Starting phenix.real_space_refine on Fri May 9 20:41:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ws5_37798/05_2025/8ws5_37798.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ws5_37798/05_2025/8ws5_37798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ws5_37798/05_2025/8ws5_37798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ws5_37798/05_2025/8ws5_37798.map" model { file = "/net/cci-nas-00/data/ceres_data/8ws5_37798/05_2025/8ws5_37798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ws5_37798/05_2025/8ws5_37798.cif" } resolution = 3.29 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= 0.001 sd= 0.014 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 74 5.49 5 S 3 5.16 5 C 2133 2.51 5 N 684 2.21 5 O 876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3770 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2226 Classifications: {'peptide': 282} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 254} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 562 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "B" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 843 Classifications: {'RNA': 40} Modifications used: {'rna2p_pyr': 6, 'rna3p_pur': 16, 'rna3p_pyr': 18} Link IDs: {'rna2p': 6, 'rna3p': 33} Chain: "D" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 139 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Time building chain proxies: 3.72, per 1000 atoms: 0.99 Number of scatterers: 3770 At special positions: 0 Unit cell: (69.3, 107.58, 93.06, 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 3 16.00 P 74 15.00 O 876 8.00 N 684 7.00 C 2133 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: 1.08 Conformation dependent library (CDL) restraints added in 253.8 milliseconds 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 516 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 2 sheets defined 39.7% alpha, 5.7% beta 17 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 75 through 89 Processing helix chain 'A' and resid 94 through 100 removed outlier: 4.093A pdb=" N ALA A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 116 removed outlier: 5.223A pdb=" N PHE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 169 removed outlier: 4.539A pdb=" N LEU A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 141 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 283 through 292 removed outlier: 4.217A pdb=" N GLU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 64 removed outlier: 3.745A pdb=" N ILE A 347 " --> pdb=" O ASP A 342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 68 83 hydrogen bonds defined for protein. 219 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 577 1.33 - 1.45: 1376 1.45 - 1.57: 1905 1.57 - 1.69: 145 1.69 - 1.80: 4 Bond restraints: 4007 Sorted by residual: bond pdb=" C ASP A 338 " pdb=" N PRO A 339 " ideal model delta sigma weight residual 1.330 1.371 -0.041 1.22e-02 6.72e+03 1.13e+01 bond pdb=" CA ASP A 338 " pdb=" C ASP A 338 " ideal model delta sigma weight residual 1.525 1.562 -0.036 1.12e-02 7.97e+03 1.05e+01 bond pdb=" C THR A 125 " pdb=" O THR A 125 " ideal model delta sigma weight residual 1.235 1.206 0.029 1.12e-02 7.97e+03 6.74e+00 bond pdb=" C ILE A 294 " pdb=" N PRO A 295 " ideal model delta sigma weight residual 1.333 1.364 -0.031 1.20e-02 6.94e+03 6.62e+00 bond pdb=" O3' DC C -11 " pdb=" P DA C -10 " ideal model delta sigma weight residual 1.607 1.638 -0.031 1.50e-02 4.44e+03 4.31e+00 ... (remaining 4002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 5522 1.98 - 3.96: 204 3.96 - 5.94: 30 5.94 - 7.91: 2 7.91 - 9.89: 2 Bond angle restraints: 5760 Sorted by residual: angle pdb=" C ILE A 296 " pdb=" N ILE A 297 " pdb=" CA ILE A 297 " ideal model delta sigma weight residual 123.10 117.81 5.29 1.36e+00 5.41e-01 1.51e+01 angle pdb=" C ILE A 132 " pdb=" CA ILE A 132 " pdb=" CB ILE A 132 " ideal model delta sigma weight residual 112.04 107.14 4.90 1.31e+00 5.83e-01 1.40e+01 angle pdb=" N ARG A 272 " pdb=" CA ARG A 272 " pdb=" C ARG A 272 " ideal model delta sigma weight residual 108.23 114.50 -6.27 1.72e+00 3.38e-01 1.33e+01 angle pdb=" C ILE A 294 " pdb=" N PRO A 295 " pdb=" CA PRO A 295 " ideal model delta sigma weight residual 120.25 115.49 4.76 1.35e+00 5.49e-01 1.24e+01 angle pdb=" NE ARG A 165 " pdb=" CZ ARG A 165 " pdb=" NH1 ARG A 165 " ideal model delta sigma weight residual 121.50 118.16 3.34 1.00e+00 1.00e+00 1.12e+01 ... (remaining 5755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 2145 34.83 - 69.66: 236 69.66 - 104.49: 17 104.49 - 139.32: 0 139.32 - 174.14: 2 Dihedral angle restraints: 2400 sinusoidal: 1596 harmonic: 804 Sorted by residual: dihedral pdb=" O4' U B 10 " pdb=" C1' U B 10 " pdb=" N1 U B 10 " pdb=" C2 U B 10 " ideal model delta sinusoidal sigma weight residual 200.00 54.15 145.85 1 1.50e+01 4.44e-03 7.80e+01 dihedral pdb=" O4' U B -9 " pdb=" C1' U B -9 " pdb=" N1 U B -9 " pdb=" C2 U B -9 " ideal model delta sinusoidal sigma weight residual 232.00 57.86 174.14 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA VAL A 279 " pdb=" C VAL A 279 " pdb=" N LEU A 280 " pdb=" CA LEU A 280 " ideal model delta harmonic sigma weight residual 180.00 156.38 23.62 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 2397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 513 0.051 - 0.101: 104 0.101 - 0.152: 36 0.152 - 0.203: 10 0.203 - 0.253: 4 Chirality restraints: 667 Sorted by residual: chirality pdb=" CA ILE A 294 " pdb=" N ILE A 294 " pdb=" C ILE A 294 " pdb=" CB ILE A 294 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA VAL A 298 " pdb=" N VAL A 298 " pdb=" C VAL A 298 " pdb=" CB VAL A 298 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C3' G B 9 " pdb=" C4' G B 9 " pdb=" O3' G B 9 " pdb=" C2' G B 9 " both_signs ideal model delta sigma weight residual False -2.48 -2.68 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 664 not shown) Planarity restraints: 472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 128 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C GLY A 128 " -0.037 2.00e-02 2.50e+03 pdb=" O GLY A 128 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 129 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 67 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C ALA A 67 " -0.032 2.00e-02 2.50e+03 pdb=" O ALA A 67 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 68 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 228 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 229 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " -0.023 5.00e-02 4.00e+02 ... (remaining 469 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 571 2.76 - 3.29: 3287 3.29 - 3.83: 6803 3.83 - 4.36: 7858 4.36 - 4.90: 11899 Nonbonded interactions: 30418 Sorted by model distance: nonbonded pdb=" NH1 ARG A 267 " pdb=" OP1 C B -15 " model vdw 2.219 3.120 nonbonded pdb=" NH2 ARG A 260 " pdb=" OP2 U B -17 " model vdw 2.260 3.120 nonbonded pdb=" OE1 GLN A 127 " pdb=" N6 DA C 1 " model vdw 2.277 3.120 nonbonded pdb=" NH1 ARG A 314 " pdb=" O4 U B -17 " model vdw 2.292 3.120 nonbonded pdb=" OE1 GLN A 202 " pdb=" N6 DA C 2 " model vdw 2.320 3.120 ... (remaining 30413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.430 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.000 Find NCS groups from input model: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 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 : 0.005 0.041 4007 Z= 0.277 Angle : 0.848 9.893 5760 Z= 0.502 Chirality : 0.053 0.253 667 Planarity : 0.006 0.041 472 Dihedral : 22.815 174.143 1884 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.30 % Favored : 92.34 % Rotamer: Outliers : 1.71 % Allowed : 3.85 % Favored : 94.44 % 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: -1.93 (0.52), residues: 274 helix: -1.08 (0.49), residues: 100 sheet: -0.79 (0.99), residues: 28 loop : -1.50 (0.57), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 249 HIS 0.004 0.001 HIS A 135 PHE 0.012 0.002 PHE A 352 TYR 0.008 0.002 TYR A 201 ARG 0.004 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.17456 ( 126) hydrogen bonds : angle 7.61178 ( 301) covalent geometry : bond 0.00487 ( 4007) covalent geometry : angle 0.84820 ( 5760) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.257 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 32 average time/residue: 0.1973 time to fit residues: 7.6449 Evaluate side-chains 27 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 50.0000 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.198008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.166246 restraints weight = 5897.759| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 1.50 r_work: 0.3984 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3850 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4007 Z= 0.242 Angle : 0.688 5.644 5760 Z= 0.368 Chirality : 0.042 0.208 667 Planarity : 0.006 0.039 472 Dihedral : 25.258 178.498 1324 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.76 % Favored : 90.88 % Rotamer: Outliers : 1.71 % Allowed : 9.40 % Favored : 88.89 % 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: -1.73 (0.52), residues: 274 helix: -0.92 (0.51), residues: 105 sheet: -0.56 (0.97), residues: 28 loop : -1.40 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 249 HIS 0.002 0.001 HIS A 214 PHE 0.008 0.002 PHE A 334 TYR 0.021 0.003 TYR A 317 ARG 0.007 0.001 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.06339 ( 126) hydrogen bonds : angle 4.79449 ( 301) covalent geometry : bond 0.00515 ( 4007) covalent geometry : angle 0.68777 ( 5760) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6226 (tm-30) cc_final: 0.5784 (tm-30) REVERT: A 323 LYS cc_start: 0.7811 (tppt) cc_final: 0.7347 (tppt) outliers start: 4 outliers final: 3 residues processed: 36 average time/residue: 0.2310 time to fit residues: 9.8230 Evaluate side-chains 35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.0010 chunk 17 optimal weight: 0.0970 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.199143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.166539 restraints weight = 5935.600| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 1.57 r_work: 0.3982 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3836 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4007 Z= 0.174 Angle : 0.617 5.605 5760 Z= 0.334 Chirality : 0.039 0.208 667 Planarity : 0.006 0.039 472 Dihedral : 25.145 178.814 1321 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.66 % Favored : 91.97 % Rotamer: Outliers : 1.28 % Allowed : 12.39 % Favored : 86.32 % 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: -1.57 (0.52), residues: 274 helix: -0.79 (0.50), residues: 105 sheet: -0.74 (0.90), residues: 33 loop : -1.24 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 249 HIS 0.002 0.001 HIS A 135 PHE 0.006 0.001 PHE A 219 TYR 0.011 0.002 TYR A 317 ARG 0.005 0.001 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.04941 ( 126) hydrogen bonds : angle 4.38642 ( 301) covalent geometry : bond 0.00370 ( 4007) covalent geometry : angle 0.61740 ( 5760) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.315 Fit side-chains REVERT: A 74 GLU cc_start: 0.6130 (tm-30) cc_final: 0.5710 (tm-30) REVERT: A 323 LYS cc_start: 0.7813 (tppt) cc_final: 0.7414 (mmmt) outliers start: 3 outliers final: 2 residues processed: 35 average time/residue: 0.2205 time to fit residues: 9.2010 Evaluate side-chains 33 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.0170 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.9822 ------------------------------------------------------------------------------- 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 = 0.4405 r_free = 0.4405 target = 0.194436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.160717 restraints weight = 5825.715| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 1.64 r_work: 0.3907 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 4007 Z= 0.300 Angle : 0.743 6.809 5760 Z= 0.394 Chirality : 0.045 0.227 667 Planarity : 0.007 0.058 472 Dihedral : 25.348 175.688 1321 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.85 % Favored : 89.78 % Rotamer: Outliers : 2.99 % Allowed : 14.96 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.50), residues: 274 helix: -1.44 (0.47), residues: 111 sheet: -0.30 (0.94), residues: 28 loop : -1.84 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 264 HIS 0.006 0.002 HIS A 135 PHE 0.013 0.003 PHE A 334 TYR 0.022 0.003 TYR A 317 ARG 0.015 0.001 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.06778 ( 126) hydrogen bonds : angle 5.08244 ( 301) covalent geometry : bond 0.00645 ( 4007) covalent geometry : angle 0.74334 ( 5760) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6682 (tm-30) cc_final: 0.5974 (tm-30) REVERT: A 323 LYS cc_start: 0.7856 (tppt) cc_final: 0.7484 (mmmt) outliers start: 7 outliers final: 5 residues processed: 42 average time/residue: 0.2293 time to fit residues: 11.3325 Evaluate side-chains 42 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 12 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 7 optimal weight: 0.3980 chunk 18 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 0.0980 chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.197983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.165321 restraints weight = 5932.484| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 1.54 r_work: 0.3960 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3817 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4007 Z= 0.158 Angle : 0.619 5.569 5760 Z= 0.336 Chirality : 0.038 0.204 667 Planarity : 0.006 0.044 472 Dihedral : 25.126 179.185 1321 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.03 % Favored : 91.61 % Rotamer: Outliers : 1.71 % Allowed : 17.52 % Favored : 80.77 % 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 (0.52), residues: 274 helix: -0.98 (0.49), residues: 111 sheet: -0.46 (0.90), residues: 33 loop : -1.50 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 304 HIS 0.002 0.001 HIS A 135 PHE 0.006 0.001 PHE A 352 TYR 0.008 0.002 TYR A 317 ARG 0.007 0.001 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 126) hydrogen bonds : angle 4.38379 ( 301) covalent geometry : bond 0.00340 ( 4007) covalent geometry : angle 0.61940 ( 5760) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.262 Fit side-chains REVERT: A 70 ARG cc_start: 0.6812 (ptt180) cc_final: 0.6583 (ptt180) REVERT: A 74 GLU cc_start: 0.6497 (tm-30) cc_final: 0.5786 (tm-30) REVERT: A 323 LYS cc_start: 0.7841 (tppt) cc_final: 0.7491 (mmmt) outliers start: 4 outliers final: 4 residues processed: 32 average time/residue: 0.2656 time to fit residues: 9.8595 Evaluate side-chains 34 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 326 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 6 optimal weight: 0.0020 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.0670 chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.3926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.198072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.165546 restraints weight = 5879.972| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 1.51 r_work: 0.3962 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4007 Z= 0.162 Angle : 0.607 5.709 5760 Z= 0.329 Chirality : 0.038 0.205 667 Planarity : 0.006 0.036 472 Dihedral : 25.017 179.306 1321 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.39 % Favored : 91.24 % Rotamer: Outliers : 2.14 % Allowed : 18.38 % Favored : 79.49 % 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: -1.43 (0.53), residues: 274 helix: -0.43 (0.51), residues: 105 sheet: -0.49 (0.90), residues: 33 loop : -1.45 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 304 HIS 0.002 0.001 HIS A 135 PHE 0.006 0.001 PHE A 137 TYR 0.008 0.002 TYR A 317 ARG 0.006 0.001 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 126) hydrogen bonds : angle 4.29395 ( 301) covalent geometry : bond 0.00348 ( 4007) covalent geometry : angle 0.60688 ( 5760) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.286 Fit side-chains REVERT: A 292 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6907 (mt-10) REVERT: A 323 LYS cc_start: 0.7802 (tppt) cc_final: 0.7417 (mmmt) outliers start: 5 outliers final: 4 residues processed: 32 average time/residue: 0.2462 time to fit residues: 9.3282 Evaluate side-chains 34 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 326 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 32 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 0.0050 chunk 18 optimal weight: 0.0670 overall best weight: 0.2332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.199647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.167277 restraints weight = 5864.412| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 1.52 r_work: 0.3983 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4007 Z= 0.136 Angle : 0.580 5.532 5760 Z= 0.315 Chirality : 0.036 0.198 667 Planarity : 0.006 0.039 472 Dihedral : 24.908 179.982 1321 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.30 % Favored : 92.34 % Rotamer: Outliers : 2.14 % Allowed : 18.38 % Favored : 79.49 % 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: -1.08 (0.54), residues: 274 helix: -0.24 (0.52), residues: 105 sheet: 0.17 (1.07), residues: 27 loop : -1.24 (0.58), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 304 HIS 0.001 0.000 HIS A 135 PHE 0.005 0.001 PHE A 137 TYR 0.006 0.001 TYR A 245 ARG 0.007 0.001 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 126) hydrogen bonds : angle 4.08888 ( 301) covalent geometry : bond 0.00293 ( 4007) covalent geometry : angle 0.57954 ( 5760) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.292 Fit side-chains REVERT: A 74 GLU cc_start: 0.6265 (tm-30) cc_final: 0.5886 (tm-30) REVERT: A 292 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6996 (mt-10) REVERT: A 323 LYS cc_start: 0.7808 (tppt) cc_final: 0.7437 (mmmt) outliers start: 5 outliers final: 3 residues processed: 32 average time/residue: 0.1972 time to fit residues: 7.7773 Evaluate side-chains 33 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 294 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 15 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.198466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.165911 restraints weight = 5924.379| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 1.52 r_work: 0.3973 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3831 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4007 Z= 0.167 Angle : 0.599 5.641 5760 Z= 0.324 Chirality : 0.038 0.218 667 Planarity : 0.006 0.034 472 Dihedral : 24.921 178.966 1321 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.76 % Favored : 90.88 % Rotamer: Outliers : 2.14 % Allowed : 18.80 % Favored : 79.06 % 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: -1.11 (0.53), residues: 274 helix: -0.25 (0.51), residues: 105 sheet: 0.08 (1.07), residues: 27 loop : -1.25 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 304 HIS 0.002 0.001 HIS A 214 PHE 0.006 0.001 PHE A 137 TYR 0.009 0.002 TYR A 140 ARG 0.005 0.000 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 126) hydrogen bonds : angle 4.19197 ( 301) covalent geometry : bond 0.00357 ( 4007) covalent geometry : angle 0.59857 ( 5760) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6013 (tm-30) REVERT: A 292 GLU cc_start: 0.7259 (mt-10) cc_final: 0.7038 (mt-10) REVERT: A 323 LYS cc_start: 0.7847 (tppt) cc_final: 0.7463 (mmmt) outliers start: 5 outliers final: 4 residues processed: 30 average time/residue: 0.2052 time to fit residues: 7.6033 Evaluate side-chains 35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 326 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 33 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 3 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 0.0470 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 overall best weight: 0.2278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.199771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.167496 restraints weight = 5816.439| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 1.52 r_work: 0.3988 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3851 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4007 Z= 0.131 Angle : 0.577 5.538 5760 Z= 0.314 Chirality : 0.036 0.213 667 Planarity : 0.006 0.037 472 Dihedral : 24.885 179.340 1321 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.93 % Favored : 92.70 % Rotamer: Outliers : 1.71 % Allowed : 19.66 % Favored : 78.63 % 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: -0.95 (0.53), residues: 274 helix: -0.12 (0.52), residues: 105 sheet: 0.14 (1.10), residues: 27 loop : -1.15 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 249 HIS 0.002 0.001 HIS A 135 PHE 0.007 0.001 PHE A 334 TYR 0.005 0.001 TYR A 245 ARG 0.005 0.001 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 126) hydrogen bonds : angle 4.04960 ( 301) covalent geometry : bond 0.00283 ( 4007) covalent geometry : angle 0.57678 ( 5760) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.6030 (tm-30) REVERT: A 292 GLU cc_start: 0.7247 (mt-10) cc_final: 0.7021 (mt-10) REVERT: A 323 LYS cc_start: 0.7823 (tppt) cc_final: 0.7444 (mmmt) outliers start: 4 outliers final: 3 residues processed: 28 average time/residue: 0.2172 time to fit residues: 7.5211 Evaluate side-chains 32 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 15 optimal weight: 0.0370 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 chunk 25 optimal weight: 0.0030 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 overall best weight: 0.1868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.200537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.168304 restraints weight = 5957.105| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 1.52 r_work: 0.4000 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3862 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4007 Z= 0.130 Angle : 0.570 5.674 5760 Z= 0.311 Chirality : 0.036 0.207 667 Planarity : 0.006 0.035 472 Dihedral : 24.782 179.820 1321 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.30 % Favored : 92.34 % Rotamer: Outliers : 1.28 % Allowed : 20.51 % Favored : 78.21 % 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: -0.76 (0.54), residues: 274 helix: 0.02 (0.52), residues: 105 sheet: 0.16 (1.11), residues: 27 loop : -1.01 (0.58), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 249 HIS 0.001 0.000 HIS A 135 PHE 0.005 0.001 PHE A 137 TYR 0.004 0.001 TYR A 245 ARG 0.005 0.000 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.03125 ( 126) hydrogen bonds : angle 3.96372 ( 301) covalent geometry : bond 0.00279 ( 4007) covalent geometry : angle 0.57027 ( 5760) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.6067 (tm-30) REVERT: A 292 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6995 (mt-10) REVERT: A 323 LYS cc_start: 0.7835 (tppt) cc_final: 0.7448 (mmmt) outliers start: 3 outliers final: 2 residues processed: 28 average time/residue: 0.2043 time to fit residues: 7.0207 Evaluate side-chains 31 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.198532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.166066 restraints weight = 5907.216| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 1.57 r_work: 0.3969 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3827 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4007 Z= 0.175 Angle : 0.604 5.454 5760 Z= 0.326 Chirality : 0.038 0.227 667 Planarity : 0.006 0.035 472 Dihedral : 24.797 178.341 1321 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.76 % Favored : 90.88 % Rotamer: Outliers : 1.71 % Allowed : 19.66 % Favored : 78.63 % 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: -1.04 (0.53), residues: 274 helix: -0.20 (0.52), residues: 105 sheet: -0.08 (1.09), residues: 27 loop : -1.16 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 249 HIS 0.002 0.001 HIS A 214 PHE 0.007 0.002 PHE A 137 TYR 0.008 0.002 TYR A 317 ARG 0.004 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 126) hydrogen bonds : angle 4.19734 ( 301) covalent geometry : bond 0.00376 ( 4007) covalent geometry : angle 0.60422 ( 5760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2735.32 seconds wall clock time: 48 minutes 10.68 seconds (2890.68 seconds total)