Starting phenix.real_space_refine on Tue Feb 11 17:12:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zaq_39884/02_2025/8zaq_39884_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zaq_39884/02_2025/8zaq_39884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zaq_39884/02_2025/8zaq_39884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zaq_39884/02_2025/8zaq_39884.map" model { file = "/net/cci-nas-00/data/ceres_data/8zaq_39884/02_2025/8zaq_39884_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zaq_39884/02_2025/8zaq_39884_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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 K 24 8.98 5 S 57 5.16 5 C 4327 2.51 5 N 965 2.21 5 O 1076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6449 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2110 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain: "B" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2110 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain: "C" Number of atoms: 2106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2106 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 16, 'TRANS': 241} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 29 Unusual residues: {' K': 8, 'RET': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 29 Unusual residues: {' K': 8, 'RET': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 29 Unusual residues: {' K': 8, 'RET': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 9.17, per 1000 atoms: 1.42 Number of scatterers: 6449 At special positions: 0 Unit cell: (74.55, 74.2, 79.45, 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) K 24 19.00 S 57 16.00 O 1076 8.00 N 965 7.00 C 4327 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 936.1 milliseconds 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1434 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 74.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 21 through 50 removed outlier: 3.750A pdb=" N GLY A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 68 through 90 Processing helix chain 'A' and resid 105 through 122 Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 149 through 178 removed outlier: 3.753A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Proline residue: A 164 - end of helix removed outlier: 3.510A pdb=" N ARG A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 199 Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.515A pdb=" N ILE A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'B' and resid 21 through 50 removed outlier: 3.750A pdb=" N GLY B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 67 Processing helix chain 'B' and resid 68 through 90 Processing helix chain 'B' and resid 105 through 122 Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 149 through 178 removed outlier: 3.751A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Proline residue: B 164 - end of helix removed outlier: 3.569A pdb=" N LEU B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 199 Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.506A pdb=" N ILE B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'C' and resid 21 through 49 Processing helix chain 'C' and resid 64 through 67 Processing helix chain 'C' and resid 68 through 90 Processing helix chain 'C' and resid 105 through 122 Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 149 through 178 removed outlier: 3.750A pdb=" N ALA C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) Proline residue: C 164 - end of helix removed outlier: 3.518A pdb=" N ARG C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 199 Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.522A pdb=" N ILE C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 Processing helix chain 'C' and resid 233 through 252 427 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.81 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1774 1.34 - 1.46: 1546 1.46 - 1.57: 3242 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 6640 Sorted by residual: bond pdb=" CA PHE A 202 " pdb=" C PHE A 202 " ideal model delta sigma weight residual 1.520 1.531 -0.011 1.23e-02 6.61e+03 7.84e-01 bond pdb=" CA PHE B 202 " pdb=" C PHE B 202 " ideal model delta sigma weight residual 1.520 1.531 -0.010 1.23e-02 6.61e+03 7.18e-01 bond pdb=" CA GLY C 158 " pdb=" C GLY C 158 " ideal model delta sigma weight residual 1.516 1.507 0.009 1.12e-02 7.97e+03 6.77e-01 bond pdb=" C LEU A 49 " pdb=" N GLY A 50 " ideal model delta sigma weight residual 1.321 1.331 -0.011 1.30e-02 5.92e+03 6.55e-01 bond pdb=" CA PHE C 202 " pdb=" C PHE C 202 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.23e-02 6.61e+03 6.50e-01 ... (remaining 6635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 8777 1.48 - 2.96: 232 2.96 - 4.44: 25 4.44 - 5.92: 13 5.92 - 7.39: 2 Bond angle restraints: 9049 Sorted by residual: angle pdb=" C GLY A 93 " pdb=" N THR A 94 " pdb=" CA THR A 94 " ideal model delta sigma weight residual 120.49 127.88 -7.39 1.42e+00 4.96e-01 2.71e+01 angle pdb=" C GLY C 93 " pdb=" N THR C 94 " pdb=" CA THR C 94 " ideal model delta sigma weight residual 120.49 127.67 -7.18 1.42e+00 4.96e-01 2.55e+01 angle pdb=" N VAL C 107 " pdb=" CA VAL C 107 " pdb=" C VAL C 107 " ideal model delta sigma weight residual 113.00 108.95 4.05 1.30e+00 5.92e-01 9.69e+00 angle pdb=" N VAL A 107 " pdb=" CA VAL A 107 " pdb=" C VAL A 107 " ideal model delta sigma weight residual 113.00 109.21 3.79 1.30e+00 5.92e-01 8.49e+00 angle pdb=" N VAL B 107 " pdb=" CA VAL B 107 " pdb=" C VAL B 107 " ideal model delta sigma weight residual 113.00 109.37 3.63 1.30e+00 5.92e-01 7.82e+00 ... (remaining 9044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.46: 3342 22.46 - 44.93: 303 44.93 - 67.39: 52 67.39 - 89.85: 6 89.85 - 112.31: 3 Dihedral angle restraints: 3706 sinusoidal: 1452 harmonic: 2254 Sorted by residual: dihedral pdb=" C1 RET B 309 " pdb=" C2 RET B 309 " pdb=" C3 RET B 309 " pdb=" C4 RET B 309 " ideal model delta sinusoidal sigma weight residual -62.54 49.77 -112.31 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C1 RET C 309 " pdb=" C2 RET C 309 " pdb=" C3 RET C 309 " pdb=" C4 RET C 309 " ideal model delta sinusoidal sigma weight residual -62.54 49.71 -112.25 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C1 RET A 309 " pdb=" C2 RET A 309 " pdb=" C3 RET A 309 " pdb=" C4 RET A 309 " ideal model delta sinusoidal sigma weight residual -62.54 49.63 -112.17 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 3703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 521 0.028 - 0.055: 274 0.055 - 0.083: 96 0.083 - 0.111: 31 0.111 - 0.138: 8 Chirality restraints: 930 Sorted by residual: chirality pdb=" CA THR B 110 " pdb=" N THR B 110 " pdb=" C THR B 110 " pdb=" CB THR B 110 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA THR C 110 " pdb=" N THR C 110 " pdb=" C THR C 110 " pdb=" CB THR C 110 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 927 not shown) Planarity restraints: 1111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 181 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO C 182 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 182 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 182 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 181 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO B 182 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 182 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 182 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 181 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO A 182 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 182 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 182 " -0.023 5.00e-02 4.00e+02 ... (remaining 1108 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.90: 6 1.90 - 2.71: 224 2.71 - 3.52: 11554 3.52 - 4.33: 22374 4.33 - 5.14: 37445 Nonbonded interactions: 71603 Sorted by model distance: nonbonded pdb=" K K B 305 " pdb=" O HOH B 409 " model vdw 1.092 2.850 nonbonded pdb=" K K C 305 " pdb=" O HOH C 409 " model vdw 1.094 2.850 nonbonded pdb=" K K A 305 " pdb=" O HOH A 409 " model vdw 1.098 2.850 nonbonded pdb=" CE2 PHE B 195 " pdb=" O HOH B 412 " model vdw 1.863 3.340 nonbonded pdb=" CE2 PHE A 195 " pdb=" O HOH A 412 " model vdw 1.869 3.340 ... (remaining 71598 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 49 or resid 51 through 260 or resid 301 through \ 309)) selection = (chain 'B' and (resid 2 through 49 or resid 51 through 260 or resid 301 through \ 309)) selection = chain 'C' } 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: 23.120 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: 0.390 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 23.340 Find NCS groups from input model: 0.260 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:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 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 0.030 6640 Z= 0.210 Angle : 0.587 7.395 9049 Z= 0.336 Chirality : 0.040 0.138 930 Planarity : 0.006 0.043 1111 Dihedral : 16.953 112.314 2272 Min Nonbonded Distance : 1.092 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.39 % Allowed : 19.28 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.30), residues: 768 helix: 1.09 (0.22), residues: 517 sheet: None (None), residues: 0 loop : 1.07 (0.43), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 190 HIS 0.002 0.001 HIS A 225 PHE 0.011 0.001 PHE C 134 TYR 0.013 0.002 TYR C 81 ARG 0.001 0.000 ARG C 151 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.689 Fit side-chains REVERT: A 76 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8667 (tp) REVERT: A 114 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8075 (mm) REVERT: A 183 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6884 (mttp) REVERT: B 183 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6941 (mttp) REVERT: C 76 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8639 (tp) REVERT: C 183 LYS cc_start: 0.7110 (OUTLIER) cc_final: 0.6898 (mttp) outliers start: 16 outliers final: 8 residues processed: 69 average time/residue: 1.0039 time to fit residues: 74.0790 Evaluate side-chains 70 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.0570 chunk 68 optimal weight: 3.9990 overall best weight: 1.3104 ------------------------------------------------------------------------------- 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 = 0.3285 r_free = 0.3285 target = 0.119343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.105168 restraints weight = 6320.928| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 0.89 r_work: 0.3278 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6640 Z= 0.278 Angle : 0.579 5.902 9049 Z= 0.294 Chirality : 0.042 0.168 930 Planarity : 0.006 0.048 1111 Dihedral : 11.820 112.304 909 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.74 % Allowed : 15.84 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.29), residues: 768 helix: 1.62 (0.20), residues: 523 sheet: None (None), residues: 0 loop : 0.88 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 138 HIS 0.002 0.001 HIS A 225 PHE 0.011 0.002 PHE C 144 TYR 0.011 0.002 TYR B 22 ARG 0.004 0.001 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.728 Fit side-chains REVERT: A 183 LYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6785 (mttp) REVERT: B 183 LYS cc_start: 0.7107 (OUTLIER) cc_final: 0.6866 (mttp) REVERT: C 183 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6815 (mttp) outliers start: 25 outliers final: 15 residues processed: 84 average time/residue: 1.0178 time to fit residues: 91.0754 Evaluate side-chains 77 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3296 r_free = 0.3296 target = 0.120350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.106063 restraints weight = 6343.517| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 0.90 r_work: 0.3288 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6640 Z= 0.232 Angle : 0.542 5.941 9049 Z= 0.272 Chirality : 0.040 0.181 930 Planarity : 0.005 0.049 1111 Dihedral : 11.557 111.123 902 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.04 % Allowed : 16.44 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.29), residues: 768 helix: 1.95 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.89 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 190 HIS 0.002 0.000 HIS A 225 PHE 0.011 0.001 PHE C 134 TYR 0.010 0.002 TYR B 22 ARG 0.002 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.692 Fit side-chains REVERT: A 183 LYS cc_start: 0.6972 (OUTLIER) cc_final: 0.6704 (mttp) REVERT: B 183 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6792 (mttp) REVERT: C 183 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6751 (mttp) outliers start: 27 outliers final: 16 residues processed: 89 average time/residue: 1.0044 time to fit residues: 95.4658 Evaluate side-chains 79 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 5 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.122304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.107809 restraints weight = 6398.339| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 0.96 r_work: 0.3337 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6640 Z= 0.203 Angle : 0.528 5.988 9049 Z= 0.263 Chirality : 0.039 0.166 930 Planarity : 0.005 0.049 1111 Dihedral : 11.496 110.768 902 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.48 % Allowed : 16.74 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.29), residues: 768 helix: 2.08 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.89 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 190 HIS 0.002 0.000 HIS A 225 PHE 0.011 0.001 PHE C 134 TYR 0.009 0.001 TYR B 22 ARG 0.002 0.000 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.689 Fit side-chains REVERT: A 183 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6752 (mttp) REVERT: B 174 LYS cc_start: 0.7868 (mttt) cc_final: 0.7652 (mttt) REVERT: B 183 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6697 (mttp) REVERT: C 183 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6615 (mttp) outliers start: 30 outliers final: 15 residues processed: 93 average time/residue: 1.0721 time to fit residues: 105.7603 Evaluate side-chains 81 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 24 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.124800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.110974 restraints weight = 6265.821| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 0.94 r_work: 0.3235 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6640 Z= 0.237 Angle : 0.546 6.004 9049 Z= 0.272 Chirality : 0.040 0.178 930 Planarity : 0.005 0.049 1111 Dihedral : 11.432 110.278 902 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.74 % Allowed : 17.34 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.29), residues: 768 helix: 2.05 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.88 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 190 HIS 0.002 0.001 HIS A 225 PHE 0.010 0.001 PHE A 134 TYR 0.011 0.002 TYR B 22 ARG 0.002 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.664 Fit side-chains REVERT: A 183 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6817 (mttp) REVERT: B 174 LYS cc_start: 0.7987 (mttt) cc_final: 0.7768 (mttt) REVERT: B 183 LYS cc_start: 0.7135 (OUTLIER) cc_final: 0.6904 (mttp) REVERT: C 183 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6818 (mttp) outliers start: 25 outliers final: 14 residues processed: 86 average time/residue: 1.0162 time to fit residues: 92.9532 Evaluate side-chains 79 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 43 optimal weight: 0.0980 chunk 62 optimal weight: 0.8980 chunk 25 optimal weight: 0.0030 chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 = 0.3319 r_free = 0.3319 target = 0.122523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.108376 restraints weight = 6216.199| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 0.88 r_work: 0.3360 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6640 Z= 0.164 Angle : 0.505 5.814 9049 Z= 0.250 Chirality : 0.038 0.158 930 Planarity : 0.005 0.047 1111 Dihedral : 11.387 110.374 902 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.74 % Allowed : 17.64 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.30), residues: 768 helix: 2.27 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.87 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 42 HIS 0.001 0.000 HIS A 225 PHE 0.011 0.001 PHE A 134 TYR 0.008 0.001 TYR B 22 ARG 0.001 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.716 Fit side-chains REVERT: B 183 LYS cc_start: 0.6986 (OUTLIER) cc_final: 0.6773 (mttp) REVERT: C 183 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6714 (mttp) outliers start: 25 outliers final: 15 residues processed: 89 average time/residue: 0.9918 time to fit residues: 94.2409 Evaluate side-chains 76 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.140448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127891 restraints weight = 5743.080| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 0.84 r_work: 0.3245 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6640 Z= 0.246 Angle : 0.551 6.017 9049 Z= 0.274 Chirality : 0.041 0.174 930 Planarity : 0.005 0.048 1111 Dihedral : 11.195 109.292 898 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 4.04 % Allowed : 17.34 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.29), residues: 768 helix: 2.11 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.86 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 138 HIS 0.002 0.001 HIS A 225 PHE 0.010 0.001 PHE A 134 TYR 0.011 0.002 TYR B 22 ARG 0.001 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 0.663 Fit side-chains REVERT: B 183 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6884 (mttp) REVERT: C 183 LYS cc_start: 0.7017 (OUTLIER) cc_final: 0.6815 (mttp) REVERT: C 230 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7057 (mp) outliers start: 27 outliers final: 17 residues processed: 83 average time/residue: 0.9935 time to fit residues: 87.9024 Evaluate side-chains 81 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 230 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.124554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111156 restraints weight = 6286.119| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 0.86 r_work: 0.3351 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6640 Z= 0.210 Angle : 0.537 5.899 9049 Z= 0.266 Chirality : 0.040 0.170 930 Planarity : 0.005 0.048 1111 Dihedral : 11.205 109.451 898 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.14 % Allowed : 18.39 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.29), residues: 768 helix: 2.13 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.89 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 190 HIS 0.002 0.000 HIS A 225 PHE 0.010 0.001 PHE A 134 TYR 0.010 0.001 TYR B 22 ARG 0.001 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.689 Fit side-chains REVERT: B 183 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6870 (mttp) REVERT: C 183 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6790 (mttp) outliers start: 21 outliers final: 17 residues processed: 80 average time/residue: 1.0606 time to fit residues: 90.1735 Evaluate side-chains 80 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 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 = 0.3598 r_free = 0.3598 target = 0.138677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.126330 restraints weight = 5929.366| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 0.82 r_work: 0.3344 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6640 Z= 0.207 Angle : 0.536 5.956 9049 Z= 0.266 Chirality : 0.040 0.168 930 Planarity : 0.005 0.047 1111 Dihedral : 11.190 109.011 898 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.29 % Allowed : 18.09 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.29), residues: 768 helix: 2.13 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.90 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 190 HIS 0.002 0.000 HIS C 225 PHE 0.025 0.001 PHE A 144 TYR 0.010 0.001 TYR B 22 ARG 0.001 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.790 Fit side-chains REVERT: B 183 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6806 (mttp) REVERT: C 183 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6722 (mttp) outliers start: 22 outliers final: 18 residues processed: 80 average time/residue: 1.1227 time to fit residues: 95.8392 Evaluate side-chains 80 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 16 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 70 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- 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 = 0.3352 r_free = 0.3352 target = 0.123759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.109992 restraints weight = 6317.127| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 0.88 r_work: 0.3334 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6640 Z= 0.213 Angle : 0.538 5.972 9049 Z= 0.267 Chirality : 0.040 0.171 930 Planarity : 0.005 0.047 1111 Dihedral : 11.182 108.580 898 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.14 % Allowed : 18.09 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.29), residues: 768 helix: 2.10 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.91 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 190 HIS 0.002 0.000 HIS C 225 PHE 0.025 0.001 PHE A 144 TYR 0.010 0.001 TYR B 22 ARG 0.001 0.000 ARG A 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.837 Fit side-chains REVERT: B 183 LYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6813 (mttp) REVERT: C 183 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6730 (mttp) outliers start: 21 outliers final: 18 residues processed: 80 average time/residue: 1.0705 time to fit residues: 91.1618 Evaluate side-chains 81 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.122867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.109315 restraints weight = 6339.547| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 0.87 r_work: 0.3310 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6640 Z= 0.268 Angle : 0.568 6.058 9049 Z= 0.284 Chirality : 0.042 0.180 930 Planarity : 0.005 0.048 1111 Dihedral : 11.199 107.901 898 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.29 % Allowed : 17.79 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.29), residues: 768 helix: 1.97 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.88 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 190 HIS 0.002 0.001 HIS A 225 PHE 0.033 0.002 PHE A 144 TYR 0.012 0.002 TYR B 22 ARG 0.001 0.000 ARG C 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5266.91 seconds wall clock time: 95 minutes 7.10 seconds (5707.10 seconds total)