Starting phenix.real_space_refine on Wed Jul 23 16:31:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ws5_37798/07_2025/8ws5_37798.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ws5_37798/07_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_37798/07_2025/8ws5_37798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ws5_37798/07_2025/8ws5_37798.map" model { file = "/net/cci-nas-00/data/ceres_data/8ws5_37798/07_2025/8ws5_37798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ws5_37798/07_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-5711/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: 4.09, per 1000 atoms: 1.08 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: 1.15 Conformation dependent library (CDL) restraints added in 287.8 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: 1.52 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: 1.06 Time building geometry restraints manager: 1.35 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: 0.010 Normalize map: mean=0, sd=1: 3.860 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: 16.110 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.260 ------------------------------------------------------------------------------- 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 : 0.292 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 32 average time/residue: 0.1956 time to fit residues: 7.6288 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 : 0.258 ------------------------------------------------------------------------------- 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 = 0.197942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.165712 restraints weight = 5919.912| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 1.53 r_work: 0.3983 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3841 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4007 Z= 0.242 Angle : 0.688 5.645 5760 Z= 0.368 Chirality : 0.042 0.208 667 Planarity : 0.006 0.039 472 Dihedral : 25.258 178.504 1324 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.91 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 0.06343 ( 126) hydrogen bonds : angle 4.79499 ( 301) covalent geometry : bond 0.00515 ( 4007) covalent geometry : angle 0.68755 ( 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 : 0.262 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6225 (tm-30) cc_final: 0.5781 (tm-30) REVERT: A 323 LYS cc_start: 0.7830 (tppt) cc_final: 0.7368 (tppt) outliers start: 4 outliers final: 3 residues processed: 36 average time/residue: 0.2302 time to fit residues: 9.7888 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 : 0.265 ------------------------------------------------------------------------------- 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: 0.9990 chunk 22 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 30.0000 chunk 15 optimal weight: 0.3980 chunk 17 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 = 0.4455 r_free = 0.4455 target = 0.198089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.165749 restraints weight = 5918.850| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 1.56 r_work: 0.3968 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.1923 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= 0.197 Angle : 0.640 5.595 5760 Z= 0.344 Chirality : 0.039 0.210 667 Planarity : 0.006 0.039 472 Dihedral : 25.128 178.681 1321 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.03 % Favored : 91.61 % Rotamer: Outliers : 1.28 % Allowed : 14.10 % Favored : 84.62 % 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 (0.52), residues: 274 helix: -0.95 (0.48), residues: 111 sheet: -0.78 (0.89), residues: 33 loop : -1.51 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 249 HIS 0.002 0.001 HIS A 135 PHE 0.006 0.002 PHE A 219 TYR 0.016 0.002 TYR A 317 ARG 0.008 0.001 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.05034 ( 126) hydrogen bonds : angle 4.45687 ( 301) covalent geometry : bond 0.00422 ( 4007) covalent geometry : angle 0.63972 ( 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 37 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6208 (tm-30) cc_final: 0.5800 (tp30) REVERT: A 323 LYS cc_start: 0.7724 (tppt) cc_final: 0.7392 (mmmt) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.2134 time to fit residues: 9.1571 Evaluate side-chains 35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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: 0.9990 chunk 11 optimal weight: 0.0670 chunk 28 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.7124 ------------------------------------------------------------------------------- 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 = 0.4423 r_free = 0.4423 target = 0.195669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.162344 restraints weight = 5812.825| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 1.61 r_work: 0.3924 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.2413 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= 0.240 Angle : 0.680 6.210 5760 Z= 0.363 Chirality : 0.041 0.210 667 Planarity : 0.007 0.039 472 Dihedral : 25.231 176.592 1321 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.22 % Favored : 89.42 % Rotamer: Outliers : 2.14 % Allowed : 15.81 % 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: -1.99 (0.51), residues: 274 helix: -1.06 (0.48), residues: 111 sheet: -0.27 (0.95), residues: 28 loop : -1.75 (0.57), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 264 HIS 0.002 0.001 HIS A 214 PHE 0.009 0.002 PHE A 334 TYR 0.019 0.003 TYR A 317 ARG 0.006 0.001 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.05608 ( 126) hydrogen bonds : angle 4.70983 ( 301) covalent geometry : bond 0.00515 ( 4007) covalent geometry : angle 0.67999 ( 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 39 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 LYS cc_start: 0.7844 (tppt) cc_final: 0.7368 (mmmt) REVERT: A 352 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.6528 (m-10) outliers start: 5 outliers final: 4 residues processed: 36 average time/residue: 0.2457 time to fit residues: 10.3157 Evaluate side-chains 39 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 352 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 12 optimal weight: 0.0030 chunk 5 optimal weight: 0.3980 chunk 7 optimal weight: 0.0970 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 overall best weight: 0.1388 ------------------------------------------------------------------------------- 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 = 0.4476 r_free = 0.4476 target = 0.200003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.167477 restraints weight = 5969.592| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 1.54 r_work: 0.3986 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3848 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.2584 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= 0.128 Angle : 0.590 5.525 5760 Z= 0.321 Chirality : 0.036 0.188 667 Planarity : 0.006 0.041 472 Dihedral : 24.988 179.824 1321 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.93 % Favored : 92.70 % Rotamer: Outliers : 1.71 % Allowed : 17.95 % Favored : 80.34 % 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: -1.48 (0.53), residues: 274 helix: -0.64 (0.50), residues: 111 sheet: -0.45 (0.91), residues: 33 loop : -1.36 (0.62), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 249 HIS 0.007 0.001 HIS A 135 PHE 0.007 0.001 PHE A 334 TYR 0.005 0.001 TYR A 245 ARG 0.006 0.001 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 126) hydrogen bonds : angle 4.11833 ( 301) covalent geometry : bond 0.00277 ( 4007) covalent geometry : angle 0.58962 ( 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 35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.300 Fit side-chains REVERT: A 74 GLU cc_start: 0.6269 (tm-30) cc_final: 0.5903 (tm-30) REVERT: A 323 LYS cc_start: 0.7811 (tppt) cc_final: 0.7380 (mmmt) REVERT: A 352 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.6570 (m-10) outliers start: 4 outliers final: 3 residues processed: 32 average time/residue: 0.2261 time to fit residues: 8.6963 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 : 0.299 ------------------------------------------------------------------------------- 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 352 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 6 optimal weight: 0.0050 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 0.0070 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.0970 chunk 22 optimal weight: 0.6980 overall best weight: 0.2610 ------------------------------------------------------------------------------- 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 = 0.4469 r_free = 0.4469 target = 0.199334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.166633 restraints weight = 5921.272| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 1.60 r_work: 0.3973 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3831 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.2711 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= 0.140 Angle : 0.586 5.666 5760 Z= 0.318 Chirality : 0.036 0.191 667 Planarity : 0.006 0.035 472 Dihedral : 24.827 179.373 1321 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.30 % Favored : 92.34 % Rotamer: Outliers : 3.42 % Allowed : 17.09 % 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: -1.09 (0.54), residues: 274 helix: -0.22 (0.52), residues: 105 sheet: 0.22 (1.05), residues: 27 loop : -1.28 (0.58), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 249 HIS 0.002 0.000 HIS A 135 PHE 0.005 0.001 PHE A 137 TYR 0.008 0.001 TYR A 140 ARG 0.006 0.001 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 126) hydrogen bonds : angle 4.05949 ( 301) covalent geometry : bond 0.00304 ( 4007) covalent geometry : angle 0.58572 ( 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 40 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.261 Fit side-chains REVERT: A 74 GLU cc_start: 0.6436 (tm-30) cc_final: 0.5992 (tm-30) REVERT: A 323 LYS cc_start: 0.7864 (tppt) cc_final: 0.7397 (mmmt) REVERT: A 352 PHE cc_start: 0.6886 (OUTLIER) cc_final: 0.6527 (m-10) outliers start: 8 outliers final: 5 residues processed: 36 average time/residue: 0.2920 time to fit residues: 12.0454 Evaluate side-chains 35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 PHE 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: 0.9980 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 0.0070 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 = 0.4453 r_free = 0.4453 target = 0.197888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.165082 restraints weight = 5892.054| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 1.57 r_work: 0.3962 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3824 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.2855 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= 0.175 Angle : 0.606 5.511 5760 Z= 0.328 Chirality : 0.038 0.210 667 Planarity : 0.006 0.034 472 Dihedral : 24.897 178.824 1321 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.39 % Favored : 91.24 % Rotamer: Outliers : 3.42 % Allowed : 16.67 % Favored : 79.91 % 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: -1.36 (0.53), residues: 274 helix: -0.47 (0.50), residues: 105 sheet: -0.45 (0.91), residues: 33 loop : -1.31 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 249 HIS 0.003 0.001 HIS A 214 PHE 0.005 0.001 PHE A 137 TYR 0.010 0.002 TYR A 140 ARG 0.005 0.001 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.05487 ( 126) hydrogen bonds : angle 4.22840 ( 301) covalent geometry : bond 0.00373 ( 4007) covalent geometry : angle 0.60594 ( 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 40 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6077 (tm-30) REVERT: A 323 LYS cc_start: 0.7856 (tppt) cc_final: 0.7487 (mmmt) REVERT: A 352 PHE cc_start: 0.6918 (OUTLIER) cc_final: 0.6489 (m-10) outliers start: 8 outliers final: 5 residues processed: 35 average time/residue: 0.2173 time to fit residues: 9.1587 Evaluate side-chains 39 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 153 LYS Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 27 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 0.0970 chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 0.0570 chunk 18 optimal weight: 0.0270 chunk 21 optimal weight: 0.8980 overall best weight: 0.2554 ------------------------------------------------------------------------------- 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 = 0.4472 r_free = 0.4472 target = 0.199546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.167135 restraints weight = 5988.775| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 1.52 r_work: 0.3992 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3855 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4007 Z= 0.136 Angle : 0.571 5.665 5760 Z= 0.312 Chirality : 0.036 0.209 667 Planarity : 0.006 0.035 472 Dihedral : 24.809 179.854 1321 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.30 % Favored : 92.34 % Rotamer: Outliers : 2.56 % Allowed : 17.52 % Favored : 79.91 % 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: -1.02 (0.53), residues: 274 helix: -0.27 (0.51), residues: 105 sheet: 0.23 (1.07), residues: 27 loop : -1.13 (0.58), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 249 HIS 0.001 0.001 HIS A 214 PHE 0.005 0.001 PHE A 137 TYR 0.005 0.001 TYR A 245 ARG 0.004 0.001 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 126) hydrogen bonds : angle 4.02499 ( 301) covalent geometry : bond 0.00294 ( 4007) covalent geometry : angle 0.57119 ( 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 39 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6106 (tm-30) REVERT: A 323 LYS cc_start: 0.7837 (tppt) cc_final: 0.7322 (mmmt) REVERT: A 352 PHE cc_start: 0.6871 (OUTLIER) cc_final: 0.6435 (m-10) outliers start: 6 outliers final: 4 residues processed: 34 average time/residue: 0.3185 time to fit residues: 13.3688 Evaluate side-chains 38 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 153 LYS Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 352 PHE 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: 0.7980 chunk 15 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 0.0870 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 0.0970 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 = 0.4466 r_free = 0.4466 target = 0.198874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.166152 restraints weight = 5831.957| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 1.56 r_work: 0.3976 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.3082 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= 0.156 Angle : 0.584 5.547 5760 Z= 0.317 Chirality : 0.037 0.219 667 Planarity : 0.006 0.035 472 Dihedral : 24.708 179.229 1321 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.39 % Favored : 91.24 % Rotamer: Outliers : 2.99 % Allowed : 16.24 % 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: -1.17 (0.53), residues: 274 helix: -0.34 (0.51), residues: 105 sheet: -0.45 (0.90), residues: 33 loop : -1.15 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 249 HIS 0.002 0.001 HIS A 214 PHE 0.006 0.001 PHE A 137 TYR 0.008 0.001 TYR A 140 ARG 0.004 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.04334 ( 126) hydrogen bonds : angle 4.11114 ( 301) covalent geometry : bond 0.00334 ( 4007) covalent geometry : angle 0.58357 ( 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 40 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6167 (tm-30) REVERT: A 323 LYS cc_start: 0.7927 (tppt) cc_final: 0.7542 (mmmt) REVERT: A 352 PHE cc_start: 0.6854 (OUTLIER) cc_final: 0.6437 (m-10) outliers start: 7 outliers final: 4 residues processed: 36 average time/residue: 0.5778 time to fit residues: 24.3094 Evaluate side-chains 39 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 351 THR Chi-restraints excluded: chain A residue 352 PHE 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: 0.0770 chunk 6 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.1980 chunk 12 optimal weight: 0.4980 chunk 16 optimal weight: 0.0870 overall best weight: 0.2116 ------------------------------------------------------------------------------- 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 = 0.4481 r_free = 0.4481 target = 0.200099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.167542 restraints weight = 5975.936| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 1.60 r_work: 0.3993 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3851 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4007 Z= 0.128 Angle : 0.570 5.659 5760 Z= 0.310 Chirality : 0.036 0.209 667 Planarity : 0.006 0.036 472 Dihedral : 24.655 179.725 1321 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.57 % Favored : 93.07 % Rotamer: Outliers : 2.56 % Allowed : 17.09 % Favored : 80.34 % 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: -0.86 (0.54), residues: 274 helix: -0.17 (0.52), residues: 105 sheet: 0.20 (1.10), residues: 27 loop : -0.98 (0.58), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 249 HIS 0.001 0.001 HIS A 135 PHE 0.005 0.001 PHE A 350 TYR 0.005 0.001 TYR A 245 ARG 0.004 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 126) hydrogen bonds : angle 3.98103 ( 301) covalent geometry : bond 0.00276 ( 4007) covalent geometry : angle 0.57021 ( 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 34 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6200 (tm-30) REVERT: A 323 LYS cc_start: 0.7911 (tppt) cc_final: 0.7523 (mmmt) REVERT: A 352 PHE cc_start: 0.6809 (OUTLIER) cc_final: 0.6382 (m-10) outliers start: 6 outliers final: 4 residues processed: 30 average time/residue: 0.3729 time to fit residues: 13.8015 Evaluate side-chains 33 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 351 THR Chi-restraints excluded: chain A residue 352 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.0770 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.4456 r_free = 0.4456 target = 0.197963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.165032 restraints weight = 5929.341| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 1.59 r_work: 0.3959 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4007 Z= 0.180 Angle : 0.609 5.600 5760 Z= 0.328 Chirality : 0.038 0.220 667 Planarity : 0.006 0.049 472 Dihedral : 24.693 178.499 1321 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.76 % Favored : 90.88 % Rotamer: Outliers : 2.56 % Allowed : 16.67 % 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: -1.26 (0.53), residues: 274 helix: -0.41 (0.50), residues: 105 sheet: -0.48 (0.93), residues: 33 loop : -1.22 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 249 HIS 0.003 0.001 HIS A 214 PHE 0.007 0.002 PHE A 137 TYR 0.010 0.002 TYR A 140 ARG 0.005 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.05101 ( 126) hydrogen bonds : angle 4.21280 ( 301) covalent geometry : bond 0.00387 ( 4007) covalent geometry : angle 0.60867 ( 5760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3303.27 seconds wall clock time: 59 minutes 19.44 seconds (3559.44 seconds total)