Starting phenix.real_space_refine on Thu Jun 5 14:18:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zaq_39884/06_2025/8zaq_39884_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zaq_39884/06_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_39884/06_2025/8zaq_39884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zaq_39884/06_2025/8zaq_39884.map" model { file = "/net/cci-nas-00/data/ceres_data/8zaq_39884/06_2025/8zaq_39884_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zaq_39884/06_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.71, per 1000 atoms: 1.51 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: 1.78 Conformation dependent library (CDL) restraints added in 902.7 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: 0.55 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: 2.21 Time building geometry restraints manager: 2.09 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: 40.150 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.910 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:15.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.170 ------------------------------------------------------------------------------- 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 6643 Z= 0.161 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 Details of bonding type rmsd hydrogen bonds : bond 0.14641 ( 427) hydrogen bonds : angle 6.74892 ( 1272) covalent geometry : bond 0.00335 ( 6640) covalent geometry : angle 0.58718 ( 9049) Misc. bond : bond 0.00062 ( 3) *********************** 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 : 0.643 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: 1.0180 time to fit residues: 75.1651 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 : 0.687 ------------------------------------------------------------------------------- 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 = 6320.929| |-----------------------------------------------------------------------------| 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 6643 Z= 0.194 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 Details of bonding type rmsd hydrogen bonds : bond 0.05342 ( 427) hydrogen bonds : angle 4.69985 ( 1272) covalent geometry : bond 0.00444 ( 6640) covalent geometry : angle 0.57885 ( 9049) Misc. bond : bond 0.00019 ( 3) *********************** 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 : 0.603 Fit side-chains REVERT: A 183 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6786 (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: 0.6816 (mttp) outliers start: 25 outliers final: 15 residues processed: 84 average time/residue: 1.2858 time to fit residues: 115.5780 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 : 0.633 ------------------------------------------------------------------------------- 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: 0.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.130851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.117455 restraints weight = 6143.057| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 0.92 r_work: 0.3334 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6643 Z= 0.159 Angle : 0.537 5.964 9049 Z= 0.270 Chirality : 0.040 0.180 930 Planarity : 0.005 0.049 1111 Dihedral : 11.545 111.170 902 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.89 % Allowed : 16.89 % Favored : 79.22 % 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: 2.37 (0.29), residues: 768 helix: 1.96 (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 0.010 0.001 TRP C 190 HIS 0.002 0.000 HIS A 225 PHE 0.011 0.001 PHE C 134 TYR 0.009 0.002 TYR B 22 ARG 0.003 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.04937 ( 427) hydrogen bonds : angle 4.56152 ( 1272) covalent geometry : bond 0.00361 ( 6640) covalent geometry : angle 0.53746 ( 9049) Misc. bond : bond 0.00017 ( 3) *********************** 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 91 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.717 Fit side-chains REVERT: A 183 LYS cc_start: 0.6915 (OUTLIER) cc_final: 0.6670 (mttp) REVERT: B 183 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6731 (mttp) REVERT: C 183 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6700 (mttp) outliers start: 26 outliers final: 14 residues processed: 87 average time/residue: 1.0260 time to fit residues: 95.4903 Evaluate side-chains 77 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 5 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.122505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.107985 restraints weight = 6394.178| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 0.96 r_work: 0.3326 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6643 Z= 0.146 Angle : 0.526 5.971 9049 Z= 0.263 Chirality : 0.040 0.165 930 Planarity : 0.005 0.048 1111 Dihedral : 11.511 110.784 902 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.63 % Allowed : 16.89 % 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: 2.52 (0.29), residues: 768 helix: 2.09 (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 176 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 427) hydrogen bonds : angle 4.46453 ( 1272) covalent geometry : bond 0.00323 ( 6640) covalent geometry : angle 0.52589 ( 9049) Misc. bond : bond 0.00015 ( 3) *********************** 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 98 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.656 Fit side-chains REVERT: A 183 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6719 (mttp) REVERT: B 183 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6792 (mttp) REVERT: C 183 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6734 (mttp) outliers start: 31 outliers final: 15 residues processed: 93 average time/residue: 0.9687 time to fit residues: 95.8948 Evaluate side-chains 80 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 24 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.125034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.111154 restraints weight = 6238.426| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 0.92 r_work: 0.3313 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6643 Z= 0.143 Angle : 0.529 5.951 9049 Z= 0.262 Chirality : 0.039 0.169 930 Planarity : 0.005 0.047 1111 Dihedral : 11.421 110.467 902 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.89 % Allowed : 17.49 % 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: 2.59 (0.29), residues: 768 helix: 2.15 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.92 (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 B 225 PHE 0.011 0.001 PHE A 134 TYR 0.009 0.001 TYR B 22 ARG 0.002 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.04700 ( 427) hydrogen bonds : angle 4.42291 ( 1272) covalent geometry : bond 0.00316 ( 6640) covalent geometry : angle 0.52850 ( 9049) Misc. bond : bond 0.00009 ( 3) *********************** 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 87 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.678 Fit side-chains REVERT: A 183 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6805 (mttp) REVERT: B 183 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6878 (mttp) REVERT: C 183 LYS cc_start: 0.6915 (OUTLIER) cc_final: 0.6643 (mttp) outliers start: 26 outliers final: 15 residues processed: 85 average time/residue: 0.9962 time to fit residues: 90.0761 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 : 0.645 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 43 optimal weight: 0.0370 chunk 62 optimal weight: 0.5980 chunk 25 optimal weight: 0.0270 chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.122060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.107832 restraints weight = 6207.528| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 0.88 r_work: 0.3369 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6643 Z= 0.122 Angle : 0.505 5.893 9049 Z= 0.250 Chirality : 0.038 0.159 930 Planarity : 0.005 0.046 1111 Dihedral : 11.360 110.382 902 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.04 % Allowed : 17.94 % Favored : 78.03 % 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: 2.73 (0.30), residues: 768 helix: 2.27 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.94 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 42 HIS 0.001 0.000 HIS A 225 PHE 0.011 0.001 PHE A 134 TYR 0.007 0.001 TYR B 45 ARG 0.002 0.000 ARG C 186 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 427) hydrogen bonds : angle 4.34735 ( 1272) covalent geometry : bond 0.00264 ( 6640) covalent geometry : angle 0.50550 ( 9049) Misc. bond : bond 0.00017 ( 3) *********************** 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 94 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.736 Fit side-chains REVERT: B 183 LYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6751 (mttp) REVERT: C 183 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6746 (mttp) outliers start: 27 outliers final: 17 residues processed: 91 average time/residue: 0.9190 time to fit residues: 89.3038 Evaluate side-chains 78 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 5 ASP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.0050 chunk 48 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 0.7994 ------------------------------------------------------------------------------- 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 = 0.3281 r_free = 0.3281 target = 0.120169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.105736 restraints weight = 6189.997| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 0.89 r_work: 0.3353 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6643 Z= 0.145 Angle : 0.533 5.955 9049 Z= 0.264 Chirality : 0.039 0.168 930 Planarity : 0.005 0.046 1111 Dihedral : 11.155 109.676 898 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.44 % Allowed : 18.09 % 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: 2.66 (0.29), residues: 768 helix: 2.21 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.94 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 138 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 C 186 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 427) hydrogen bonds : angle 4.35950 ( 1272) covalent geometry : bond 0.00327 ( 6640) covalent geometry : angle 0.53316 ( 9049) Misc. bond : bond 0.00013 ( 3) *********************** 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 84 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.611 Fit side-chains REVERT: B 183 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6821 (mttp) REVERT: C 183 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6773 (mttp) REVERT: C 230 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.6948 (mp) outliers start: 23 outliers final: 16 residues processed: 80 average time/residue: 1.0497 time to fit residues: 89.3542 Evaluate side-chains 78 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3281 r_free = 0.3281 target = 0.120153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.105678 restraints weight = 6242.705| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 0.89 r_work: 0.3351 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6643 Z= 0.146 Angle : 0.536 6.721 9049 Z= 0.265 Chirality : 0.040 0.168 930 Planarity : 0.005 0.046 1111 Dihedral : 11.166 109.546 898 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.14 % Allowed : 18.24 % 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: 2.64 (0.29), residues: 768 helix: 2.18 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.97 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 190 HIS 0.002 0.000 HIS C 225 PHE 0.023 0.001 PHE A 144 TYR 0.010 0.001 TYR B 22 ARG 0.001 0.000 ARG C 186 Details of bonding type rmsd hydrogen bonds : bond 0.04655 ( 427) hydrogen bonds : angle 4.36565 ( 1272) covalent geometry : bond 0.00328 ( 6640) covalent geometry : angle 0.53583 ( 9049) Misc. bond : bond 0.00011 ( 3) *********************** 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 83 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.642 Fit side-chains REVERT: B 183 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6818 (mttp) REVERT: C 183 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6759 (mttp) outliers start: 21 outliers final: 17 residues processed: 80 average time/residue: 0.9509 time to fit residues: 81.1639 Evaluate side-chains 81 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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: 0.6980 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3274 r_free = 0.3274 target = 0.119544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.105033 restraints weight = 6260.292| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 0.90 r_work: 0.3345 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6643 Z= 0.153 Angle : 0.535 5.976 9049 Z= 0.266 Chirality : 0.040 0.170 930 Planarity : 0.005 0.046 1111 Dihedral : 11.160 109.120 898 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.99 % Allowed : 18.24 % 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: 2.61 (0.29), residues: 768 helix: 2.15 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.96 (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 0.027 0.001 PHE A 144 TYR 0.010 0.001 TYR B 22 ARG 0.002 0.000 ARG B 176 Details of bonding type rmsd hydrogen bonds : bond 0.04743 ( 427) hydrogen bonds : angle 4.37378 ( 1272) covalent geometry : bond 0.00346 ( 6640) covalent geometry : angle 0.53471 ( 9049) Misc. bond : bond 0.00011 ( 3) *********************** 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 81 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.924 Fit side-chains REVERT: B 170 MET cc_start: 0.8223 (tmm) cc_final: 0.7894 (tpt) REVERT: B 183 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6852 (mttp) REVERT: C 183 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6794 (mttp) outliers start: 20 outliers final: 16 residues processed: 78 average time/residue: 1.3637 time to fit residues: 113.3583 Evaluate side-chains 79 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- 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: 0.7980 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 26 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.120904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.106571 restraints weight = 6242.665| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 0.90 r_work: 0.3262 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6643 Z= 0.149 Angle : 0.532 5.964 9049 Z= 0.265 Chirality : 0.040 0.170 930 Planarity : 0.005 0.046 1111 Dihedral : 11.165 109.017 898 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.44 % Allowed : 18.09 % 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: 2.61 (0.29), residues: 768 helix: 2.15 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.96 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 190 HIS 0.002 0.000 HIS C 225 PHE 0.027 0.001 PHE A 144 TYR 0.010 0.001 TYR B 22 ARG 0.001 0.000 ARG B 176 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 427) hydrogen bonds : angle 4.39351 ( 1272) covalent geometry : bond 0.00335 ( 6640) covalent geometry : angle 0.53235 ( 9049) Misc. bond : bond 0.00010 ( 3) ********************** 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: 23 poor density : 60 time to evaluate : 0.707 Fit side-chains REVERT: B 170 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7893 (tpt) REVERT: B 183 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6833 (mttp) outliers start: 23 outliers final: 18 residues processed: 79 average time/residue: 1.4563 time to fit residues: 123.1186 Evaluate side-chains 79 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 1.793 ------------------------------------------------------------------------------- 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 109 THR 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 170 MET 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 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: 0.0570 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- 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 = 0.3289 r_free = 0.3289 target = 0.119976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.105597 restraints weight = 6292.171| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 0.90 r_work: 0.3249 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6643 Z= 0.163 Angle : 0.546 5.997 9049 Z= 0.273 Chirality : 0.041 0.174 930 Planarity : 0.005 0.046 1111 Dihedral : 10.981 108.464 894 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.44 % Allowed : 18.24 % 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: 2.53 (0.29), residues: 768 helix: 2.08 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.95 (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 0.028 0.002 PHE A 144 TYR 0.011 0.002 TYR B 22 ARG 0.001 0.000 ARG B 176 Details of bonding type rmsd hydrogen bonds : bond 0.04864 ( 427) hydrogen bonds : angle 4.42455 ( 1272) covalent geometry : bond 0.00372 ( 6640) covalent geometry : angle 0.54603 ( 9049) Misc. bond : bond 0.00011 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7412.65 seconds wall clock time: 132 minutes 48.06 seconds (7968.06 seconds total)