Starting phenix.real_space_refine on Tue Mar 3 11:46:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hj9_34835/03_2026/8hj9_34835_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hj9_34835/03_2026/8hj9_34835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hj9_34835/03_2026/8hj9_34835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hj9_34835/03_2026/8hj9_34835.map" model { file = "/net/cci-nas-00/data/ceres_data/8hj9_34835/03_2026/8hj9_34835_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hj9_34835/03_2026/8hj9_34835_neut.cif" } resolution = 3.12 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= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2083 2.51 5 N 553 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3274 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3226 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.85, per 1000 atoms: 0.26 Number of scatterers: 3274 At special positions: 0 Unit cell: (67.048, 75.922, 70.992, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 3 15.00 O 621 8.00 N 553 7.00 C 2083 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: 0.23 Conformation dependent library (CDL) restraints added in 94.6 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 56.5% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 Processing helix chain 'A' and resid 24 through 33 Processing helix chain 'A' and resid 79 through 96 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 removed outlier: 3.568A pdb=" N MET A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 removed outlier: 4.041A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.908A pdb=" N ALA A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 339 through 344 removed outlier: 3.536A pdb=" N ASN A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 361 removed outlier: 4.479A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.376A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279 removed outlier: 6.405A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) 191 hydrogen bonds defined for protein. 549 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: 0.57 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1063 1.34 - 1.46: 676 1.46 - 1.57: 1580 1.57 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3351 Sorted by residual: bond pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 1.736 1.615 0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" C1D NAP A 501 " pdb=" O4D NAP A 501 " ideal model delta sigma weight residual 1.375 1.427 -0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" C5D NAP A 501 " pdb=" O5D NAP A 501 " ideal model delta sigma weight residual 1.403 1.450 -0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" O5D NAP A 501 " pdb=" PN NAP A 501 " ideal model delta sigma weight residual 1.649 1.604 0.045 2.00e-02 2.50e+03 5.07e+00 bond pdb=" O3 NAP A 501 " pdb=" PA NAP A 501 " ideal model delta sigma weight residual 1.647 1.605 0.042 2.00e-02 2.50e+03 4.48e+00 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 4397 1.56 - 3.12: 136 3.12 - 4.68: 23 4.68 - 6.24: 3 6.24 - 7.79: 2 Bond angle restraints: 4561 Sorted by residual: angle pdb=" C VAL A 146 " pdb=" N TYR A 147 " pdb=" CA TYR A 147 " ideal model delta sigma weight residual 123.47 127.83 -4.36 1.53e+00 4.27e-01 8.13e+00 angle pdb=" C2B NAP A 501 " pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 117.19 109.40 7.79 3.00e+00 1.11e-01 6.75e+00 angle pdb=" N GLY A 219 " pdb=" CA GLY A 219 " pdb=" C GLY A 219 " ideal model delta sigma weight residual 113.18 107.69 5.49 2.37e+00 1.78e-01 5.37e+00 angle pdb=" N VAL A 97 " pdb=" CA VAL A 97 " pdb=" C VAL A 97 " ideal model delta sigma weight residual 112.83 110.54 2.29 9.90e-01 1.02e+00 5.34e+00 angle pdb=" N ASP A 145 " pdb=" CA ASP A 145 " pdb=" C ASP A 145 " ideal model delta sigma weight residual 108.19 110.98 -2.79 1.29e+00 6.01e-01 4.69e+00 ... (remaining 4556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 1780 17.07 - 34.15: 174 34.15 - 51.22: 51 51.22 - 68.29: 17 68.29 - 85.36: 10 Dihedral angle restraints: 2032 sinusoidal: 843 harmonic: 1189 Sorted by residual: dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 162.79 17.21 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CB LYS A 32 " pdb=" CG LYS A 32 " pdb=" CD LYS A 32 " pdb=" CE LYS A 32 " ideal model delta sinusoidal sigma weight residual -180.00 -122.52 -57.48 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CG LYS A 214 " pdb=" CD LYS A 214 " pdb=" CE LYS A 214 " pdb=" NZ LYS A 214 " ideal model delta sinusoidal sigma weight residual -60.00 -115.05 55.05 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 2029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 290 0.027 - 0.054: 120 0.054 - 0.081: 43 0.081 - 0.108: 37 0.108 - 0.135: 11 Chirality restraints: 501 Sorted by residual: chirality pdb=" CA ILE A 37 " pdb=" N ILE A 37 " pdb=" C ILE A 37 " pdb=" CB ILE A 37 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE A 108 " pdb=" N ILE A 108 " pdb=" C ILE A 108 " pdb=" CB ILE A 108 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 chirality pdb=" CA ILE A 313 " pdb=" N ILE A 313 " pdb=" C ILE A 313 " pdb=" CB ILE A 313 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 498 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAP A 501 " -0.032 2.00e-02 2.50e+03 7.06e-02 9.96e+01 pdb=" C2N NAP A 501 " 0.113 2.00e-02 2.50e+03 pdb=" C3N NAP A 501 " 0.032 2.00e-02 2.50e+03 pdb=" C4N NAP A 501 " 0.087 2.00e-02 2.50e+03 pdb=" C5N NAP A 501 " -0.037 2.00e-02 2.50e+03 pdb=" C6N NAP A 501 " -0.059 2.00e-02 2.50e+03 pdb=" C7N NAP A 501 " -0.113 2.00e-02 2.50e+03 pdb=" N1N NAP A 501 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO A 142 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 150 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " -0.020 5.00e-02 4.00e+02 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 549 2.77 - 3.30: 3323 3.30 - 3.83: 5835 3.83 - 4.37: 6712 4.37 - 4.90: 11533 Nonbonded interactions: 27952 Sorted by model distance: nonbonded pdb=" OH TYR A 408 " pdb=" O LYS A 419 " model vdw 2.234 3.040 nonbonded pdb=" NE1 TRP A 263 " pdb=" O LYS A 271 " model vdw 2.255 3.120 nonbonded pdb=" OG1 THR A 68 " pdb=" OD1 ASP A 140 " model vdw 2.257 3.040 nonbonded pdb=" OD2 ASP A 244 " pdb=" OG SER A 269 " model vdw 2.281 3.040 nonbonded pdb=" O ASP A 209 " pdb=" NZ LYS A 213 " model vdw 2.290 3.120 ... (remaining 27947 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: 1.260 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: 0.010 Set scattering table: 0.010 Process input model: 5.030 Find NCS groups from input model: 0.020 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 3351 Z= 0.207 Angle : 0.648 7.795 4561 Z= 0.363 Chirality : 0.042 0.135 501 Planarity : 0.005 0.071 579 Dihedral : 16.737 85.364 1274 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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 are not related in a simple way. whole: 1.80 (0.43), residues: 414 helix: 2.39 (0.35), residues: 205 sheet: 0.15 (0.69), residues: 64 loop : -0.00 (0.57), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 16 TYR 0.019 0.001 TYR A 250 PHE 0.010 0.001 PHE A 381 TRP 0.015 0.001 TRP A 263 HIS 0.005 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 3351) covalent geometry : angle 0.64814 ( 4561) hydrogen bonds : bond 0.12091 ( 191) hydrogen bonds : angle 4.83940 ( 549) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.072 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6037 (mpp) cc_final: 0.5769 (mmt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0489 time to fit residues: 3.5728 Evaluate side-chains 43 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.156554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.132740 restraints weight = 7216.593| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 3.00 r_work: 0.3727 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3351 Z= 0.119 Angle : 0.476 6.830 4561 Z= 0.246 Chirality : 0.042 0.131 501 Planarity : 0.004 0.047 579 Dihedral : 9.767 67.230 517 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.91 % Allowed : 6.36 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.43), residues: 414 helix: 2.42 (0.35), residues: 210 sheet: -0.17 (0.66), residues: 70 loop : 0.15 (0.61), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 58 TYR 0.015 0.001 TYR A 250 PHE 0.006 0.001 PHE A 381 TRP 0.007 0.001 TRP A 63 HIS 0.006 0.002 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3351) covalent geometry : angle 0.47576 ( 4561) hydrogen bonds : bond 0.03607 ( 191) hydrogen bonds : angle 4.26302 ( 549) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.119 Fit side-chains REVERT: A 153 MET cc_start: 0.6863 (mpp) cc_final: 0.6274 (mmt) REVERT: A 230 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7338 (mm) outliers start: 3 outliers final: 1 residues processed: 50 average time/residue: 0.0476 time to fit residues: 3.1145 Evaluate side-chains 47 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 291 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.0060 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- 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 = 0.4135 r_free = 0.4135 target = 0.153533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.129310 restraints weight = 7167.469| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.91 r_work: 0.3680 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3351 Z= 0.153 Angle : 0.488 5.269 4561 Z= 0.251 Chirality : 0.042 0.128 501 Planarity : 0.004 0.051 579 Dihedral : 8.323 58.818 517 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.12 % Allowed : 7.88 % Favored : 90.00 % 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 are not related in a simple way. whole: 1.69 (0.43), residues: 414 helix: 2.31 (0.35), residues: 209 sheet: -0.06 (0.67), residues: 68 loop : -0.06 (0.59), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 396 TYR 0.010 0.001 TYR A 132 PHE 0.006 0.001 PHE A 381 TRP 0.005 0.001 TRP A 63 HIS 0.009 0.002 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 3351) covalent geometry : angle 0.48780 ( 4561) hydrogen bonds : bond 0.03554 ( 191) hydrogen bonds : angle 4.19898 ( 549) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.128 Fit side-chains REVERT: A 153 MET cc_start: 0.6906 (mpp) cc_final: 0.6351 (mmt) REVERT: A 230 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7277 (mm) REVERT: A 259 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7679 (pm20) outliers start: 7 outliers final: 3 residues processed: 49 average time/residue: 0.0496 time to fit residues: 3.2136 Evaluate side-chains 49 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 291 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 0.0970 chunk 28 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.4164 r_free = 0.4164 target = 0.155676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.132040 restraints weight = 7077.197| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.95 r_work: 0.3722 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3351 Z= 0.100 Angle : 0.445 7.284 4561 Z= 0.228 Chirality : 0.041 0.128 501 Planarity : 0.004 0.050 579 Dihedral : 7.715 59.381 517 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.12 % Allowed : 10.61 % Favored : 87.27 % 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 are not related in a simple way. whole: 1.78 (0.43), residues: 414 helix: 2.43 (0.35), residues: 209 sheet: -0.19 (0.67), residues: 70 loop : 0.01 (0.59), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 396 TYR 0.018 0.001 TYR A 250 PHE 0.011 0.001 PHE A 381 TRP 0.006 0.001 TRP A 63 HIS 0.008 0.002 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 3351) covalent geometry : angle 0.44457 ( 4561) hydrogen bonds : bond 0.03149 ( 191) hydrogen bonds : angle 4.08737 ( 549) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.135 Fit side-chains REVERT: A 153 MET cc_start: 0.7034 (mpp) cc_final: 0.6622 (mmt) REVERT: A 193 GLN cc_start: 0.9223 (tp-100) cc_final: 0.8783 (tp-100) REVERT: A 230 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7282 (mm) REVERT: A 259 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7542 (pm20) outliers start: 7 outliers final: 2 residues processed: 53 average time/residue: 0.0504 time to fit residues: 3.5293 Evaluate side-chains 48 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 291 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.0470 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.155773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.131921 restraints weight = 7146.894| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.98 r_work: 0.3725 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3351 Z= 0.100 Angle : 0.446 6.132 4561 Z= 0.231 Chirality : 0.041 0.128 501 Planarity : 0.004 0.051 579 Dihedral : 7.226 56.390 517 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.12 % Allowed : 12.73 % Favored : 85.15 % 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 are not related in a simple way. whole: 1.82 (0.43), residues: 414 helix: 2.40 (0.35), residues: 211 sheet: -0.37 (0.66), residues: 73 loop : 0.26 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 396 TYR 0.006 0.001 TYR A 408 PHE 0.011 0.001 PHE A 381 TRP 0.005 0.001 TRP A 63 HIS 0.007 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 3351) covalent geometry : angle 0.44567 ( 4561) hydrogen bonds : bond 0.03059 ( 191) hydrogen bonds : angle 3.99280 ( 549) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: A 193 GLN cc_start: 0.9235 (tp-100) cc_final: 0.8763 (tp-100) REVERT: A 230 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7251 (mm) outliers start: 7 outliers final: 3 residues processed: 53 average time/residue: 0.0465 time to fit residues: 3.3259 Evaluate side-chains 52 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 291 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.148542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.123775 restraints weight = 7190.691| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.89 r_work: 0.3594 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3351 Z= 0.263 Angle : 0.587 5.814 4561 Z= 0.305 Chirality : 0.044 0.135 501 Planarity : 0.005 0.051 579 Dihedral : 7.231 52.384 517 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.52 % Allowed : 13.64 % Favored : 84.85 % 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 are not related in a simple way. whole: 1.29 (0.42), residues: 414 helix: 2.05 (0.34), residues: 206 sheet: -0.45 (0.67), residues: 71 loop : -0.17 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.019 0.002 TYR A 250 PHE 0.011 0.002 PHE A 381 TRP 0.010 0.002 TRP A 30 HIS 0.008 0.002 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00602 ( 3351) covalent geometry : angle 0.58656 ( 4561) hydrogen bonds : bond 0.04099 ( 191) hydrogen bonds : angle 4.43592 ( 549) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.128 Fit side-chains REVERT: A 193 GLN cc_start: 0.9211 (tp-100) cc_final: 0.8811 (tp-100) REVERT: A 230 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7418 (mm) outliers start: 5 outliers final: 4 residues processed: 50 average time/residue: 0.0443 time to fit residues: 2.9447 Evaluate side-chains 46 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 401 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.3980 chunk 31 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.153370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.129424 restraints weight = 7202.814| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.93 r_work: 0.3690 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3351 Z= 0.105 Angle : 0.484 8.612 4561 Z= 0.247 Chirality : 0.042 0.127 501 Planarity : 0.004 0.052 579 Dihedral : 6.768 50.759 517 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.21 % Allowed : 15.45 % Favored : 83.33 % 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 are not related in a simple way. whole: 1.65 (0.43), residues: 414 helix: 2.25 (0.35), residues: 209 sheet: -0.22 (0.69), residues: 71 loop : 0.07 (0.59), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 396 TYR 0.020 0.001 TYR A 250 PHE 0.012 0.001 PHE A 381 TRP 0.006 0.001 TRP A 63 HIS 0.009 0.002 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 3351) covalent geometry : angle 0.48398 ( 4561) hydrogen bonds : bond 0.03244 ( 191) hydrogen bonds : angle 4.11840 ( 549) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.073 Fit side-chains REVERT: A 193 GLN cc_start: 0.9226 (tp-100) cc_final: 0.8788 (tp-100) REVERT: A 230 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7445 (mm) REVERT: A 234 GLN cc_start: 0.6956 (tt0) cc_final: 0.6711 (tt0) outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.0378 time to fit residues: 2.5800 Evaluate side-chains 49 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 291 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.152912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.128933 restraints weight = 7292.031| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.94 r_work: 0.3686 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3351 Z= 0.117 Angle : 0.484 8.396 4561 Z= 0.247 Chirality : 0.041 0.122 501 Planarity : 0.004 0.053 579 Dihedral : 6.534 48.669 517 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.52 % Allowed : 15.15 % Favored : 83.33 % 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 are not related in a simple way. whole: 1.71 (0.43), residues: 414 helix: 2.32 (0.34), residues: 209 sheet: -0.16 (0.70), residues: 71 loop : 0.06 (0.59), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 396 TYR 0.007 0.001 TYR A 132 PHE 0.011 0.001 PHE A 381 TRP 0.005 0.001 TRP A 30 HIS 0.007 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 3351) covalent geometry : angle 0.48445 ( 4561) hydrogen bonds : bond 0.03250 ( 191) hydrogen bonds : angle 4.07160 ( 549) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.168 Fit side-chains REVERT: A 193 GLN cc_start: 0.9239 (tp-100) cc_final: 0.8793 (tp-100) REVERT: A 230 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7409 (mm) REVERT: A 234 GLN cc_start: 0.7003 (tt0) cc_final: 0.6773 (tt0) outliers start: 5 outliers final: 2 residues processed: 50 average time/residue: 0.0448 time to fit residues: 3.0501 Evaluate side-chains 48 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 291 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 34 optimal weight: 0.0170 chunk 24 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.1820 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.152554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.128652 restraints weight = 7208.290| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.90 r_work: 0.3673 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3351 Z= 0.128 Angle : 0.488 8.131 4561 Z= 0.249 Chirality : 0.042 0.122 501 Planarity : 0.004 0.053 579 Dihedral : 6.415 46.888 517 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.52 % Allowed : 14.85 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.43), residues: 414 helix: 2.32 (0.34), residues: 209 sheet: -0.16 (0.70), residues: 71 loop : -0.02 (0.58), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 396 TYR 0.022 0.001 TYR A 250 PHE 0.012 0.001 PHE A 381 TRP 0.006 0.001 TRP A 30 HIS 0.007 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3351) covalent geometry : angle 0.48762 ( 4561) hydrogen bonds : bond 0.03276 ( 191) hydrogen bonds : angle 4.08603 ( 549) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.102 Fit side-chains REVERT: A 193 GLN cc_start: 0.9230 (tp-100) cc_final: 0.8772 (tp-100) REVERT: A 230 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7414 (mm) outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 0.0464 time to fit residues: 3.1199 Evaluate side-chains 49 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 291 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.151807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.127655 restraints weight = 7100.348| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.88 r_work: 0.3664 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3351 Z= 0.141 Angle : 0.504 8.024 4561 Z= 0.257 Chirality : 0.042 0.123 501 Planarity : 0.004 0.053 579 Dihedral : 6.356 47.989 517 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.82 % Allowed : 15.15 % Favored : 83.03 % 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 are not related in a simple way. whole: 1.64 (0.43), residues: 414 helix: 2.29 (0.34), residues: 209 sheet: -0.23 (0.70), residues: 71 loop : -0.02 (0.58), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 396 TYR 0.009 0.001 TYR A 132 PHE 0.012 0.001 PHE A 381 TRP 0.007 0.001 TRP A 30 HIS 0.007 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3351) covalent geometry : angle 0.50410 ( 4561) hydrogen bonds : bond 0.03375 ( 191) hydrogen bonds : angle 4.13484 ( 549) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.128 Fit side-chains REVERT: A 193 GLN cc_start: 0.9233 (tp-100) cc_final: 0.8785 (tp-100) REVERT: A 230 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7429 (mm) outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 0.0368 time to fit residues: 2.5511 Evaluate side-chains 49 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 291 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 0.2980 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 16 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 15 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 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.154164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.130485 restraints weight = 7258.175| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.95 r_work: 0.3700 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3351 Z= 0.106 Angle : 0.484 7.894 4561 Z= 0.245 Chirality : 0.041 0.124 501 Planarity : 0.004 0.052 579 Dihedral : 6.227 50.102 517 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.21 % Allowed : 16.06 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.44), residues: 414 helix: 2.41 (0.35), residues: 209 sheet: -0.14 (0.71), residues: 71 loop : 0.02 (0.58), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 396 TYR 0.019 0.001 TYR A 250 PHE 0.011 0.001 PHE A 381 TRP 0.005 0.001 TRP A 92 HIS 0.006 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 3351) covalent geometry : angle 0.48441 ( 4561) hydrogen bonds : bond 0.03118 ( 191) hydrogen bonds : angle 4.07768 ( 549) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 936.42 seconds wall clock time: 16 minutes 39.80 seconds (999.80 seconds total)