Starting phenix.real_space_refine on Fri May 9 19:32:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ws6_37799/05_2025/8ws6_37799.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ws6_37799/05_2025/8ws6_37799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ws6_37799/05_2025/8ws6_37799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ws6_37799/05_2025/8ws6_37799.map" model { file = "/net/cci-nas-00/data/ceres_data/8ws6_37799/05_2025/8ws6_37799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ws6_37799/05_2025/8ws6_37799.cif" } resolution = 3.21 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= 0.015 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 58 5.49 5 S 3 5.16 5 C 2058 2.51 5 N 645 2.21 5 O 794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 3558 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2348 Classifications: {'peptide': 298} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 268} 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: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 401 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "B" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 650 Classifications: {'RNA': 31} Modifications used: {'rna2p_pyr': 6, 'rna3p_pur': 11, 'rna3p_pyr': 14} Link IDs: {'rna2p': 6, 'rna3p': 24} Chain: "D" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 159 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Time building chain proxies: 3.74, per 1000 atoms: 1.05 Number of scatterers: 3558 At special positions: 0 Unit cell: (65.34, 88.44, 91.74, 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 58 15.00 O 794 8.00 N 645 7.00 C 2058 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: 1.10 Conformation dependent library (CDL) restraints added in 307.5 milliseconds 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 542 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 1 sheets defined 35.6% alpha, 8.7% beta 13 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 75 through 89 Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.635A pdb=" N ALA A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 removed outlier: 3.894A pdb=" N ALA A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 132 through 149 removed outlier: 4.143A pdb=" N PHE A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 169 removed outlier: 3.750A pdb=" N SER A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 287 through 292 removed outlier: 3.817A pdb=" N LYS A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 287 through 292' Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.891A pdb=" N ALA A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.538A pdb=" N LEU A 341 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 347 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASN A 64 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL A 306 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLN A 68 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N TRP A 304 " --> pdb=" O GLN A 68 " (cutoff:3.500A) 76 hydrogen bonds defined for protein. 204 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 844 1.33 - 1.45: 1012 1.45 - 1.57: 1789 1.57 - 1.69: 113 1.69 - 1.81: 4 Bond restraints: 3762 Sorted by residual: bond pdb=" CA LEU A 217 " pdb=" C LEU A 217 " ideal model delta sigma weight residual 1.524 1.552 -0.028 1.26e-02 6.30e+03 5.04e+00 bond pdb=" CA GLU A 176 " pdb=" C GLU A 176 " ideal model delta sigma weight residual 1.528 1.542 -0.014 1.01e-02 9.80e+03 1.86e+00 bond pdb=" N PRO A 324 " pdb=" CA PRO A 324 " ideal model delta sigma weight residual 1.472 1.454 0.018 1.32e-02 5.74e+03 1.78e+00 bond pdb=" C LEU A 217 " pdb=" N PRO A 218 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.76e+00 bond pdb=" C GLU A 152 " pdb=" O GLU A 152 " ideal model delta sigma weight residual 1.237 1.222 0.015 1.17e-02 7.31e+03 1.63e+00 ... (remaining 3757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 5097 1.44 - 2.88: 221 2.88 - 4.32: 35 4.32 - 5.77: 5 5.77 - 7.21: 2 Bond angle restraints: 5360 Sorted by residual: angle pdb=" N ARG A 150 " pdb=" CA ARG A 150 " pdb=" C ARG A 150 " ideal model delta sigma weight residual 113.55 108.80 4.75 1.26e+00 6.30e-01 1.42e+01 angle pdb=" N GLY A 244 " pdb=" CA GLY A 244 " pdb=" C GLY A 244 " ideal model delta sigma weight residual 114.95 110.19 4.76 1.41e+00 5.03e-01 1.14e+01 angle pdb=" C GLU A 176 " pdb=" N PRO A 177 " pdb=" CA PRO A 177 " ideal model delta sigma weight residual 119.84 115.76 4.08 1.25e+00 6.40e-01 1.07e+01 angle pdb=" N LYS A 157 " pdb=" CA LYS A 157 " pdb=" C LYS A 157 " ideal model delta sigma weight residual 111.36 107.95 3.41 1.09e+00 8.42e-01 9.76e+00 angle pdb=" C GLN A 242 " pdb=" N PRO A 243 " pdb=" CA PRO A 243 " ideal model delta sigma weight residual 119.84 123.65 -3.81 1.25e+00 6.40e-01 9.28e+00 ... (remaining 5355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.53: 2059 34.53 - 69.07: 180 69.07 - 103.60: 16 103.60 - 138.13: 0 138.13 - 172.67: 2 Dihedral angle restraints: 2257 sinusoidal: 1408 harmonic: 849 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 58.29 141.71 1 1.50e+01 4.44e-03 7.62e+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 59.33 172.67 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" CA GLU A 148 " pdb=" C GLU A 148 " pdb=" N THR A 149 " pdb=" CA THR A 149 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 2254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 420 0.029 - 0.058: 125 0.058 - 0.087: 37 0.087 - 0.117: 22 0.117 - 0.146: 6 Chirality restraints: 610 Sorted by residual: chirality pdb=" CA ILE A 347 " pdb=" N ILE A 347 " pdb=" C ILE A 347 " pdb=" CB ILE A 347 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" C1' U B 10 " pdb=" O4' U B 10 " pdb=" C2' U B 10 " pdb=" N1 U B 10 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CB ILE A 261 " pdb=" CA ILE A 261 " pdb=" CG1 ILE A 261 " pdb=" CG2 ILE A 261 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 607 not shown) Planarity restraints: 484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 338 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO A 339 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 191 " 0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO A 192 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 238 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 239 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 239 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 239 " 0.028 5.00e-02 4.00e+02 ... (remaining 481 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 387 2.74 - 3.28: 3109 3.28 - 3.82: 6018 3.82 - 4.36: 7409 4.36 - 4.90: 11478 Nonbonded interactions: 28401 Sorted by model distance: nonbonded pdb=" O ASP A 110 " pdb=" OD1 ASP A 110 " model vdw 2.204 3.040 nonbonded pdb=" O TRP A 112 " pdb=" OG1 THR A 116 " model vdw 2.243 3.040 nonbonded pdb=" NH1 ARG A 314 " pdb=" O4 U B -17 " model vdw 2.250 3.120 nonbonded pdb=" ND2 ASN A 138 " pdb=" OP1 DG C -2 " model vdw 2.312 3.120 nonbonded pdb=" NH1 ARG A 260 " pdb=" O6 G B -16 " model vdw 2.353 3.120 ... (remaining 28396 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: 3.840 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.980 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 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 : 0.003 0.031 3762 Z= 0.179 Angle : 0.665 7.208 5360 Z= 0.410 Chirality : 0.036 0.146 610 Planarity : 0.007 0.073 484 Dihedral : 21.116 172.666 1715 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: -1.69 (0.46), residues: 296 helix: -1.76 (0.47), residues: 95 sheet: -0.73 (1.04), residues: 29 loop : -0.72 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 304 HIS 0.001 0.000 HIS A 214 PHE 0.010 0.001 PHE A 219 TYR 0.006 0.001 TYR A 265 ARG 0.002 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.26783 ( 106) hydrogen bonds : angle 10.01247 ( 260) covalent geometry : bond 0.00316 ( 3762) covalent geometry : angle 0.66540 ( 5360) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 104 THR cc_start: 0.7057 (p) cc_final: 0.6844 (p) REVERT: A 331 LEU cc_start: 0.7261 (tp) cc_final: 0.6999 (tt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.3168 time to fit residues: 16.3011 Evaluate side-chains 41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 24 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.148077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.124639 restraints weight = 5127.119| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.55 r_work: 0.3456 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3762 Z= 0.243 Angle : 0.675 5.394 5360 Z= 0.364 Chirality : 0.044 0.138 610 Planarity : 0.008 0.054 484 Dihedral : 24.197 173.178 1121 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.21 % Allowed : 11.34 % Favored : 87.45 % 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: -1.12 (0.48), residues: 296 helix: -1.18 (0.49), residues: 97 sheet: -0.08 (1.06), residues: 31 loop : -0.51 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 112 HIS 0.006 0.001 HIS A 214 PHE 0.013 0.002 PHE A 335 TYR 0.016 0.003 TYR A 265 ARG 0.004 0.001 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.05859 ( 106) hydrogen bonds : angle 4.94242 ( 260) covalent geometry : bond 0.00542 ( 3762) covalent geometry : angle 0.67525 ( 5360) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.239 Fit side-chains REVERT: A 134 ARG cc_start: 0.7842 (tmm-80) cc_final: 0.7628 (ttp-110) REVERT: A 261 ILE cc_start: 0.7806 (tt) cc_final: 0.7574 (pt) outliers start: 3 outliers final: 2 residues processed: 44 average time/residue: 0.2243 time to fit residues: 11.4845 Evaluate side-chains 44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 255 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.146599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.123196 restraints weight = 5126.090| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.55 r_work: 0.3430 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3762 Z= 0.265 Angle : 0.694 5.815 5360 Z= 0.373 Chirality : 0.046 0.154 610 Planarity : 0.008 0.050 484 Dihedral : 24.530 173.538 1121 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.62 % Allowed : 14.98 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.28 (0.47), residues: 296 helix: -1.40 (0.47), residues: 103 sheet: -0.20 (1.09), residues: 30 loop : -0.48 (0.47), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 264 HIS 0.003 0.001 HIS A 135 PHE 0.013 0.003 PHE A 335 TYR 0.013 0.002 TYR A 265 ARG 0.003 0.001 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.05114 ( 106) hydrogen bonds : angle 4.59792 ( 260) covalent geometry : bond 0.00593 ( 3762) covalent geometry : angle 0.69427 ( 5360) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.284 Fit side-chains REVERT: A 134 ARG cc_start: 0.7930 (tmm-80) cc_final: 0.7714 (ttp-110) REVERT: A 139 ARG cc_start: 0.7653 (mtm-85) cc_final: 0.7435 (mtm-85) outliers start: 4 outliers final: 4 residues processed: 44 average time/residue: 0.2339 time to fit residues: 12.0466 Evaluate side-chains 46 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 255 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 3 optimal weight: 0.3980 chunk 16 optimal weight: 0.0670 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 chunk 14 optimal weight: 0.0070 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.0770 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 overall best weight: 0.1494 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.155562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.133586 restraints weight = 5091.863| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.35 r_work: 0.3529 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3762 Z= 0.122 Angle : 0.557 6.858 5360 Z= 0.302 Chirality : 0.038 0.136 610 Planarity : 0.006 0.042 484 Dihedral : 24.164 173.714 1121 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.83 % Allowed : 14.98 % Favored : 82.19 % 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: -0.46 (0.49), residues: 296 helix: -0.67 (0.50), residues: 103 sheet: 0.29 (1.07), residues: 32 loop : -0.03 (0.50), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 264 HIS 0.002 0.001 HIS A 135 PHE 0.007 0.001 PHE A 352 TYR 0.007 0.001 TYR A 265 ARG 0.002 0.000 ARG A 150 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 106) hydrogen bonds : angle 4.10759 ( 260) covalent geometry : bond 0.00271 ( 3762) covalent geometry : angle 0.55681 ( 5360) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7888 (tmm-80) cc_final: 0.7553 (ttp-110) REVERT: A 331 LEU cc_start: 0.7491 (tp) cc_final: 0.7083 (tt) outliers start: 7 outliers final: 2 residues processed: 47 average time/residue: 0.2367 time to fit residues: 13.0553 Evaluate side-chains 40 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 166 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 28 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 0.0370 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 8 optimal weight: 0.2980 overall best weight: 0.3258 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.150208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.126990 restraints weight = 5228.625| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.52 r_work: 0.3487 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3762 Z= 0.149 Angle : 0.565 6.457 5360 Z= 0.303 Chirality : 0.039 0.132 610 Planarity : 0.006 0.040 484 Dihedral : 24.110 173.440 1121 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.81 % Allowed : 16.60 % Favored : 82.59 % 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: -0.23 (0.49), residues: 296 helix: -0.43 (0.53), residues: 97 sheet: 0.15 (1.07), residues: 30 loop : 0.10 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 264 HIS 0.001 0.000 HIS A 135 PHE 0.008 0.002 PHE A 350 TYR 0.009 0.001 TYR A 265 ARG 0.002 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 106) hydrogen bonds : angle 4.03447 ( 260) covalent geometry : bond 0.00334 ( 3762) covalent geometry : angle 0.56457 ( 5360) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7961 (tmm-80) cc_final: 0.7603 (ttp-110) REVERT: A 331 LEU cc_start: 0.7472 (tp) cc_final: 0.7097 (tt) outliers start: 2 outliers final: 2 residues processed: 38 average time/residue: 0.2879 time to fit residues: 12.5064 Evaluate side-chains 38 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 166 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 30.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.147127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.123607 restraints weight = 5229.860| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.55 r_work: 0.3431 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3762 Z= 0.240 Angle : 0.642 6.239 5360 Z= 0.341 Chirality : 0.044 0.146 610 Planarity : 0.006 0.040 484 Dihedral : 24.302 173.059 1121 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.43 % Allowed : 16.60 % Favored : 80.97 % 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: -0.48 (0.49), residues: 296 helix: -0.57 (0.52), residues: 97 sheet: -0.31 (1.02), residues: 30 loop : -0.03 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 264 HIS 0.001 0.001 HIS A 214 PHE 0.013 0.002 PHE A 350 TYR 0.010 0.002 TYR A 87 ARG 0.004 0.001 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.04818 ( 106) hydrogen bonds : angle 4.20911 ( 260) covalent geometry : bond 0.00541 ( 3762) covalent geometry : angle 0.64246 ( 5360) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8012 (tmm-80) cc_final: 0.7649 (ttp-110) REVERT: A 279 VAL cc_start: 0.6722 (OUTLIER) cc_final: 0.6421 (p) outliers start: 6 outliers final: 3 residues processed: 43 average time/residue: 0.2369 time to fit residues: 11.8054 Evaluate side-chains 43 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 279 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.0270 chunk 14 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 26 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 overall best weight: 0.2376 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.149383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126134 restraints weight = 5157.115| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.52 r_work: 0.3473 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3762 Z= 0.138 Angle : 0.570 6.595 5360 Z= 0.305 Chirality : 0.039 0.132 610 Planarity : 0.006 0.039 484 Dihedral : 24.228 172.433 1121 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.02 % Allowed : 19.43 % Favored : 78.54 % 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: -0.20 (0.50), residues: 296 helix: -0.32 (0.53), residues: 97 sheet: -0.07 (1.04), residues: 30 loop : 0.11 (0.50), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 264 HIS 0.002 0.001 HIS A 214 PHE 0.010 0.001 PHE A 350 TYR 0.011 0.001 TYR A 265 ARG 0.002 0.000 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 106) hydrogen bonds : angle 4.05887 ( 260) covalent geometry : bond 0.00307 ( 3762) covalent geometry : angle 0.57042 ( 5360) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8004 (tmm-80) cc_final: 0.7717 (ttp-110) REVERT: A 279 VAL cc_start: 0.6697 (OUTLIER) cc_final: 0.6432 (p) outliers start: 5 outliers final: 4 residues processed: 40 average time/residue: 0.2440 time to fit residues: 11.4634 Evaluate side-chains 40 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 326 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.0040 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.0170 chunk 16 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 24 optimal weight: 0.4980 chunk 9 optimal weight: 0.0980 overall best weight: 0.2030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** 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 = 0.3898 r_free = 0.3898 target = 0.151336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.127971 restraints weight = 5172.022| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.54 r_work: 0.3501 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3762 Z= 0.121 Angle : 0.538 7.072 5360 Z= 0.289 Chirality : 0.037 0.135 610 Planarity : 0.006 0.041 484 Dihedral : 24.059 172.836 1121 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.62 % Allowed : 20.24 % Favored : 78.14 % 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: 0.11 (0.50), residues: 296 helix: -0.05 (0.53), residues: 97 sheet: 0.16 (1.04), residues: 30 loop : 0.29 (0.51), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 264 HIS 0.001 0.001 HIS A 214 PHE 0.008 0.001 PHE A 335 TYR 0.008 0.001 TYR A 265 ARG 0.003 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 106) hydrogen bonds : angle 3.94420 ( 260) covalent geometry : bond 0.00271 ( 3762) covalent geometry : angle 0.53824 ( 5360) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8010 (tmm-80) cc_final: 0.7714 (ttp-110) REVERT: A 279 VAL cc_start: 0.6753 (OUTLIER) cc_final: 0.6491 (p) outliers start: 4 outliers final: 3 residues processed: 39 average time/residue: 0.2764 time to fit residues: 12.5023 Evaluate side-chains 40 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 279 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 7 optimal weight: 0.0070 chunk 12 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.0870 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.149632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.126354 restraints weight = 5103.698| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.52 r_work: 0.3474 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3762 Z= 0.164 Angle : 0.565 6.939 5360 Z= 0.301 Chirality : 0.039 0.136 610 Planarity : 0.006 0.039 484 Dihedral : 24.105 172.869 1121 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.43 % Allowed : 19.03 % Favored : 78.54 % 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: 0.06 (0.50), residues: 296 helix: -0.08 (0.53), residues: 97 sheet: 0.03 (1.02), residues: 30 loop : 0.27 (0.51), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 264 HIS 0.001 0.000 HIS A 214 PHE 0.009 0.002 PHE A 137 TYR 0.009 0.002 TYR A 265 ARG 0.003 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 106) hydrogen bonds : angle 3.98126 ( 260) covalent geometry : bond 0.00370 ( 3762) covalent geometry : angle 0.56510 ( 5360) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8033 (tmm-80) cc_final: 0.7736 (ttp-110) REVERT: A 279 VAL cc_start: 0.6756 (OUTLIER) cc_final: 0.6472 (p) REVERT: A 331 LEU cc_start: 0.7462 (tp) cc_final: 0.7072 (tt) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 0.2464 time to fit residues: 12.2891 Evaluate side-chains 43 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 0.0770 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.152004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129539 restraints weight = 5142.220| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.36 r_work: 0.3468 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3762 Z= 0.191 Angle : 0.595 6.907 5360 Z= 0.316 Chirality : 0.041 0.134 610 Planarity : 0.006 0.038 484 Dihedral : 24.176 172.356 1121 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.02 % Allowed : 19.43 % Favored : 78.54 % 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: -0.05 (0.50), residues: 296 helix: -0.12 (0.53), residues: 97 sheet: -0.15 (1.01), residues: 30 loop : 0.19 (0.50), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 264 HIS 0.001 0.000 HIS A 214 PHE 0.011 0.002 PHE A 137 TYR 0.009 0.002 TYR A 265 ARG 0.003 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 106) hydrogen bonds : angle 4.01299 ( 260) covalent geometry : bond 0.00432 ( 3762) covalent geometry : angle 0.59540 ( 5360) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8043 (tmm-80) cc_final: 0.7730 (ttp-110) REVERT: A 279 VAL cc_start: 0.6776 (OUTLIER) cc_final: 0.6500 (p) outliers start: 5 outliers final: 4 residues processed: 43 average time/residue: 0.2397 time to fit residues: 11.9625 Evaluate side-chains 44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 1 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 28 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 0.0470 chunk 20 optimal weight: 0.1980 chunk 6 optimal weight: 0.0570 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** 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 = 0.3936 r_free = 0.3936 target = 0.156290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.134261 restraints weight = 5167.561| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.37 r_work: 0.3537 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3762 Z= 0.108 Angle : 0.526 7.279 5360 Z= 0.280 Chirality : 0.037 0.134 610 Planarity : 0.005 0.037 484 Dihedral : 24.009 172.003 1121 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.21 % Allowed : 20.24 % Favored : 78.54 % 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: 0.06 (0.50), residues: 296 helix: -0.00 (0.52), residues: 105 sheet: 0.04 (0.96), residues: 32 loop : 0.24 (0.52), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 264 HIS 0.001 0.001 HIS A 253 PHE 0.007 0.001 PHE A 335 TYR 0.007 0.001 TYR A 265 ARG 0.003 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 106) hydrogen bonds : angle 3.80444 ( 260) covalent geometry : bond 0.00239 ( 3762) covalent geometry : angle 0.52624 ( 5360) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2575.64 seconds wall clock time: 45 minutes 9.09 seconds (2709.09 seconds total)