Starting phenix.real_space_refine on Fri Dec 27 08:14:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hj9_34835/12_2024/8hj9_34835_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hj9_34835/12_2024/8hj9_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_34835/12_2024/8hj9_34835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hj9_34835/12_2024/8hj9_34835.map" model { file = "/net/cci-nas-00/data/ceres_data/8hj9_34835/12_2024/8hj9_34835_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hj9_34835/12_2024/8hj9_34835_neut.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP: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: 2.97, per 1000 atoms: 0.91 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: 0.92 Conformation dependent library (CDL) restraints added in 415.4 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: 0.37 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: 1.01 Time building geometry restraints manager: 1.04 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.530 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.260 ------------------------------------------------------------------------------- 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= 0.228 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (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 TRP 0.015 0.001 TRP A 263 HIS 0.005 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.019 0.001 TYR A 250 ARG 0.002 0.000 ARG A 16 *********************** 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 : 0.398 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: 0.1353 time to fit residues: 9.7584 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 : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3351 Z= 0.196 Angle : 0.487 6.810 4561 Z= 0.251 Chirality : 0.042 0.130 501 Planarity : 0.004 0.047 579 Dihedral : 9.575 63.786 517 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.21 % Allowed : 6.36 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.43), residues: 414 helix: 2.38 (0.35), residues: 210 sheet: -0.21 (0.66), residues: 70 loop : 0.12 (0.61), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.007 0.002 HIS A 388 PHE 0.007 0.001 PHE A 381 TYR 0.015 0.002 TYR A 250 ARG 0.001 0.000 ARG A 58 *********************** 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: 4 poor density : 49 time to evaluate : 0.379 Fit side-chains REVERT: A 153 MET cc_start: 0.6360 (mpp) cc_final: 0.5979 (mmt) REVERT: A 230 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7305 (mm) outliers start: 4 outliers final: 2 residues processed: 49 average time/residue: 0.1406 time to fit residues: 8.9695 Evaluate side-chains 46 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 249 ILE 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 20 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1349 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= 0.162 Angle : 0.456 5.156 4561 Z= 0.234 Chirality : 0.041 0.129 501 Planarity : 0.004 0.050 579 Dihedral : 8.142 58.471 517 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.82 % Allowed : 8.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.43), residues: 414 helix: 2.41 (0.35), residues: 209 sheet: -0.13 (0.67), residues: 70 loop : 0.06 (0.60), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.009 0.002 HIS A 388 PHE 0.006 0.001 PHE A 381 TYR 0.011 0.001 TYR A 132 ARG 0.002 0.000 ARG A 396 *********************** 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 56 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6416 (mpp) cc_final: 0.5913 (mmt) REVERT: A 230 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7248 (mm) REVERT: A 259 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7608 (pm20) outliers start: 6 outliers final: 2 residues processed: 52 average time/residue: 0.1323 time to fit residues: 8.7738 Evaluate side-chains 47 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 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 36 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 0.3980 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3351 Z= 0.173 Angle : 0.454 7.091 4561 Z= 0.233 Chirality : 0.041 0.128 501 Planarity : 0.004 0.051 579 Dihedral : 7.711 59.038 517 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.42 % Allowed : 10.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.43), residues: 414 helix: 2.41 (0.35), residues: 209 sheet: -0.15 (0.66), residues: 71 loop : 0.06 (0.59), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 63 HIS 0.008 0.001 HIS A 388 PHE 0.011 0.001 PHE A 381 TYR 0.017 0.001 TYR A 250 ARG 0.001 0.000 ARG A 396 *********************** 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 56 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 193 GLN cc_start: 0.8997 (tp-100) cc_final: 0.8547 (tp-100) REVERT: A 230 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7249 (mm) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 0.1130 time to fit residues: 7.7196 Evaluate side-chains 50 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3351 Z= 0.179 Angle : 0.462 6.216 4561 Z= 0.240 Chirality : 0.041 0.126 501 Planarity : 0.004 0.052 579 Dihedral : 7.258 56.031 517 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.82 % Allowed : 13.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.43), residues: 414 helix: 2.33 (0.34), residues: 211 sheet: -0.14 (0.66), residues: 71 loop : 0.17 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 30 HIS 0.008 0.001 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.007 0.001 TYR A 132 ARG 0.002 0.000 ARG A 396 *********************** 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 54 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.332 Fit side-chains REVERT: A 193 GLN cc_start: 0.8998 (tp-100) cc_final: 0.8537 (tp-100) REVERT: A 230 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7309 (mm) outliers start: 6 outliers final: 3 residues processed: 50 average time/residue: 0.1266 time to fit residues: 8.1685 Evaluate side-chains 50 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 23 optimal weight: 9.9990 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 0.0970 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3351 Z= 0.150 Angle : 0.453 5.634 4561 Z= 0.235 Chirality : 0.041 0.127 501 Planarity : 0.004 0.052 579 Dihedral : 6.906 53.841 517 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.52 % Allowed : 13.94 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.43), residues: 414 helix: 2.39 (0.35), residues: 211 sheet: -0.13 (0.67), residues: 71 loop : 0.17 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 63 HIS 0.009 0.002 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.006 0.001 TYR A 400 ARG 0.001 0.000 ARG A 396 *********************** 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 53 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.402 Fit side-chains REVERT: A 193 GLN cc_start: 0.9003 (tp-100) cc_final: 0.8517 (tp-100) REVERT: A 230 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7368 (mm) outliers start: 5 outliers final: 3 residues processed: 50 average time/residue: 0.1106 time to fit residues: 7.4913 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 : 0.367 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3351 Z= 0.268 Angle : 0.516 5.332 4561 Z= 0.267 Chirality : 0.042 0.125 501 Planarity : 0.004 0.052 579 Dihedral : 6.765 50.972 517 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.82 % Allowed : 14.24 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.43), residues: 414 helix: 2.24 (0.34), residues: 208 sheet: -0.20 (0.67), residues: 71 loop : 0.03 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 HIS 0.007 0.001 HIS A 388 PHE 0.011 0.001 PHE A 381 TYR 0.020 0.001 TYR A 250 ARG 0.003 0.000 ARG A 200 *********************** 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 50 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.401 Fit side-chains REVERT: A 193 GLN cc_start: 0.9000 (tp-100) cc_final: 0.8542 (tp-100) REVERT: A 230 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7416 (mm) outliers start: 6 outliers final: 5 residues processed: 48 average time/residue: 0.1230 time to fit residues: 7.8002 Evaluate side-chains 49 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 53 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 31 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 0.1980 chunk 28 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3351 Z= 0.151 Angle : 0.469 8.724 4561 Z= 0.240 Chirality : 0.041 0.128 501 Planarity : 0.004 0.054 579 Dihedral : 6.520 49.266 517 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.94 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.43), residues: 414 helix: 2.35 (0.34), residues: 211 sheet: -0.07 (0.69), residues: 71 loop : 0.22 (0.60), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.008 0.002 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.020 0.001 TYR A 250 ARG 0.001 0.000 ARG A 200 *********************** 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 50 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.352 Fit side-chains REVERT: A 193 GLN cc_start: 0.8989 (tp-100) cc_final: 0.8506 (tp-100) REVERT: A 230 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7397 (mm) outliers start: 5 outliers final: 3 residues processed: 49 average time/residue: 0.1143 time to fit residues: 7.5357 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 : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.0770 chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3351 Z= 0.172 Angle : 0.481 8.565 4561 Z= 0.245 Chirality : 0.042 0.126 501 Planarity : 0.004 0.053 579 Dihedral : 6.379 47.322 517 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.91 % Allowed : 15.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.43), residues: 414 helix: 2.35 (0.34), residues: 211 sheet: -0.08 (0.69), residues: 71 loop : 0.17 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 30 HIS 0.007 0.001 HIS A 388 PHE 0.011 0.001 PHE A 381 TYR 0.008 0.001 TYR A 132 ARG 0.001 0.000 ARG A 396 *********************** 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 48 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.380 Fit side-chains REVERT: A 193 GLN cc_start: 0.8991 (tp-100) cc_final: 0.8508 (tp-100) REVERT: A 230 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7361 (mm) outliers start: 3 outliers final: 2 residues processed: 47 average time/residue: 0.1287 time to fit residues: 7.9724 Evaluate side-chains 47 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.0870 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3351 Z= 0.173 Angle : 0.486 8.468 4561 Z= 0.247 Chirality : 0.042 0.126 501 Planarity : 0.004 0.052 579 Dihedral : 6.290 47.273 517 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.91 % Allowed : 15.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.43), residues: 414 helix: 2.36 (0.34), residues: 211 sheet: 0.01 (0.69), residues: 70 loop : 0.11 (0.58), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 30 HIS 0.007 0.001 HIS A 388 PHE 0.011 0.001 PHE A 381 TYR 0.020 0.001 TYR A 250 ARG 0.001 0.000 ARG A 396 ********************** 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 47 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.289 Fit side-chains REVERT: A 193 GLN cc_start: 0.8986 (tp-100) cc_final: 0.8494 (tp-100) REVERT: A 230 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7368 (mm) outliers start: 3 outliers final: 2 residues processed: 46 average time/residue: 0.0964 time to fit residues: 6.2410 Evaluate side-chains 47 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 9.9990 chunk 1 optimal weight: 0.0770 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 27 optimal weight: 0.0020 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 overall best weight: 0.7748 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.154949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.131406 restraints weight = 7127.649| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.89 r_work: 0.3715 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3351 Z= 0.159 Angle : 0.484 8.328 4561 Z= 0.246 Chirality : 0.041 0.126 501 Planarity : 0.004 0.053 579 Dihedral : 6.165 49.390 517 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.21 % Allowed : 15.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.43), residues: 414 helix: 2.42 (0.35), residues: 211 sheet: 0.02 (0.70), residues: 70 loop : 0.11 (0.59), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 63 HIS 0.006 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.007 0.001 TYR A 132 ARG 0.001 0.000 ARG A 396 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1058.52 seconds wall clock time: 19 minutes 59.09 seconds (1199.09 seconds total)