Starting phenix.real_space_refine on Fri May 9 15:15:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtb_36639/05_2025/8jtb_36639.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtb_36639/05_2025/8jtb_36639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jtb_36639/05_2025/8jtb_36639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtb_36639/05_2025/8jtb_36639.map" model { file = "/net/cci-nas-00/data/ceres_data/8jtb_36639/05_2025/8jtb_36639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtb_36639/05_2025/8jtb_36639.cif" } resolution = 2.93 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= -0.003 sd= 0.076 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 27 5.16 5 C 1875 2.51 5 N 432 2.21 5 O 474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2808 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2797 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 23, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.59, per 1000 atoms: 0.92 Number of scatterers: 2808 At special positions: 0 Unit cell: (57.8, 62.9, 71.4, 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 27 16.00 O 474 8.00 N 432 7.00 C 1875 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: 0.75 Conformation dependent library (CDL) restraints added in 363.7 milliseconds 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 676 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 92.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 19 through 49 removed outlier: 3.534A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 132 through 157 removed outlier: 4.248A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 4.103A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 179 Processing helix chain 'A' and resid 181 through 211 Processing helix chain 'A' and resid 213 through 245 removed outlier: 3.662A pdb=" N ILE A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 249 through 270 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 291 through 323 removed outlier: 3.751A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix removed outlier: 3.517A pdb=" N GLU A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.619A pdb=" N GLY A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 4.601A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 380 through 414 removed outlier: 4.638A pdb=" N ALA A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 418 through 447 removed outlier: 3.775A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.551A pdb=" N ARG A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) 241 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.74 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 522 1.33 - 1.45: 662 1.45 - 1.57: 1646 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 2876 Sorted by residual: bond pdb=" N SER A 179 " pdb=" CA SER A 179 " ideal model delta sigma weight residual 1.454 1.497 -0.043 1.17e-02 7.31e+03 1.34e+01 bond pdb=" N ILE A 44 " pdb=" CA ILE A 44 " ideal model delta sigma weight residual 1.463 1.500 -0.037 1.20e-02 6.94e+03 9.59e+00 bond pdb=" C SER A 179 " pdb=" O SER A 179 " ideal model delta sigma weight residual 1.234 1.270 -0.036 1.16e-02 7.43e+03 9.53e+00 bond pdb=" N VAL A 39 " pdb=" CA VAL A 39 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.46e+00 bond pdb=" N VAL A 41 " pdb=" CA VAL A 41 " ideal model delta sigma weight residual 1.463 1.499 -0.036 1.20e-02 6.94e+03 9.03e+00 ... (remaining 2871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 3716 2.08 - 4.15: 167 4.15 - 6.23: 29 6.23 - 8.30: 1 8.30 - 10.38: 2 Bond angle restraints: 3915 Sorted by residual: angle pdb=" CA ILE A 44 " pdb=" C ILE A 44 " pdb=" N PRO A 45 " ideal model delta sigma weight residual 120.83 123.82 -2.99 6.10e-01 2.69e+00 2.41e+01 angle pdb=" N SER A 179 " pdb=" CA SER A 179 " pdb=" C SER A 179 " ideal model delta sigma weight residual 109.86 116.49 -6.63 1.55e+00 4.16e-01 1.83e+01 angle pdb=" CA VAL A 41 " pdb=" C VAL A 41 " pdb=" N PRO A 42 " ideal model delta sigma weight residual 120.83 123.31 -2.48 6.10e-01 2.69e+00 1.66e+01 angle pdb=" CA ILE A 44 " pdb=" C ILE A 44 " pdb=" O ILE A 44 " ideal model delta sigma weight residual 118.69 116.06 2.63 6.70e-01 2.23e+00 1.54e+01 angle pdb=" N GLN A 192 " pdb=" CA GLN A 192 " pdb=" C GLN A 192 " ideal model delta sigma weight residual 111.28 107.11 4.17 1.09e+00 8.42e-01 1.47e+01 ... (remaining 3910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 1492 17.36 - 34.73: 130 34.73 - 52.09: 46 52.09 - 69.45: 7 69.45 - 86.82: 3 Dihedral angle restraints: 1678 sinusoidal: 616 harmonic: 1062 Sorted by residual: dihedral pdb=" C ILE A 44 " pdb=" N ILE A 44 " pdb=" CA ILE A 44 " pdb=" CB ILE A 44 " ideal model delta harmonic sigma weight residual -122.00 -132.73 10.73 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" C PHE A 178 " pdb=" N PHE A 178 " pdb=" CA PHE A 178 " pdb=" CB PHE A 178 " ideal model delta harmonic sigma weight residual -122.60 -132.61 10.01 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CA ILE A 44 " pdb=" CB ILE A 44 " ideal model delta harmonic sigma weight residual 123.40 132.53 -9.13 0 2.50e+00 1.60e-01 1.33e+01 ... (remaining 1675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 384 0.064 - 0.127: 66 0.127 - 0.190: 16 0.190 - 0.254: 2 0.254 - 0.317: 2 Chirality restraints: 470 Sorted by residual: chirality pdb=" CA PHE A 178 " pdb=" N PHE A 178 " pdb=" C PHE A 178 " pdb=" CB PHE A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.18 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA PHE A 176 " pdb=" N PHE A 176 " pdb=" C PHE A 176 " pdb=" CB PHE A 176 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 467 not shown) Planarity restraints: 479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 176 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.27e+00 pdb=" C PHE A 176 " -0.053 2.00e-02 2.50e+03 pdb=" O PHE A 176 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA A 177 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 179 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.31e+00 pdb=" C SER A 179 " -0.050 2.00e-02 2.50e+03 pdb=" O SER A 179 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 180 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 165 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.73e+00 pdb=" C GLY A 165 " -0.038 2.00e-02 2.50e+03 pdb=" O GLY A 165 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 166 " 0.013 2.00e-02 2.50e+03 ... (remaining 476 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 309 2.75 - 3.29: 2832 3.29 - 3.82: 4501 3.82 - 4.36: 5253 4.36 - 4.90: 9287 Nonbonded interactions: 22182 Sorted by model distance: nonbonded pdb=" O PRO A 236 " pdb=" OG SER A 240 " model vdw 2.211 3.040 nonbonded pdb=" O PRO A 336 " pdb=" OG SER A 340 " model vdw 2.249 3.040 nonbonded pdb=" O GLN A 142 " pdb=" ND2 ASN A 146 " model vdw 2.295 3.120 nonbonded pdb=" O ILE A 367 " pdb=" OG SER A 371 " model vdw 2.432 3.040 nonbonded pdb=" O GLN A 192 " pdb=" OG SER A 196 " model vdw 2.492 3.040 ... (remaining 22177 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.880 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:10.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 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 0.048 2876 Z= 0.424 Angle : 0.936 10.379 3915 Z= 0.622 Chirality : 0.057 0.317 470 Planarity : 0.007 0.047 479 Dihedral : 15.619 86.816 1002 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.08 % Favored : 98.39 % Rotamer: Outliers : 1.35 % Allowed : 25.25 % Favored : 73.40 % Cbeta Deviations : 0.30 % 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: 0.86 (0.43), residues: 372 helix: 1.10 (0.29), residues: 315 sheet: None (None), residues: 0 loop : -2.20 (0.63), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 451 HIS 0.001 0.001 HIS A 414 PHE 0.017 0.002 PHE A 238 TYR 0.014 0.002 TYR A 422 ARG 0.004 0.001 ARG A 413 Details of bonding type rmsd hydrogen bonds : bond 0.17015 ( 241) hydrogen bonds : angle 6.12959 ( 714) covalent geometry : bond 0.00618 ( 2876) covalent geometry : angle 0.93580 ( 3915) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.285 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 1.0125 time to fit residues: 56.4001 Evaluate side-chains 45 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 371 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 15 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.0270 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.137562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.119085 restraints weight = 3279.641| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.45 r_work: 0.3199 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2876 Z= 0.149 Angle : 0.652 10.090 3915 Z= 0.325 Chirality : 0.041 0.143 470 Planarity : 0.006 0.045 479 Dihedral : 5.255 39.920 400 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.70 % Allowed : 23.57 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.63 (0.44), residues: 372 helix: 1.61 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -2.26 (0.68), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.001 0.000 HIS A 353 PHE 0.012 0.001 PHE A 238 TYR 0.012 0.001 TYR A 422 ARG 0.001 0.000 ARG A 413 Details of bonding type rmsd hydrogen bonds : bond 0.05828 ( 241) hydrogen bonds : angle 4.63598 ( 714) covalent geometry : bond 0.00282 ( 2876) covalent geometry : angle 0.65225 ( 3915) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.304 Fit side-chains outliers start: 11 outliers final: 0 residues processed: 60 average time/residue: 0.9539 time to fit residues: 59.1636 Evaluate side-chains 47 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.134612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.117264 restraints weight = 3339.933| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.26 r_work: 0.3168 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2876 Z= 0.175 Angle : 0.667 10.203 3915 Z= 0.332 Chirality : 0.043 0.148 470 Planarity : 0.006 0.045 479 Dihedral : 4.830 36.451 396 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.04 % Allowed : 21.21 % Favored : 74.75 % 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: 1.65 (0.44), residues: 372 helix: 1.61 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -2.15 (0.70), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 451 HIS 0.001 0.001 HIS A 414 PHE 0.022 0.002 PHE A 238 TYR 0.016 0.002 TYR A 422 ARG 0.001 0.000 ARG A 413 Details of bonding type rmsd hydrogen bonds : bond 0.06260 ( 241) hydrogen bonds : angle 4.55678 ( 714) covalent geometry : bond 0.00397 ( 2876) covalent geometry : angle 0.66735 ( 3915) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.288 Fit side-chains REVERT: A 242 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7083 (mm) outliers start: 12 outliers final: 3 residues processed: 52 average time/residue: 1.0390 time to fit residues: 55.6861 Evaluate side-chains 48 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 365 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 0.0570 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 overall best weight: 0.3856 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.139175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.122249 restraints weight = 3451.238| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.26 r_work: 0.3210 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2876 Z= 0.142 Angle : 0.619 9.951 3915 Z= 0.305 Chirality : 0.041 0.137 470 Planarity : 0.006 0.046 479 Dihedral : 4.648 34.940 396 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.03 % Allowed : 22.22 % Favored : 74.75 % 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: 2.04 (0.45), residues: 372 helix: 1.88 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -2.10 (0.72), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 358 HIS 0.001 0.000 HIS A 353 PHE 0.017 0.001 PHE A 238 TYR 0.012 0.001 TYR A 422 ARG 0.001 0.000 ARG A 413 Details of bonding type rmsd hydrogen bonds : bond 0.05251 ( 241) hydrogen bonds : angle 4.36054 ( 714) covalent geometry : bond 0.00289 ( 2876) covalent geometry : angle 0.61862 ( 3915) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.297 Fit side-chains REVERT: A 262 ASP cc_start: 0.7595 (t0) cc_final: 0.7347 (t70) REVERT: A 275 VAL cc_start: 0.7880 (OUTLIER) cc_final: 0.7635 (t) outliers start: 9 outliers final: 3 residues processed: 54 average time/residue: 0.9846 time to fit residues: 54.9461 Evaluate side-chains 49 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 381 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.135137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.117912 restraints weight = 3389.458| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.26 r_work: 0.3182 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2876 Z= 0.171 Angle : 0.650 10.151 3915 Z= 0.321 Chirality : 0.043 0.134 470 Planarity : 0.006 0.046 479 Dihedral : 4.733 35.458 396 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.71 % Allowed : 20.20 % Favored : 75.08 % 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: 1.63 (0.45), residues: 372 helix: 1.61 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.73 (0.75), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.002 0.001 HIS A 414 PHE 0.023 0.002 PHE A 238 TYR 0.017 0.002 TYR A 422 ARG 0.002 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.05962 ( 241) hydrogen bonds : angle 4.44889 ( 714) covalent geometry : bond 0.00390 ( 2876) covalent geometry : angle 0.65030 ( 3915) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.321 Fit side-chains REVERT: A 275 VAL cc_start: 0.7905 (OUTLIER) cc_final: 0.7665 (t) outliers start: 14 outliers final: 6 residues processed: 57 average time/residue: 0.9591 time to fit residues: 56.4969 Evaluate side-chains 54 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.0270 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.135617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.118154 restraints weight = 3432.982| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.29 r_work: 0.3179 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2876 Z= 0.154 Angle : 0.640 9.991 3915 Z= 0.312 Chirality : 0.042 0.130 470 Planarity : 0.006 0.045 479 Dihedral : 4.653 34.353 396 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 4.04 % Allowed : 20.54 % Favored : 75.42 % 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: 1.75 (0.45), residues: 372 helix: 1.69 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.75 (0.75), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 358 HIS 0.001 0.001 HIS A 353 PHE 0.020 0.001 PHE A 238 TYR 0.015 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.05612 ( 241) hydrogen bonds : angle 4.39430 ( 714) covalent geometry : bond 0.00338 ( 2876) covalent geometry : angle 0.63950 ( 3915) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.287 Fit side-chains REVERT: A 275 VAL cc_start: 0.7893 (OUTLIER) cc_final: 0.7665 (t) outliers start: 12 outliers final: 7 residues processed: 57 average time/residue: 0.9296 time to fit residues: 54.7743 Evaluate side-chains 54 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 14 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.136456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.118840 restraints weight = 3493.663| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.31 r_work: 0.3223 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2876 Z= 0.151 Angle : 0.639 9.946 3915 Z= 0.312 Chirality : 0.042 0.129 470 Planarity : 0.006 0.045 479 Dihedral : 4.632 33.352 396 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.70 % Allowed : 21.89 % Favored : 74.41 % 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: 1.75 (0.45), residues: 372 helix: 1.70 (0.30), residues: 327 sheet: None (None), residues: 0 loop : -2.94 (0.76), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 358 HIS 0.001 0.000 HIS A 414 PHE 0.020 0.001 PHE A 238 TYR 0.015 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.05498 ( 241) hydrogen bonds : angle 4.36743 ( 714) covalent geometry : bond 0.00330 ( 2876) covalent geometry : angle 0.63851 ( 3915) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.311 Fit side-chains REVERT: A 275 VAL cc_start: 0.7869 (OUTLIER) cc_final: 0.7645 (t) outliers start: 11 outliers final: 4 residues processed: 56 average time/residue: 0.9387 time to fit residues: 54.3067 Evaluate side-chains 51 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.134302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.116741 restraints weight = 3428.383| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.30 r_work: 0.3144 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2876 Z= 0.170 Angle : 0.675 10.073 3915 Z= 0.331 Chirality : 0.043 0.128 470 Planarity : 0.006 0.047 479 Dihedral : 4.703 34.273 396 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.37 % Allowed : 22.56 % Favored : 74.07 % 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: 1.54 (0.45), residues: 372 helix: 1.57 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -3.06 (0.75), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.001 0.001 HIS A 414 PHE 0.027 0.002 PHE A 238 TYR 0.017 0.002 TYR A 422 ARG 0.001 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.05909 ( 241) hydrogen bonds : angle 4.43661 ( 714) covalent geometry : bond 0.00390 ( 2876) covalent geometry : angle 0.67505 ( 3915) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.290 Fit side-chains REVERT: A 275 VAL cc_start: 0.7864 (OUTLIER) cc_final: 0.7634 (t) outliers start: 10 outliers final: 6 residues processed: 53 average time/residue: 1.0327 time to fit residues: 56.4070 Evaluate side-chains 51 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.120021 restraints weight = 3433.306| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.28 r_work: 0.3164 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2876 Z= 0.153 Angle : 0.647 9.936 3915 Z= 0.316 Chirality : 0.042 0.128 470 Planarity : 0.006 0.045 479 Dihedral : 4.634 32.525 396 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.69 % Allowed : 23.23 % Favored : 74.07 % 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: 1.68 (0.45), residues: 372 helix: 1.68 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.10 (0.74), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 328 HIS 0.001 0.000 HIS A 414 PHE 0.024 0.001 PHE A 238 TYR 0.015 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.05526 ( 241) hydrogen bonds : angle 4.36532 ( 714) covalent geometry : bond 0.00334 ( 2876) covalent geometry : angle 0.64709 ( 3915) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.339 Fit side-chains REVERT: A 275 VAL cc_start: 0.7820 (OUTLIER) cc_final: 0.7606 (t) outliers start: 8 outliers final: 5 residues processed: 50 average time/residue: 1.0893 time to fit residues: 56.1196 Evaluate side-chains 49 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.0970 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.138349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.120951 restraints weight = 3413.373| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.28 r_work: 0.3188 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2876 Z= 0.149 Angle : 0.648 9.850 3915 Z= 0.318 Chirality : 0.042 0.126 470 Planarity : 0.006 0.045 479 Dihedral : 4.584 31.441 396 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.02 % Allowed : 24.24 % Favored : 73.74 % 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: 1.77 (0.45), residues: 372 helix: 1.75 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.10 (0.75), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 358 HIS 0.001 0.000 HIS A 414 PHE 0.023 0.001 PHE A 238 TYR 0.014 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.05345 ( 241) hydrogen bonds : angle 4.35162 ( 714) covalent geometry : bond 0.00318 ( 2876) covalent geometry : angle 0.64758 ( 3915) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.285 Fit side-chains REVERT: A 275 VAL cc_start: 0.7848 (OUTLIER) cc_final: 0.7635 (t) outliers start: 6 outliers final: 5 residues processed: 51 average time/residue: 1.0517 time to fit residues: 55.2812 Evaluate side-chains 51 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 21 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 12 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 = 0.3532 r_free = 0.3532 target = 0.137607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.120348 restraints weight = 3355.689| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.24 r_work: 0.3187 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2876 Z= 0.155 Angle : 0.652 9.930 3915 Z= 0.318 Chirality : 0.042 0.126 470 Planarity : 0.006 0.045 479 Dihedral : 4.627 32.435 396 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.36 % Allowed : 23.23 % Favored : 74.41 % 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: 1.70 (0.45), residues: 372 helix: 1.71 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.18 (0.74), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 358 HIS 0.001 0.001 HIS A 414 PHE 0.024 0.001 PHE A 238 TYR 0.016 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.05536 ( 241) hydrogen bonds : angle 4.37124 ( 714) covalent geometry : bond 0.00344 ( 2876) covalent geometry : angle 0.65208 ( 3915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2190.46 seconds wall clock time: 38 minutes 32.31 seconds (2312.31 seconds total)