Starting phenix.real_space_refine on Sat Apr 26 22:04:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ws6_37799/04_2025/8ws6_37799.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ws6_37799/04_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_37799/04_2025/8ws6_37799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ws6_37799/04_2025/8ws6_37799.map" model { file = "/net/cci-nas-00/data/ceres_data/8ws6_37799/04_2025/8ws6_37799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ws6_37799/04_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-5669/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: 6.23, per 1000 atoms: 1.75 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: 1.09 Conformation dependent library (CDL) restraints added in 301.3 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: 1.46 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: 1.11 Time building geometry restraints manager: 1.27 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: 7.420 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.580 Find NCS groups from input model: 0.050 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:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.530 ------------------------------------------------------------------------------- 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 : 0.329 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: 0.2850 time to fit residues: 14.7399 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 : 0.269 ------------------------------------------------------------------------------- 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: 0.9990 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: 1.9990 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.147508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124041 restraints weight = 5130.802| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.57 r_work: 0.3445 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3762 Z= 0.278 Angle : 0.709 5.282 5360 Z= 0.382 Chirality : 0.046 0.177 610 Planarity : 0.008 0.055 484 Dihedral : 24.294 173.081 1121 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.21 % Allowed : 11.74 % Favored : 87.04 % 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: -1.37 (0.48), residues: 296 helix: -1.53 (0.47), residues: 103 sheet: -0.12 (1.06), residues: 31 loop : -0.52 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 112 HIS 0.005 0.001 HIS A 214 PHE 0.015 0.003 PHE A 335 TYR 0.018 0.003 TYR A 140 ARG 0.004 0.001 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.05840 ( 106) hydrogen bonds : angle 4.95476 ( 260) covalent geometry : bond 0.00622 ( 3762) covalent geometry : angle 0.70911 ( 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 : 0.275 Fit side-chains REVERT: A 134 ARG cc_start: 0.7849 (tmm-80) cc_final: 0.7636 (ttp-110) REVERT: A 261 ILE cc_start: 0.7814 (tt) cc_final: 0.7566 (pt) outliers start: 3 outliers final: 2 residues processed: 44 average time/residue: 0.2321 time to fit residues: 11.9669 Evaluate side-chains 45 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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: 0.0870 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 0.0370 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 24 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 overall best weight: 0.2436 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.154993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.132801 restraints weight = 5135.720| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.36 r_work: 0.3521 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3762 Z= 0.134 Angle : 0.574 6.547 5360 Z= 0.312 Chirality : 0.039 0.136 610 Planarity : 0.006 0.045 484 Dihedral : 24.241 173.919 1121 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.62 % Allowed : 14.17 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.49), residues: 296 helix: -0.86 (0.50), residues: 103 sheet: 0.42 (1.08), residues: 31 loop : -0.31 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 264 HIS 0.002 0.001 HIS A 135 PHE 0.008 0.001 PHE A 335 TYR 0.009 0.001 TYR A 265 ARG 0.002 0.000 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 106) hydrogen bonds : angle 4.27228 ( 260) covalent geometry : bond 0.00296 ( 3762) covalent geometry : angle 0.57448 ( 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 45 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.301 Fit side-chains REVERT: A 106 ARG cc_start: 0.8036 (tpt90) cc_final: 0.7820 (tpt90) REVERT: A 134 ARG cc_start: 0.7809 (tmm-80) cc_final: 0.7502 (ttp-110) outliers start: 4 outliers final: 1 residues processed: 42 average time/residue: 0.2320 time to fit residues: 11.3609 Evaluate side-chains 39 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.0030 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 26 optimal weight: 0.0040 chunk 21 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 overall best weight: 0.2000 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.155608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.133673 restraints weight = 5103.950| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.36 r_work: 0.3532 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3762 Z= 0.127 Angle : 0.553 6.356 5360 Z= 0.299 Chirality : 0.038 0.140 610 Planarity : 0.006 0.042 484 Dihedral : 24.158 173.879 1121 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.02 % Allowed : 14.17 % Favored : 83.81 % 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: -0.35 (0.50), residues: 296 helix: -0.50 (0.51), residues: 103 sheet: 0.64 (1.17), residues: 29 loop : -0.08 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 264 HIS 0.002 0.001 HIS A 135 PHE 0.007 0.001 PHE A 335 TYR 0.007 0.001 TYR A 265 ARG 0.009 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 106) hydrogen bonds : angle 4.03767 ( 260) covalent geometry : bond 0.00282 ( 3762) covalent geometry : angle 0.55272 ( 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 47 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7852 (tmm-80) cc_final: 0.7520 (ttp-110) REVERT: A 331 LEU cc_start: 0.7517 (tp) cc_final: 0.7171 (tt) outliers start: 5 outliers final: 4 residues processed: 45 average time/residue: 0.2527 time to fit residues: 13.1990 Evaluate side-chains 44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 166 GLU Chi-restraints excluded: chain A residue 255 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.148928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.125525 restraints weight = 5232.832| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.54 r_work: 0.3454 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3762 Z= 0.197 Angle : 0.605 6.142 5360 Z= 0.322 Chirality : 0.041 0.135 610 Planarity : 0.006 0.039 484 Dihedral : 24.153 173.488 1121 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.64 % Allowed : 13.77 % 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: -0.49 (0.49), residues: 296 helix: -0.80 (0.51), residues: 103 sheet: 0.10 (1.08), residues: 30 loop : 0.08 (0.49), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 264 HIS 0.002 0.001 HIS A 135 PHE 0.013 0.002 PHE A 350 TYR 0.009 0.002 TYR A 265 ARG 0.005 0.000 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 106) hydrogen bonds : angle 4.16562 ( 260) covalent geometry : bond 0.00440 ( 3762) covalent geometry : angle 0.60501 ( 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 50 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7975 (tmm-80) cc_final: 0.7629 (ttp-110) REVERT: A 279 VAL cc_start: 0.6683 (OUTLIER) cc_final: 0.6417 (p) REVERT: A 331 LEU cc_start: 0.7482 (tp) cc_final: 0.7133 (tt) outliers start: 9 outliers final: 3 residues processed: 46 average time/residue: 0.2542 time to fit residues: 13.4718 Evaluate side-chains 44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 30.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.146402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.122893 restraints weight = 5246.910| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.57 r_work: 0.3423 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3762 Z= 0.284 Angle : 0.679 6.089 5360 Z= 0.360 Chirality : 0.046 0.165 610 Planarity : 0.007 0.042 484 Dihedral : 24.340 173.000 1121 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.21 % Allowed : 17.81 % 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: -0.58 (0.49), residues: 296 helix: -0.64 (0.52), residues: 97 sheet: -0.35 (1.05), residues: 30 loop : -0.09 (0.48), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 264 HIS 0.002 0.001 HIS A 214 PHE 0.013 0.003 PHE A 350 TYR 0.014 0.003 TYR A 265 ARG 0.005 0.001 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.05191 ( 106) hydrogen bonds : angle 4.28060 ( 260) covalent geometry : bond 0.00637 ( 3762) covalent geometry : angle 0.67889 ( 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 40 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8034 (tmm-80) cc_final: 0.7668 (ttp-110) outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 0.2618 time to fit residues: 11.8309 Evaluate side-chains 40 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.0970 chunk 14 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.0570 chunk 26 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.2896 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.149333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126034 restraints weight = 5165.858| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.54 r_work: 0.3475 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2561 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= 0.142 Angle : 0.570 6.789 5360 Z= 0.307 Chirality : 0.039 0.130 610 Planarity : 0.006 0.039 484 Dihedral : 24.238 172.622 1121 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.43 % Allowed : 17.41 % Favored : 80.16 % 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: -0.26 (0.50), residues: 296 helix: -0.34 (0.53), residues: 97 sheet: -0.09 (1.04), residues: 30 loop : 0.06 (0.50), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 264 HIS 0.002 0.001 HIS A 135 PHE 0.009 0.002 PHE A 350 TYR 0.011 0.001 TYR A 265 ARG 0.002 0.000 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 106) hydrogen bonds : angle 4.06999 ( 260) covalent geometry : bond 0.00318 ( 3762) covalent geometry : angle 0.57040 ( 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 44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8002 (tmm-80) cc_final: 0.7704 (ttp-110) REVERT: A 279 VAL cc_start: 0.6647 (OUTLIER) cc_final: 0.6388 (p) outliers start: 6 outliers final: 4 residues processed: 42 average time/residue: 0.2375 time to fit residues: 11.6095 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 : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 0.1980 chunk 15 optimal weight: 0.0170 chunk 11 optimal weight: 0.0040 chunk 14 optimal weight: 0.0050 chunk 16 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 0.0570 overall best weight: 0.0562 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.158125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.135883 restraints weight = 5199.115| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.41 r_work: 0.3560 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2895 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= 0.109 Angle : 0.526 7.507 5360 Z= 0.282 Chirality : 0.037 0.131 610 Planarity : 0.006 0.035 484 Dihedral : 23.914 173.210 1121 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.43 % Allowed : 17.81 % Favored : 79.76 % 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: 0.12 (0.51), residues: 296 helix: -0.12 (0.52), residues: 104 sheet: 0.28 (0.98), residues: 31 loop : 0.36 (0.54), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 264 HIS 0.001 0.000 HIS A 214 PHE 0.007 0.001 PHE A 335 TYR 0.008 0.001 TYR A 201 ARG 0.002 0.000 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.03169 ( 106) hydrogen bonds : angle 3.76764 ( 260) covalent geometry : bond 0.00239 ( 3762) covalent geometry : angle 0.52561 ( 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 44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7989 (tmm-80) cc_final: 0.7607 (ttp-110) REVERT: A 279 VAL cc_start: 0.6661 (OUTLIER) cc_final: 0.6429 (p) outliers start: 6 outliers final: 3 residues processed: 42 average time/residue: 0.2500 time to fit residues: 12.1785 Evaluate side-chains 41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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: 0.9980 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.149236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.126276 restraints weight = 5127.069| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.52 r_work: 0.3457 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3762 Z= 0.194 Angle : 0.597 6.707 5360 Z= 0.316 Chirality : 0.041 0.143 610 Planarity : 0.006 0.037 484 Dihedral : 24.095 172.419 1121 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.62 % Allowed : 18.22 % Favored : 80.16 % 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: -0.11 (0.53), residues: 97 sheet: -0.01 (1.00), residues: 30 loop : 0.16 (0.50), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 264 HIS 0.001 0.001 HIS A 214 PHE 0.012 0.002 PHE A 350 TYR 0.009 0.002 TYR A 87 ARG 0.004 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.04445 ( 106) hydrogen bonds : angle 3.92866 ( 260) covalent geometry : bond 0.00440 ( 3762) covalent geometry : angle 0.59667 ( 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 42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8045 (tmm-80) cc_final: 0.7649 (ttp-110) REVERT: A 279 VAL cc_start: 0.6636 (OUTLIER) cc_final: 0.6379 (p) REVERT: A 331 LEU cc_start: 0.7472 (tp) cc_final: 0.7124 (tt) outliers start: 4 outliers final: 3 residues processed: 41 average time/residue: 0.2814 time to fit residues: 13.2069 Evaluate side-chains 42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 0.0870 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.0370 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 23 optimal weight: 0.0870 overall best weight: 0.2014 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.151848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.129033 restraints weight = 5114.784| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.51 r_work: 0.3518 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3762 Z= 0.119 Angle : 0.536 7.303 5360 Z= 0.285 Chirality : 0.037 0.147 610 Planarity : 0.006 0.037 484 Dihedral : 24.044 171.965 1121 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.02 % Allowed : 17.81 % Favored : 80.16 % 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: 0.17 (0.50), residues: 296 helix: 0.09 (0.54), residues: 97 sheet: 0.05 (1.00), residues: 30 loop : 0.30 (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 0.006 0.001 PHE A 335 TYR 0.008 0.001 TYR A 265 ARG 0.002 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 106) hydrogen bonds : angle 3.79073 ( 260) covalent geometry : bond 0.00268 ( 3762) covalent geometry : angle 0.53589 ( 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 42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8017 (tmm-80) cc_final: 0.7618 (ttp-110) REVERT: A 279 VAL cc_start: 0.6639 (OUTLIER) cc_final: 0.6408 (p) outliers start: 5 outliers final: 4 residues processed: 40 average time/residue: 0.2890 time to fit residues: 13.2354 Evaluate side-chains 42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 263 LYS Chi-restraints excluded: chain A residue 279 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 1 optimal weight: 0.0060 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.150290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.127102 restraints weight = 5149.662| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.55 r_work: 0.3485 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3762 Z= 0.155 Angle : 0.561 6.945 5360 Z= 0.297 Chirality : 0.039 0.146 610 Planarity : 0.006 0.038 484 Dihedral : 24.076 172.021 1121 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.02 % Allowed : 17.81 % Favored : 80.16 % 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: 0.13 (0.50), residues: 296 helix: 0.06 (0.54), residues: 97 sheet: 0.02 (1.00), residues: 30 loop : 0.26 (0.50), 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 350 TYR 0.009 0.001 TYR A 265 ARG 0.003 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 106) hydrogen bonds : angle 3.83474 ( 260) covalent geometry : bond 0.00351 ( 3762) covalent geometry : angle 0.56064 ( 5360) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2715.78 seconds wall clock time: 47 minutes 5.32 seconds (2825.32 seconds total)