Starting phenix.real_space_refine on Wed Mar 5 16:37:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtb_36639/03_2025/8jtb_36639.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtb_36639/03_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_36639/03_2025/8jtb_36639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtb_36639/03_2025/8jtb_36639.map" model { file = "/net/cci-nas-00/data/ceres_data/8jtb_36639/03_2025/8jtb_36639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtb_36639/03_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-5624/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: 2.93, per 1000 atoms: 1.04 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: 0.78 Conformation dependent library (CDL) restraints added in 379.1 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: 0.25 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: 0.73 Time building geometry restraints manager: 0.91 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.830 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.350 ------------------------------------------------------------------------------- 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= 0.415 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 *********************** 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 : 0.323 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 1.0014 time to fit residues: 55.8513 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 : 0.315 ------------------------------------------------------------------------------- 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: 3.51 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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= 0.187 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 *********************** 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 : 0.317 Fit side-chains outliers start: 11 outliers final: 0 residues processed: 60 average time/residue: 0.9583 time to fit residues: 59.4952 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 : 0.278 ------------------------------------------------------------------------------- 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: 0.7980 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 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: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.134569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.117203 restraints weight = 3343.134| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.27 r_work: 0.3167 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1478 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= 0.268 Angle : 0.668 10.205 3915 Z= 0.332 Chirality : 0.043 0.149 470 Planarity : 0.006 0.046 479 Dihedral : 4.839 36.780 396 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.70 % Allowed : 21.21 % 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: 1.64 (0.44), residues: 372 helix: 1.60 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -2.16 (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 0.002 0.000 ARG A 413 *********************** 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 57 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.237 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 51 average time/residue: 1.0889 time to fit residues: 57.1500 Evaluate side-chains 47 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE 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: 0.0870 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 28 optimal weight: 0.1980 overall best weight: 0.3358 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.139178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.121884 restraints weight = 3452.657| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.30 r_work: 0.3222 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2876 Z= 0.182 Angle : 0.614 9.958 3915 Z= 0.302 Chirality : 0.041 0.133 470 Planarity : 0.006 0.046 479 Dihedral : 4.620 34.390 396 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.69 % Allowed : 22.90 % 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: 2.10 (0.45), residues: 372 helix: 1.92 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -2.11 (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 414 PHE 0.016 0.001 PHE A 238 TYR 0.012 0.001 TYR A 422 ARG 0.001 0.000 ARG A 413 *********************** 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: 8 poor density : 49 time to evaluate : 0.269 Fit side-chains REVERT: A 262 ASP cc_start: 0.7612 (t0) cc_final: 0.7352 (t70) outliers start: 8 outliers final: 3 residues processed: 54 average time/residue: 0.9861 time to fit residues: 54.9617 Evaluate side-chains 50 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.136348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.119109 restraints weight = 3375.364| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.27 r_work: 0.3213 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2876 Z= 0.234 Angle : 0.637 10.054 3915 Z= 0.314 Chirality : 0.042 0.134 470 Planarity : 0.006 0.045 479 Dihedral : 4.660 34.569 396 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.71 % Allowed : 20.88 % 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: 1.79 (0.45), residues: 372 helix: 1.71 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.68 (0.76), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 451 HIS 0.001 0.001 HIS A 414 PHE 0.023 0.001 PHE A 238 TYR 0.016 0.002 TYR A 422 ARG 0.001 0.000 ARG A 217 *********************** 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 : 0.317 Fit side-chains REVERT: A 275 VAL cc_start: 0.7894 (OUTLIER) cc_final: 0.7632 (t) outliers start: 14 outliers final: 6 residues processed: 57 average time/residue: 0.9691 time to fit residues: 57.0675 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 : 0.254 ------------------------------------------------------------------------------- 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: 0.5980 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.0980 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.136489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118974 restraints weight = 3437.616| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.30 r_work: 0.3188 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1873 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= 0.213 Angle : 0.636 9.969 3915 Z= 0.310 Chirality : 0.042 0.130 470 Planarity : 0.006 0.045 479 Dihedral : 4.609 33.760 396 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 4.38 % Allowed : 20.54 % 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: 1.83 (0.45), residues: 372 helix: 1.75 (0.30), residues: 327 sheet: None (None), residues: 0 loop : -2.85 (0.76), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 328 HIS 0.001 0.000 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 *********************** 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 61 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.312 Fit side-chains REVERT: A 275 VAL cc_start: 0.7916 (OUTLIER) cc_final: 0.7651 (t) outliers start: 13 outliers final: 6 residues processed: 58 average time/residue: 0.9294 time to fit residues: 55.7042 Evaluate side-chains 53 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.137048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.119631 restraints weight = 3475.819| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.30 r_work: 0.3204 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1967 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= 0.214 Angle : 0.641 9.934 3915 Z= 0.311 Chirality : 0.042 0.128 470 Planarity : 0.006 0.045 479 Dihedral : 4.599 33.017 396 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.03 % Allowed : 22.56 % 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: 1.74 (0.45), residues: 372 helix: 1.71 (0.30), residues: 326 sheet: None (None), residues: 0 loop : -3.01 (0.74), residues: 46 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 0.025 0.001 PHE A 238 TYR 0.014 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 *********************** 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 55 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.306 Fit side-chains REVERT: A 275 VAL cc_start: 0.7908 (OUTLIER) cc_final: 0.7638 (t) outliers start: 9 outliers final: 4 residues processed: 53 average time/residue: 1.0000 time to fit residues: 54.7149 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 : 0.276 ------------------------------------------------------------------------------- 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: 0.8980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 0.0970 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.137090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.119732 restraints weight = 3402.423| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.28 r_work: 0.3220 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2002 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= 0.215 Angle : 0.644 9.925 3915 Z= 0.314 Chirality : 0.042 0.127 470 Planarity : 0.006 0.045 479 Dihedral : 4.579 32.878 396 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.03 % Allowed : 22.56 % 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: 1.76 (0.45), residues: 372 helix: 1.73 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.02 (0.75), 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 *********************** 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: 9 poor density : 46 time to evaluate : 0.343 Fit side-chains REVERT: A 275 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7595 (t) outliers start: 9 outliers final: 5 residues processed: 53 average time/residue: 0.9338 time to fit residues: 51.1507 Evaluate side-chains 52 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 2 optimal weight: 0.0770 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.137399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.120176 restraints weight = 3422.409| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.26 r_work: 0.3193 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2137 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= 0.210 Angle : 0.642 9.877 3915 Z= 0.313 Chirality : 0.042 0.125 470 Planarity : 0.006 0.046 479 Dihedral : 4.564 32.431 396 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.37 % Allowed : 22.22 % 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: 1.84 (0.45), residues: 372 helix: 1.78 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -3.06 (0.77), 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 0.023 0.001 PHE A 238 TYR 0.014 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 *********************** 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 55 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.298 Fit side-chains REVERT: A 275 VAL cc_start: 0.7878 (OUTLIER) cc_final: 0.7606 (t) outliers start: 10 outliers final: 5 residues processed: 54 average time/residue: 1.0147 time to fit residues: 56.5223 Evaluate side-chains 52 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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: 0.4980 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 0.0770 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 0.0040 chunk 19 optimal weight: 0.9980 overall best weight: 0.3950 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.138245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.120839 restraints weight = 3399.667| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.27 r_work: 0.3245 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2876 Z= 0.189 Angle : 0.634 9.784 3915 Z= 0.310 Chirality : 0.041 0.124 470 Planarity : 0.006 0.046 479 Dihedral : 4.484 30.775 396 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.35 % Allowed : 24.58 % 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: 2.00 (0.45), residues: 372 helix: 1.89 (0.30), residues: 326 sheet: None (None), residues: 0 loop : -2.97 (0.76), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 328 HIS 0.000 0.000 HIS A 414 PHE 0.022 0.001 PHE A 238 TYR 0.013 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 ********************** 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 52 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.284 Fit side-chains REVERT: A 275 VAL cc_start: 0.7831 (OUTLIER) cc_final: 0.7559 (t) outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 1.0255 time to fit residues: 55.0580 Evaluate side-chains 49 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 334 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 21 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 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 = 0.3523 r_free = 0.3523 target = 0.137062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.119671 restraints weight = 3340.030| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.27 r_work: 0.3185 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2876 Z= 0.231 Angle : 0.649 9.913 3915 Z= 0.318 Chirality : 0.042 0.123 470 Planarity : 0.006 0.046 479 Dihedral : 4.564 32.278 396 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: 1.89 (0.45), residues: 372 helix: 1.80 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -2.94 (0.77), residues: 45 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 0.023 0.001 PHE A 238 TYR 0.016 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2249.56 seconds wall clock time: 39 minutes 3.92 seconds (2343.92 seconds total)