-02 7.72e+00 angle pdb=" C ASN A 171 " pdb=" CA ASN A 171 " pdb=" CB ASN A 171 " ideal model delta sigma weight residual 110.24 114.05 -3.81 1.46e+00 4.69e-01 6.83e+00 ... (remaining 3312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 1188 17.92 - 35.83: 183 35.83 - 53.75: 36 53.75 - 71.67: 4 71.67 - 89.59: 3 Dihedral angle restraints: 1414 sinusoidal: 560 harmonic: 854 Sorted by residual: dihedral pdb=" CB CYS A 100 " pdb=" SG CYS A 100 " pdb=" SG CYS A 177 " pdb=" CB CYS A 177 " ideal model delta sinusoidal sigma weight residual -86.00 -156.72 70.72 1 1.00e+01 1.00e-02 6.43e+01 dihedral pdb=" CB GLU A 190 " pdb=" CG GLU A 190 " pdb=" CD GLU A 190 " pdb=" OE1 GLU A 190 " ideal model delta sinusoidal sigma weight residual 0.00 89.59 -89.59 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ARG A 90 " pdb=" CB ARG A 90 " pdb=" CG ARG A 90 " pdb=" CD ARG A 90 " ideal model delta sinusoidal sigma weight residual 180.00 125.46 54.54 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 1411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 221 0.031 - 0.062: 93 0.062 - 0.093: 37 0.093 - 0.124: 22 0.124 - 0.155: 5 Chirality restraints: 378 Sorted by residual: chirality pdb=" CB ILE A 78 " pdb=" CA ILE A 78 " pdb=" CG1 ILE A 78 " pdb=" CG2 ILE A 78 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CG LEU A 195 " pdb=" CB LEU A 195 " pdb=" CD1 LEU A 195 " pdb=" CD2 LEU A 195 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CA ASN A 171 " pdb=" N ASN A 171 " pdb=" C ASN A 171 " pdb=" CB ASN A 171 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 375 not shown) Planarity restraints: 403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 171 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C ASN A 171 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN A 171 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 172 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 199 " -0.028 5.00e-02 4.00e+02 4.33e-02 2.99e+00 pdb=" N PRO A 200 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 30 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A 31 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.021 5.00e-02 4.00e+02 ... (remaining 400 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 320 2.75 - 3.29: 2488 3.29 - 3.83: 3930 3.83 - 4.36: 4310 4.36 - 4.90: 7723 Nonbonded interactions: 18771 Sorted by model distance: nonbonded pdb=" O ASN A 171 " pdb=" ND2 ASN A 171 " model vdw 2.213 3.120 nonbonded pdb=" O PHE A 276 " pdb=" OG1 THR A 279 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR A 284 " pdb=" O2 NIO A 401 " model vdw 2.276 3.040 nonbonded pdb=" OG SER A 140 " pdb=" OG1 THR A 143 " model vdw 2.294 3.040 nonbonded pdb=" O SER A 298 " pdb=" OG SER A 298 " model vdw 2.335 3.040 ... (remaining 18766 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.260 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 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 : 0.004 0.041 2446 Z= 0.178 Angle : 0.729 9.727 3321 Z= 0.388 Chirality : 0.046 0.155 378 Planarity : 0.005 0.043 403 Dihedral : 17.218 89.586 850 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.18 % Allowed : 29.13 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.51), residues: 289 helix: 0.93 (0.37), residues: 206 sheet: None (None), residues: 0 loop : -1.43 (0.70), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 93 HIS 0.004 0.001 HIS A 184 PHE 0.021 0.001 PHE A 95 TYR 0.012 0.001 TYR A 295 ARG 0.002 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.12821 ( 161) hydrogen bonds : angle 6.13303 ( 477) SS BOND : bond 0.00430 ( 2) SS BOND : angle 2.70124 ( 4) covalent geometry : bond 0.00391 ( 2444) covalent geometry : angle 0.72342 ( 3317) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.276 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 65 average time/residue: 0.1264 time to fit residues: 9.9006 Evaluate side-chains 62 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.0050 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.172356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.150303 restraints weight = 3306.896| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.03 r_work: 0.3624 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2446 Z= 0.157 Angle : 0.594 6.529 3321 Z= 0.319 Chirality : 0.043 0.134 378 Planarity : 0.004 0.040 403 Dihedral : 4.703 35.048 316 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 9.06 % Allowed : 22.44 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.52), residues: 289 helix: 1.24 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -1.86 (0.74), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 93 HIS 0.003 0.001 HIS A 55 PHE 0.011 0.001 PHE A 197 TYR 0.010 0.002 TYR A 295 ARG 0.002 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.05081 ( 161) hydrogen bonds : angle 4.81633 ( 477) SS BOND : bond 0.00374 ( 2) SS BOND : angle 0.73238 ( 4) covalent geometry : bond 0.00348 ( 2444) covalent geometry : angle 0.59406 ( 3317) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.276 Fit side-chains REVERT: A 205 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6197 (tt) REVERT: A 273 ASP cc_start: 0.6905 (t0) cc_final: 0.6697 (m-30) REVERT: A 274 LEU cc_start: 0.8220 (tp) cc_final: 0.7932 (mp) outliers start: 23 outliers final: 10 residues processed: 88 average time/residue: 0.1206 time to fit residues: 12.8773 Evaluate side-chains 77 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 293 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.169966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147652 restraints weight = 3287.767| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.02 r_work: 0.3596 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2446 Z= 0.172 Angle : 0.610 6.483 3321 Z= 0.327 Chirality : 0.044 0.133 378 Planarity : 0.004 0.040 403 Dihedral : 4.604 30.992 314 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 10.63 % Allowed : 19.69 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.52), residues: 289 helix: 1.18 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -1.80 (0.74), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 93 HIS 0.003 0.001 HIS A 55 PHE 0.012 0.001 PHE A 244 TYR 0.009 0.002 TYR A 295 ARG 0.002 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.04922 ( 161) hydrogen bonds : angle 4.72416 ( 477) SS BOND : bond 0.00371 ( 2) SS BOND : angle 0.63147 ( 4) covalent geometry : bond 0.00396 ( 2444) covalent geometry : angle 0.60972 ( 3317) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.243 Fit side-chains REVERT: A 187 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.7112 (mm-40) REVERT: A 205 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6234 (tt) REVERT: A 274 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8097 (mp) outliers start: 27 outliers final: 19 residues processed: 81 average time/residue: 0.1076 time to fit residues: 10.8249 Evaluate side-chains 83 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 293 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.170413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.148468 restraints weight = 3312.913| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.04 r_work: 0.3599 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2446 Z= 0.155 Angle : 0.604 6.590 3321 Z= 0.320 Chirality : 0.044 0.150 378 Planarity : 0.004 0.041 403 Dihedral : 4.540 28.067 314 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 10.63 % Allowed : 21.65 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.52), residues: 289 helix: 1.20 (0.37), residues: 212 sheet: None (None), residues: 0 loop : -1.75 (0.75), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 93 HIS 0.002 0.001 HIS A 161 PHE 0.011 0.001 PHE A 244 TYR 0.008 0.002 TYR A 87 ARG 0.002 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.04681 ( 161) hydrogen bonds : angle 4.63419 ( 477) SS BOND : bond 0.00318 ( 2) SS BOND : angle 0.46261 ( 4) covalent geometry : bond 0.00349 ( 2444) covalent geometry : angle 0.60409 ( 3317) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.222 Fit side-chains REVERT: A 205 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6191 (tt) REVERT: A 274 LEU cc_start: 0.8197 (tp) cc_final: 0.7988 (mp) outliers start: 27 outliers final: 18 residues processed: 86 average time/residue: 0.1040 time to fit residues: 10.8842 Evaluate side-chains 85 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 293 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.169867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.147861 restraints weight = 3347.145| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.04 r_work: 0.3600 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2446 Z= 0.160 Angle : 0.615 7.545 3321 Z= 0.325 Chirality : 0.045 0.150 378 Planarity : 0.004 0.041 403 Dihedral : 4.493 23.413 314 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 11.02 % Allowed : 23.23 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.52), residues: 289 helix: 1.19 (0.37), residues: 212 sheet: None (None), residues: 0 loop : -1.73 (0.75), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 93 HIS 0.003 0.001 HIS A 161 PHE 0.010 0.001 PHE A 232 TYR 0.008 0.002 TYR A 87 ARG 0.002 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.04638 ( 161) hydrogen bonds : angle 4.67505 ( 477) SS BOND : bond 0.00325 ( 2) SS BOND : angle 0.46736 ( 4) covalent geometry : bond 0.00364 ( 2444) covalent geometry : angle 0.61549 ( 3317) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.247 Fit side-chains REVERT: A 205 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6201 (tt) outliers start: 28 outliers final: 20 residues processed: 87 average time/residue: 0.1088 time to fit residues: 11.6225 Evaluate side-chains 86 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 287 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.172257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.150570 restraints weight = 3239.956| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.98 r_work: 0.3623 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2446 Z= 0.156 Angle : 0.668 13.267 3321 Z= 0.343 Chirality : 0.046 0.155 378 Planarity : 0.004 0.041 403 Dihedral : 4.534 22.205 314 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 10.63 % Allowed : 25.20 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.52), residues: 289 helix: 1.39 (0.37), residues: 206 sheet: None (None), residues: 0 loop : -1.75 (0.73), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 93 HIS 0.003 0.001 HIS A 161 PHE 0.010 0.001 PHE A 197 TYR 0.008 0.001 TYR A 87 ARG 0.002 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.04610 ( 161) hydrogen bonds : angle 4.76707 ( 477) SS BOND : bond 0.00392 ( 2) SS BOND : angle 1.28414 ( 4) covalent geometry : bond 0.00349 ( 2444) covalent geometry : angle 0.66646 ( 3317) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.311 Fit side-chains REVERT: A 205 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6204 (tt) REVERT: A 239 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8432 (p) outliers start: 27 outliers final: 19 residues processed: 87 average time/residue: 0.1127 time to fit residues: 11.9101 Evaluate side-chains 87 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 287 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 28 optimal weight: 0.0170 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN A 259 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.172593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.150613 restraints weight = 3350.514| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.03 r_work: 0.3614 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2446 Z= 0.155 Angle : 0.663 8.185 3321 Z= 0.348 Chirality : 0.046 0.151 378 Planarity : 0.004 0.041 403 Dihedral : 4.572 20.744 314 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 8.66 % Allowed : 26.77 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.53), residues: 289 helix: 1.39 (0.38), residues: 207 sheet: None (None), residues: 0 loop : -1.65 (0.74), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 93 HIS 0.002 0.001 HIS A 55 PHE 0.010 0.001 PHE A 197 TYR 0.011 0.001 TYR A 87 ARG 0.003 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.04627 ( 161) hydrogen bonds : angle 4.70001 ( 477) SS BOND : bond 0.00648 ( 2) SS BOND : angle 2.35523 ( 4) covalent geometry : bond 0.00345 ( 2444) covalent geometry : angle 0.65823 ( 3317) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.245 Fit side-chains REVERT: A 205 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6515 (tt) REVERT: A 239 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8417 (p) outliers start: 22 outliers final: 16 residues processed: 82 average time/residue: 0.1060 time to fit residues: 10.7453 Evaluate side-chains 85 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 287 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN A 259 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.172122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.149791 restraints weight = 3435.163| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.08 r_work: 0.3612 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2446 Z= 0.164 Angle : 0.677 10.963 3321 Z= 0.351 Chirality : 0.047 0.142 378 Planarity : 0.004 0.040 403 Dihedral : 4.535 19.084 314 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 8.27 % Allowed : 26.77 % Favored : 64.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.53), residues: 289 helix: 1.36 (0.38), residues: 206 sheet: None (None), residues: 0 loop : -1.73 (0.72), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 93 HIS 0.003 0.001 HIS A 55 PHE 0.010 0.001 PHE A 197 TYR 0.008 0.001 TYR A 294 ARG 0.003 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.04682 ( 161) hydrogen bonds : angle 4.78090 ( 477) SS BOND : bond 0.00356 ( 2) SS BOND : angle 1.68403 ( 4) covalent geometry : bond 0.00375 ( 2444) covalent geometry : angle 0.67533 ( 3317) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.282 Fit side-chains REVERT: A 205 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6088 (tt) REVERT: A 239 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8419 (p) REVERT: A 288 MET cc_start: 0.7793 (tmm) cc_final: 0.7508 (tmm) outliers start: 21 outliers final: 16 residues processed: 78 average time/residue: 0.1013 time to fit residues: 9.8097 Evaluate side-chains 84 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 287 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.2980 chunk 2 optimal weight: 0.0980 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN A 259 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.173104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.151110 restraints weight = 3306.127| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.03 r_work: 0.3627 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2446 Z= 0.156 Angle : 0.676 11.851 3321 Z= 0.349 Chirality : 0.046 0.144 378 Planarity : 0.004 0.041 403 Dihedral : 4.543 18.233 314 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 8.66 % Allowed : 25.98 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.53), residues: 289 helix: 1.35 (0.38), residues: 206 sheet: None (None), residues: 0 loop : -1.73 (0.73), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 93 HIS 0.002 0.001 HIS A 161 PHE 0.010 0.001 PHE A 197 TYR 0.007 0.001 TYR A 294 ARG 0.003 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 161) hydrogen bonds : angle 4.78993 ( 477) SS BOND : bond 0.00334 ( 2) SS BOND : angle 1.20158 ( 4) covalent geometry : bond 0.00349 ( 2444) covalent geometry : angle 0.67466 ( 3317) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.270 Fit side-chains REVERT: A 205 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6600 (tt) REVERT: A 239 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8431 (p) outliers start: 22 outliers final: 16 residues processed: 80 average time/residue: 0.1104 time to fit residues: 11.0216 Evaluate side-chains 84 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN A 259 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.173435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151489 restraints weight = 3299.804| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.00 r_work: 0.3634 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2446 Z= 0.151 Angle : 0.678 12.460 3321 Z= 0.350 Chirality : 0.046 0.138 378 Planarity : 0.004 0.041 403 Dihedral : 4.534 17.612 314 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 7.09 % Allowed : 26.77 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.53), residues: 289 helix: 1.35 (0.38), residues: 206 sheet: None (None), residues: 0 loop : -1.70 (0.74), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 93 HIS 0.002 0.001 HIS A 161 PHE 0.011 0.001 PHE A 38 TYR 0.006 0.001 TYR A 294 ARG 0.003 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.04582 ( 161) hydrogen bonds : angle 4.78990 ( 477) SS BOND : bond 0.00291 ( 2) SS BOND : angle 1.14144 ( 4) covalent geometry : bond 0.00336 ( 2444) covalent geometry : angle 0.67766 ( 3317) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.249 Fit side-chains REVERT: A 205 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6582 (tt) REVERT: A 239 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8434 (p) outliers start: 18 outliers final: 16 residues processed: 76 average time/residue: 0.1106 time to fit residues: 10.2847 Evaluate side-chains 84 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 22 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN A 259 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.172921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.150363 restraints weight = 3309.396| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.08 r_work: 0.3627 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2446 Z= 0.161 Angle : 0.693 12.419 3321 Z= 0.359 Chirality : 0.047 0.139 378 Planarity : 0.004 0.042 403 Dihedral : 4.521 17.729 314 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 7.48 % Allowed : 26.77 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.52), residues: 289 helix: 1.29 (0.38), residues: 206 sheet: None (None), residues: 0 loop : -1.68 (0.73), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 59 HIS 0.003 0.001 HIS A 55 PHE 0.011 0.001 PHE A 38 TYR 0.011 0.002 TYR A 295 ARG 0.002 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.04695 ( 161) hydrogen bonds : angle 4.79528 ( 477) SS BOND : bond 0.00272 ( 2) SS BOND : angle 1.12391 ( 4) covalent geometry : bond 0.00366 ( 2444) covalent geometry : angle 0.69276 ( 3317) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1546.13 seconds wall clock time: 27 minutes 34.36 seconds (1654.36 seconds total)