Starting phenix.real_space_refine on Fri Aug 22 12:59:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtb_36639/08_2025/8jtb_36639.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtb_36639/08_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_36639/08_2025/8jtb_36639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtb_36639/08_2025/8jtb_36639.map" model { file = "/net/cci-nas-00/data/ceres_data/8jtb_36639/08_2025/8jtb_36639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtb_36639/08_2025/8jtb_36639.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 0.88, per 1000 atoms: 0.31 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: 0.24 Conformation dependent library (CDL) restraints added in 116.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.09 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: 0.28 Time building geometry restraints manager: 0.31 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: 1.980 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.470 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:5.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.000 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (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 ARG 0.004 0.001 ARG A 413 TYR 0.014 0.002 TYR A 422 PHE 0.017 0.002 PHE A 238 TRP 0.008 0.001 TRP A 451 HIS 0.001 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00618 ( 2876) covalent geometry : angle 0.93580 ( 3915) hydrogen bonds : bond 0.17015 ( 241) hydrogen bonds : angle 6.12959 ( 714) *********************** 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 : 0.101 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 0.3957 time to fit residues: 22.0104 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 : 0.109 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.136431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.118461 restraints weight = 3379.492| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.37 r_work: 0.3151 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2876 Z= 0.175 Angle : 0.687 10.320 3915 Z= 0.345 Chirality : 0.043 0.153 470 Planarity : 0.006 0.045 479 Dihedral : 5.433 41.810 400 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 5.05 % Allowed : 21.55 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.43), residues: 372 helix: 1.34 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -2.25 (0.68), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 19 TYR 0.014 0.002 TYR A 422 PHE 0.013 0.002 PHE A 238 TRP 0.006 0.001 TRP A 451 HIS 0.000 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 2876) covalent geometry : angle 0.68716 ( 3915) hydrogen bonds : bond 0.06476 ( 241) hydrogen bonds : angle 4.73491 ( 714) *********************** 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 64 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.106 Fit side-chains outliers start: 15 outliers final: 3 residues processed: 59 average time/residue: 0.4435 time to fit residues: 26.9725 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 : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 345 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.134700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.117142 restraints weight = 3426.117| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.28 r_work: 0.3132 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1474 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= 0.168 Angle : 0.659 10.164 3915 Z= 0.327 Chirality : 0.042 0.139 470 Planarity : 0.006 0.045 479 Dihedral : 4.858 37.237 396 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.04 % Allowed : 21.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.44), residues: 372 helix: 1.57 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -2.31 (0.68), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 155 TYR 0.015 0.002 TYR A 422 PHE 0.022 0.002 PHE A 238 TRP 0.004 0.001 TRP A 451 HIS 0.001 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 2876) covalent geometry : angle 0.65911 ( 3915) hydrogen bonds : bond 0.06105 ( 241) hydrogen bonds : angle 4.56282 ( 714) *********************** 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: 12 poor density : 45 time to evaluate : 0.104 Fit side-chains REVERT: A 242 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6720 (mm) outliers start: 12 outliers final: 5 residues processed: 51 average time/residue: 0.4895 time to fit residues: 25.6525 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 : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 431 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 31 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 = 0.3487 r_free = 0.3487 target = 0.134692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.117550 restraints weight = 3424.978| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.24 r_work: 0.3147 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1691 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= 0.176 Angle : 0.662 10.187 3915 Z= 0.330 Chirality : 0.043 0.139 470 Planarity : 0.006 0.046 479 Dihedral : 4.856 36.914 396 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 4.71 % Allowed : 20.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.44), residues: 372 helix: 1.46 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.94 (0.70), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.017 0.002 TYR A 422 PHE 0.018 0.001 PHE A 238 TRP 0.004 0.001 TRP A 451 HIS 0.001 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 2876) covalent geometry : angle 0.66224 ( 3915) hydrogen bonds : bond 0.06113 ( 241) hydrogen bonds : angle 4.52750 ( 714) *********************** 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 60 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.107 Fit side-chains REVERT: A 275 VAL cc_start: 0.7893 (OUTLIER) cc_final: 0.7665 (t) outliers start: 14 outliers final: 8 residues processed: 55 average time/residue: 0.4506 time to fit residues: 25.5302 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 : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 169 MET 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 345 THR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 431 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 21 optimal weight: 0.0370 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.137520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120196 restraints weight = 3386.209| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.27 r_work: 0.3158 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1796 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= 0.158 Angle : 0.635 10.063 3915 Z= 0.314 Chirality : 0.042 0.138 470 Planarity : 0.006 0.046 479 Dihedral : 4.732 35.141 396 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.45), residues: 372 helix: 1.59 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.07 (0.70), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.015 0.001 TYR A 422 PHE 0.018 0.001 PHE A 238 TRP 0.003 0.001 TRP A 358 HIS 0.001 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 2876) covalent geometry : angle 0.63532 ( 3915) hydrogen bonds : bond 0.05691 ( 241) hydrogen bonds : angle 4.44191 ( 714) *********************** 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 63 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.107 Fit side-chains REVERT: A 275 VAL cc_start: 0.7900 (OUTLIER) cc_final: 0.7665 (t) outliers start: 14 outliers final: 6 residues processed: 58 average time/residue: 0.4011 time to fit residues: 24.0269 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 : 0.102 ------------------------------------------------------------------------------- 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 275 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 365 MET 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 23 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 0.0470 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.136990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.118897 restraints weight = 3389.341| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.39 r_work: 0.3225 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1947 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= 0.145 Angle : 0.631 9.872 3915 Z= 0.309 Chirality : 0.041 0.130 470 Planarity : 0.006 0.046 479 Dihedral : 4.630 33.496 396 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.14 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.45), residues: 372 helix: 1.70 (0.30), residues: 327 sheet: None (None), residues: 0 loop : -2.99 (0.74), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.014 0.001 TYR A 422 PHE 0.016 0.001 PHE A 238 TRP 0.003 0.001 TRP A 358 HIS 0.000 0.000 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 2876) covalent geometry : angle 0.63067 ( 3915) hydrogen bonds : bond 0.05311 ( 241) hydrogen bonds : angle 4.35870 ( 714) *********************** 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: 12 poor density : 49 time to evaluate : 0.111 Fit side-chains REVERT: A 275 VAL cc_start: 0.7891 (OUTLIER) cc_final: 0.7656 (t) outliers start: 12 outliers final: 7 residues processed: 57 average time/residue: 0.4447 time to fit residues: 26.0957 Evaluate side-chains 56 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.106 ------------------------------------------------------------------------------- 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 268 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 365 MET 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 1 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.0370 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.0170 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 overall best weight: 0.3296 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.140546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.122676 restraints weight = 3393.498| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.40 r_work: 0.3211 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2876 Z= 0.134 Angle : 0.614 9.762 3915 Z= 0.299 Chirality : 0.040 0.128 470 Planarity : 0.006 0.046 479 Dihedral : 4.498 31.580 396 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.96 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.45), residues: 372 helix: 1.85 (0.30), residues: 326 sheet: None (None), residues: 0 loop : -3.02 (0.75), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 357 TYR 0.012 0.001 TYR A 422 PHE 0.016 0.001 PHE A 238 TRP 0.004 0.001 TRP A 328 HIS 0.000 0.000 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 2876) covalent geometry : angle 0.61408 ( 3915) hydrogen bonds : bond 0.04837 ( 241) hydrogen bonds : angle 4.25430 ( 714) *********************** 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 56 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.106 Fit side-chains REVERT: A 275 VAL cc_start: 0.7842 (OUTLIER) cc_final: 0.7610 (t) outliers start: 10 outliers final: 3 residues processed: 53 average time/residue: 0.4142 time to fit residues: 22.6610 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 : 0.084 ------------------------------------------------------------------------------- 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 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 2 optimal weight: 0.0570 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 0.1980 chunk 35 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.3298 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.140244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.122976 restraints weight = 3432.849| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.27 r_work: 0.3254 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2273 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= 0.134 Angle : 0.624 9.753 3915 Z= 0.302 Chirality : 0.040 0.128 470 Planarity : 0.006 0.046 479 Dihedral : 4.468 31.321 396 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.45), residues: 372 helix: 1.91 (0.30), residues: 326 sheet: None (None), residues: 0 loop : -2.98 (0.77), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 413 TYR 0.013 0.001 TYR A 422 PHE 0.024 0.001 PHE A 238 TRP 0.004 0.001 TRP A 328 HIS 0.000 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 2876) covalent geometry : angle 0.62414 ( 3915) hydrogen bonds : bond 0.04802 ( 241) hydrogen bonds : angle 4.22600 ( 714) *********************** 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 : 0.069 Fit side-chains REVERT: A 275 VAL cc_start: 0.7811 (OUTLIER) cc_final: 0.7577 (t) outliers start: 9 outliers final: 2 residues processed: 52 average time/residue: 0.4003 time to fit residues: 21.4586 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 : 0.106 ------------------------------------------------------------------------------- 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 381 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 33 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.138634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.120995 restraints weight = 3486.242| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.32 r_work: 0.3190 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2182 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= 0.146 Angle : 0.635 9.869 3915 Z= 0.309 Chirality : 0.041 0.127 470 Planarity : 0.006 0.045 479 Dihedral : 4.542 32.273 396 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.69 % Allowed : 22.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.45), residues: 372 helix: 1.84 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.06 (0.75), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.016 0.001 TYR A 422 PHE 0.024 0.001 PHE A 238 TRP 0.003 0.001 TRP A 358 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 2876) covalent geometry : angle 0.63468 ( 3915) hydrogen bonds : bond 0.05250 ( 241) hydrogen bonds : angle 4.29004 ( 714) *********************** 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 54 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.065 Fit side-chains REVERT: A 275 VAL cc_start: 0.7824 (OUTLIER) cc_final: 0.7575 (t) outliers start: 8 outliers final: 4 residues processed: 53 average time/residue: 0.3755 time to fit residues: 20.4917 Evaluate side-chains 50 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.074 ------------------------------------------------------------------------------- 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 381 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 2 optimal weight: 0.0470 chunk 25 optimal weight: 0.0030 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 0.0970 chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 overall best weight: 0.1486 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.144571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127081 restraints weight = 3445.883| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.36 r_work: 0.3294 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2876 Z= 0.129 Angle : 0.611 9.788 3915 Z= 0.297 Chirality : 0.040 0.127 470 Planarity : 0.006 0.045 479 Dihedral : 4.380 29.538 396 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.35 % Allowed : 24.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.46), residues: 372 helix: 2.18 (0.30), residues: 327 sheet: None (None), residues: 0 loop : -2.81 (0.80), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 357 TYR 0.008 0.001 TYR A 422 PHE 0.021 0.001 PHE A 238 TRP 0.004 0.001 TRP A 328 HIS 0.000 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 2876) covalent geometry : angle 0.61124 ( 3915) hydrogen bonds : bond 0.04302 ( 241) hydrogen bonds : angle 4.17593 ( 714) ********************** 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 54 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.105 Fit side-chains REVERT: A 262 ASP cc_start: 0.7854 (t0) cc_final: 0.7489 (t70) REVERT: A 275 VAL cc_start: 0.7792 (OUTLIER) cc_final: 0.7532 (t) outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 0.4152 time to fit residues: 23.0963 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 : 0.062 ------------------------------------------------------------------------------- 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 381 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.5980 chunk 21 optimal weight: 0.0870 chunk 13 optimal weight: 0.0970 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 0.0570 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.2274 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.143975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.126218 restraints weight = 3355.589| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.38 r_work: 0.3266 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2876 Z= 0.129 Angle : 0.617 9.705 3915 Z= 0.299 Chirality : 0.041 0.155 470 Planarity : 0.006 0.045 479 Dihedral : 4.316 27.965 396 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.02 % Allowed : 23.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.46), residues: 372 helix: 2.23 (0.30), residues: 326 sheet: None (None), residues: 0 loop : -2.86 (0.78), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 357 TYR 0.011 0.001 TYR A 422 PHE 0.021 0.001 PHE A 238 TRP 0.003 0.001 TRP A 328 HIS 0.000 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 2876) covalent geometry : angle 0.61718 ( 3915) hydrogen bonds : bond 0.04454 ( 241) hydrogen bonds : angle 4.18635 ( 714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 993.35 seconds wall clock time: 17 minutes 37.52 seconds (1057.52 seconds total)