Starting phenix.real_space_refine on Wed Mar 12 06:22:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aw5_15691/03_2025/8aw5_15691.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aw5_15691/03_2025/8aw5_15691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8aw5_15691/03_2025/8aw5_15691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aw5_15691/03_2025/8aw5_15691.map" model { file = "/net/cci-nas-00/data/ceres_data/8aw5_15691/03_2025/8aw5_15691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aw5_15691/03_2025/8aw5_15691.cif" } resolution = 2.8 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= 0.004 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: 6 Type Number sf(0) Gaussians Fe 3 7.16 5 P 9 5.49 5 S 21 5.16 5 C 4887 2.51 5 N 975 2.21 5 O 1128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7023 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2142 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 9, 'TRANS': 256} Chain breaks: 1 Chain: "B" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2142 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 9, 'TRANS': 256} Chain breaks: 1 Chain: "C" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2142 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 9, 'TRANS': 256} Chain breaks: 1 Chain: "A" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 199 Unusual residues: {'HEM': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 199 Unusual residues: {'HEM': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 199 Unusual residues: {'HEM': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.48, per 1000 atoms: 0.64 Number of scatterers: 7023 At special positions: 0 Unit cell: (88.56, 93.48, 72.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 3 26.01 S 21 16.00 P 9 15.00 O 1128 8.00 N 975 7.00 C 4887 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: 2.29 Conformation dependent library (CDL) restraints added in 887.8 milliseconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 82.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 10 through 33 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 74 through 101 removed outlier: 3.801A pdb=" N GLU A 78 " --> pdb=" O GLN A 74 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 126 Processing helix chain 'A' and resid 133 through 167 removed outlier: 3.642A pdb=" N LEU A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 200 Processing helix chain 'A' and resid 203 through 231 removed outlier: 4.082A pdb=" N GLY A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 256 Processing helix chain 'A' and resid 259 through 287 Proline residue: A 283 - end of helix Processing helix chain 'B' and resid 11 through 33 Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 74 through 101 removed outlier: 3.800A pdb=" N GLU B 78 " --> pdb=" O GLN B 74 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 126 Processing helix chain 'B' and resid 133 through 167 removed outlier: 3.643A pdb=" N LEU B 149 " --> pdb=" O THR B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 200 Processing helix chain 'B' and resid 203 through 231 removed outlier: 4.081A pdb=" N GLY B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 256 Processing helix chain 'B' and resid 259 through 287 Proline residue: B 283 - end of helix Processing helix chain 'C' and resid 11 through 33 Processing helix chain 'C' and resid 52 through 56 Processing helix chain 'C' and resid 74 through 101 removed outlier: 3.800A pdb=" N GLU C 78 " --> pdb=" O GLN C 74 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 101 " --> pdb=" O PHE C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 126 Processing helix chain 'C' and resid 133 through 167 removed outlier: 3.642A pdb=" N LEU C 149 " --> pdb=" O THR C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 200 Processing helix chain 'C' and resid 203 through 231 removed outlier: 4.081A pdb=" N GLY C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE C 219 " --> pdb=" O THR C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 256 Processing helix chain 'C' and resid 259 through 287 Proline residue: C 283 - end of helix 523 hydrogen bonds defined for protein. 1551 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: 1.83 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 2444 1.38 - 1.55: 4708 1.55 - 1.72: 21 1.72 - 1.89: 36 1.89 - 2.06: 12 Bond restraints: 7221 Sorted by residual: bond pdb=" C21 POV C 404 " pdb=" O22 POV C 404 " ideal model delta sigma weight residual 1.205 1.438 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C21 POV A 402 " pdb=" O22 POV A 402 " ideal model delta sigma weight residual 1.205 1.438 -0.233 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C21 POV B 402 " pdb=" O22 POV B 402 " ideal model delta sigma weight residual 1.205 1.438 -0.233 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C21 POV A 404 " pdb=" O22 POV A 404 " ideal model delta sigma weight residual 1.205 1.434 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C21 POV A 403 " pdb=" O22 POV A 403 " ideal model delta sigma weight residual 1.205 1.434 -0.229 2.00e-02 2.50e+03 1.31e+02 ... (remaining 7216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 9472 3.45 - 6.90: 219 6.90 - 10.35: 29 10.35 - 13.80: 24 13.80 - 17.25: 48 Bond angle restraints: 9792 Sorted by residual: angle pdb=" N GLU C 204 " pdb=" CA GLU C 204 " pdb=" C GLU C 204 " ideal model delta sigma weight residual 111.69 99.00 12.69 1.23e+00 6.61e-01 1.07e+02 angle pdb=" N GLU A 204 " pdb=" CA GLU A 204 " pdb=" C GLU A 204 " ideal model delta sigma weight residual 111.69 99.01 12.68 1.23e+00 6.61e-01 1.06e+02 angle pdb=" N GLU B 204 " pdb=" CA GLU B 204 " pdb=" C GLU B 204 " ideal model delta sigma weight residual 112.45 98.98 13.47 1.39e+00 5.18e-01 9.39e+01 angle pdb=" N VAL C 32 " pdb=" CA VAL C 32 " pdb=" C VAL C 32 " ideal model delta sigma weight residual 111.45 103.72 7.73 9.30e-01 1.16e+00 6.92e+01 angle pdb=" N VAL B 32 " pdb=" CA VAL B 32 " pdb=" C VAL B 32 " ideal model delta sigma weight residual 111.45 103.73 7.72 9.30e-01 1.16e+00 6.89e+01 ... (remaining 9787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.36: 3951 28.36 - 56.72: 150 56.72 - 85.07: 45 85.07 - 113.43: 18 113.43 - 141.79: 6 Dihedral angle restraints: 4170 sinusoidal: 1827 harmonic: 2343 Sorted by residual: dihedral pdb=" C3 POV C 404 " pdb=" C31 POV C 404 " pdb=" O31 POV C 404 " pdb=" C32 POV C 404 " ideal model delta sinusoidal sigma weight residual 172.61 -45.60 -141.79 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" C3 POV A 402 " pdb=" C31 POV A 402 " pdb=" O31 POV A 402 " pdb=" C32 POV A 402 " ideal model delta sinusoidal sigma weight residual 172.61 -45.64 -141.75 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" C3 POV B 402 " pdb=" C31 POV B 402 " pdb=" O31 POV B 402 " pdb=" C32 POV B 402 " ideal model delta sinusoidal sigma weight residual 172.61 -45.67 -141.72 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 4167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 779 0.062 - 0.123: 235 0.123 - 0.185: 65 0.185 - 0.247: 10 0.247 - 0.309: 12 Chirality restraints: 1101 Sorted by residual: chirality pdb=" CA GLU A 204 " pdb=" N GLU A 204 " pdb=" C GLU A 204 " pdb=" CB GLU A 204 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA GLU B 204 " pdb=" N GLU B 204 " pdb=" C GLU B 204 " pdb=" CB GLU B 204 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA GLU C 204 " pdb=" N GLU C 204 " pdb=" C GLU C 204 " pdb=" CB GLU C 204 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 1098 not shown) Planarity restraints: 1095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV C 402 " -0.151 2.00e-02 2.50e+03 2.72e-01 7.38e+02 pdb=" C29 POV C 402 " 0.352 2.00e-02 2.50e+03 pdb="C210 POV C 402 " -0.354 2.00e-02 2.50e+03 pdb="C211 POV C 402 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 403 " -0.151 2.00e-02 2.50e+03 2.72e-01 7.37e+02 pdb=" C29 POV A 403 " 0.352 2.00e-02 2.50e+03 pdb="C210 POV A 403 " -0.354 2.00e-02 2.50e+03 pdb="C211 POV A 403 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B 403 " 0.150 2.00e-02 2.50e+03 2.72e-01 7.37e+02 pdb=" C29 POV B 403 " -0.352 2.00e-02 2.50e+03 pdb="C210 POV B 403 " 0.354 2.00e-02 2.50e+03 pdb="C211 POV B 403 " -0.152 2.00e-02 2.50e+03 ... (remaining 1092 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 2862 2.92 - 3.42: 7633 3.42 - 3.91: 12228 3.91 - 4.41: 13913 4.41 - 4.90: 22736 Nonbonded interactions: 59372 Sorted by model distance: nonbonded pdb=" OG SER A 157 " pdb=" OH TYR A 184 " model vdw 2.427 3.040 nonbonded pdb=" OG SER B 157 " pdb=" OH TYR B 184 " model vdw 2.427 3.040 nonbonded pdb=" OG SER C 157 " pdb=" OH TYR C 184 " model vdw 2.428 3.040 nonbonded pdb=" O GLY B 29 " pdb=" OG1 THR B 33 " model vdw 2.446 3.040 nonbonded pdb=" O GLY A 29 " pdb=" OG1 THR A 33 " model vdw 2.446 3.040 ... (remaining 59367 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 1.410 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.260 Find NCS groups from input model: 0.120 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:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 0.017 0.233 7221 Z= 0.943 Angle : 1.758 17.246 9792 Z= 0.905 Chirality : 0.070 0.309 1101 Planarity : 0.036 0.272 1095 Dihedral : 18.375 141.787 2676 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.58 % Favored : 95.04 % Rotamer: Outliers : 0.43 % Allowed : 6.06 % Favored : 93.51 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.31), residues: 786 helix: 1.25 (0.21), residues: 621 sheet: None (None), residues: 0 loop : -3.62 (0.42), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 276 HIS 0.002 0.001 HIS C 81 PHE 0.014 0.002 PHE A 272 TYR 0.010 0.001 TYR B 164 ARG 0.002 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 178 time to evaluate : 0.668 Fit side-chains REVERT: A 14 LEU cc_start: 0.8819 (mt) cc_final: 0.8500 (mt) REVERT: A 171 GLU cc_start: 0.8036 (mp0) cc_final: 0.7750 (mp0) REVERT: B 143 VAL cc_start: 0.8928 (t) cc_final: 0.8700 (t) REVERT: B 203 LEU cc_start: 0.8183 (tp) cc_final: 0.7942 (tp) REVERT: B 246 GLN cc_start: 0.9056 (tp40) cc_final: 0.8711 (tp40) REVERT: C 243 MET cc_start: 0.8768 (mmt) cc_final: 0.8409 (mmt) outliers start: 3 outliers final: 0 residues processed: 178 average time/residue: 1.0912 time to fit residues: 205.1653 Evaluate side-chains 105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 HIS C 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.133487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.096219 restraints weight = 7964.220| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.57 r_work: 0.2793 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7221 Z= 0.281 Angle : 0.672 12.934 9792 Z= 0.318 Chirality : 0.041 0.197 1101 Planarity : 0.004 0.045 1095 Dihedral : 19.676 133.384 1278 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.46 % Allowed : 14.86 % Favored : 81.67 % 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: 2.23 (0.30), residues: 786 helix: 2.45 (0.20), residues: 627 sheet: None (None), residues: 0 loop : -2.82 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 44 HIS 0.004 0.001 HIS B 213 PHE 0.016 0.002 PHE B 272 TYR 0.015 0.001 TYR C 199 ARG 0.001 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.728 Fit side-chains REVERT: A 14 LEU cc_start: 0.8839 (mt) cc_final: 0.8488 (mt) REVERT: A 78 GLU cc_start: 0.8014 (tp30) cc_final: 0.7720 (tp30) REVERT: A 171 GLU cc_start: 0.8424 (mp0) cc_final: 0.7981 (mp0) REVERT: A 172 ARG cc_start: 0.6735 (tpm170) cc_final: 0.6312 (tpp-160) REVERT: A 201 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8080 (mmtp) REVERT: B 171 GLU cc_start: 0.8001 (mp0) cc_final: 0.7766 (mp0) REVERT: B 172 ARG cc_start: 0.6761 (tpm170) cc_final: 0.6422 (tpp-160) REVERT: C 243 MET cc_start: 0.9213 (mmt) cc_final: 0.8869 (mmt) outliers start: 24 outliers final: 6 residues processed: 116 average time/residue: 1.4157 time to fit residues: 171.9041 Evaluate side-chains 95 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain C residue 181 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 141 HIS B 246 GLN C 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.132399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.095261 restraints weight = 8083.677| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.55 r_work: 0.2774 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7221 Z= 0.263 Angle : 0.622 13.179 9792 Z= 0.297 Chirality : 0.039 0.194 1101 Planarity : 0.004 0.043 1095 Dihedral : 18.626 130.058 1278 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.18 % Allowed : 14.14 % Favored : 81.67 % 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: 2.72 (0.30), residues: 786 helix: 2.80 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.66 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 44 HIS 0.003 0.001 HIS C 213 PHE 0.016 0.002 PHE B 272 TYR 0.014 0.001 TYR C 199 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.747 Fit side-chains REVERT: A 14 LEU cc_start: 0.8849 (mt) cc_final: 0.8503 (mt) REVERT: A 78 GLU cc_start: 0.8113 (tp30) cc_final: 0.7720 (tp30) REVERT: A 171 GLU cc_start: 0.8481 (mp0) cc_final: 0.8179 (mp0) REVERT: A 172 ARG cc_start: 0.6935 (tpm170) cc_final: 0.6533 (tpp-160) REVERT: A 201 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8098 (mmtm) REVERT: A 258 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.7128 (t80) REVERT: B 78 GLU cc_start: 0.7843 (tp30) cc_final: 0.7557 (tp30) REVERT: B 143 VAL cc_start: 0.9075 (t) cc_final: 0.8818 (t) REVERT: B 172 ARG cc_start: 0.6894 (tpm170) cc_final: 0.6635 (tpp-160) REVERT: B 234 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8389 (ptmm) REVERT: C 243 MET cc_start: 0.9213 (mmt) cc_final: 0.8938 (mmt) REVERT: C 258 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.6974 (t80) outliers start: 29 outliers final: 11 residues processed: 117 average time/residue: 1.3624 time to fit residues: 166.9660 Evaluate side-chains 109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TRP Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 41 optimal weight: 0.0870 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 HIS B 246 GLN C 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.131722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.095316 restraints weight = 8220.652| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.52 r_work: 0.2792 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7221 Z= 0.231 Angle : 0.587 6.724 9792 Z= 0.283 Chirality : 0.038 0.133 1101 Planarity : 0.004 0.039 1095 Dihedral : 17.924 127.987 1278 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.17 % Allowed : 15.44 % Favored : 81.39 % 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: 2.91 (0.30), residues: 786 helix: 2.92 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.53 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 276 HIS 0.003 0.001 HIS B 213 PHE 0.014 0.002 PHE C 272 TYR 0.012 0.001 TYR C 164 ARG 0.003 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.727 Fit side-chains REVERT: A 14 LEU cc_start: 0.8848 (mt) cc_final: 0.8503 (mt) REVERT: A 78 GLU cc_start: 0.8196 (tp30) cc_final: 0.7775 (tp30) REVERT: A 171 GLU cc_start: 0.8554 (mp0) cc_final: 0.8229 (mp0) REVERT: A 201 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8258 (mmtp) REVERT: A 258 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.7061 (t80) REVERT: B 78 GLU cc_start: 0.7832 (tp30) cc_final: 0.7521 (tp30) REVERT: B 143 VAL cc_start: 0.9003 (t) cc_final: 0.8767 (t) REVERT: B 172 ARG cc_start: 0.6893 (tpm170) cc_final: 0.6572 (tpp-160) REVERT: B 234 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8403 (ptmm) REVERT: C 78 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7724 (tp30) REVERT: C 243 MET cc_start: 0.9199 (mmt) cc_final: 0.8942 (mmt) REVERT: C 258 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.6966 (t80) outliers start: 22 outliers final: 8 residues processed: 109 average time/residue: 1.5039 time to fit residues: 171.4320 Evaluate side-chains 106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 0.0000 chunk 75 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 overall best weight: 0.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 141 HIS C 74 GLN C 141 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.133877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.097234 restraints weight = 8046.250| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.52 r_work: 0.2807 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7221 Z= 0.213 Angle : 0.571 6.503 9792 Z= 0.277 Chirality : 0.037 0.129 1101 Planarity : 0.004 0.041 1095 Dihedral : 17.408 121.247 1278 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.46 % Allowed : 15.30 % Favored : 81.24 % 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: 3.00 (0.30), residues: 786 helix: 2.99 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.54 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 276 HIS 0.003 0.001 HIS B 213 PHE 0.014 0.001 PHE C 272 TYR 0.012 0.001 TYR C 199 ARG 0.004 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.720 Fit side-chains REVERT: A 14 LEU cc_start: 0.8842 (mt) cc_final: 0.8517 (mt) REVERT: A 78 GLU cc_start: 0.8195 (tp30) cc_final: 0.7849 (tp30) REVERT: A 171 GLU cc_start: 0.8508 (mp0) cc_final: 0.8237 (mp0) REVERT: A 258 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.7047 (t80) REVERT: B 78 GLU cc_start: 0.7852 (tp30) cc_final: 0.7549 (tp30) REVERT: B 143 VAL cc_start: 0.9021 (t) cc_final: 0.8790 (t) REVERT: B 172 ARG cc_start: 0.6822 (tpm170) cc_final: 0.6219 (mmp80) REVERT: B 201 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8256 (mmtt) REVERT: B 234 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8429 (ptmm) REVERT: C 78 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7462 (tp30) REVERT: C 82 ARG cc_start: 0.7969 (mtp180) cc_final: 0.7349 (mmm-85) REVERT: C 243 MET cc_start: 0.9168 (mmt) cc_final: 0.8954 (mmt) REVERT: C 258 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.6906 (t80) outliers start: 24 outliers final: 10 residues processed: 114 average time/residue: 1.3874 time to fit residues: 165.5814 Evaluate side-chains 109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 56 optimal weight: 0.0060 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 141 HIS C 141 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.132237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.096516 restraints weight = 8206.862| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.49 r_work: 0.2790 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7221 Z= 0.230 Angle : 0.585 6.463 9792 Z= 0.284 Chirality : 0.038 0.133 1101 Planarity : 0.004 0.041 1095 Dihedral : 17.256 119.177 1278 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.54 % Favored : 97.07 % Rotamer: Outliers : 3.03 % Allowed : 16.02 % Favored : 80.95 % 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: 2.93 (0.30), residues: 786 helix: 2.93 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.50 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.003 0.001 HIS A 266 PHE 0.015 0.002 PHE C 272 TYR 0.013 0.001 TYR C 199 ARG 0.003 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.657 Fit side-chains REVERT: A 14 LEU cc_start: 0.8863 (mt) cc_final: 0.8539 (mt) REVERT: A 78 GLU cc_start: 0.8214 (tp30) cc_final: 0.7808 (tp30) REVERT: A 171 GLU cc_start: 0.8532 (mp0) cc_final: 0.8254 (mp0) REVERT: A 258 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.7084 (t80) REVERT: A 287 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8066 (ptpp) REVERT: B 78 GLU cc_start: 0.7811 (tp30) cc_final: 0.7513 (tp30) REVERT: B 143 VAL cc_start: 0.9025 (t) cc_final: 0.8792 (t) REVERT: B 172 ARG cc_start: 0.6932 (tpm170) cc_final: 0.6338 (mmp80) REVERT: B 201 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8168 (mmtm) REVERT: B 234 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8449 (ptmm) REVERT: B 260 LEU cc_start: 0.8991 (mt) cc_final: 0.8715 (mp) REVERT: C 78 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7572 (tp30) REVERT: C 243 MET cc_start: 0.9147 (mmt) cc_final: 0.8923 (mmt) REVERT: C 258 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.6811 (t80) outliers start: 21 outliers final: 8 residues processed: 107 average time/residue: 1.3995 time to fit residues: 156.5847 Evaluate side-chains 105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TRP Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 10 optimal weight: 0.0040 chunk 40 optimal weight: 0.7980 chunk 58 optimal weight: 0.3980 chunk 44 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 141 HIS B 141 HIS C 74 GLN C 141 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.134177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.097842 restraints weight = 8131.326| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.53 r_work: 0.2851 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7221 Z= 0.198 Angle : 0.564 6.480 9792 Z= 0.276 Chirality : 0.037 0.125 1101 Planarity : 0.004 0.039 1095 Dihedral : 16.810 112.657 1278 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.54 % Favored : 97.07 % Rotamer: Outliers : 2.45 % Allowed : 16.88 % Favored : 80.66 % 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: 3.02 (0.30), residues: 786 helix: 3.01 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.54 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 276 HIS 0.003 0.001 HIS C 213 PHE 0.012 0.001 PHE C 272 TYR 0.011 0.001 TYR C 164 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.732 Fit side-chains REVERT: A 14 LEU cc_start: 0.8857 (mt) cc_final: 0.8530 (mt) REVERT: A 78 GLU cc_start: 0.8198 (tp30) cc_final: 0.7783 (tp30) REVERT: A 171 GLU cc_start: 0.8488 (mp0) cc_final: 0.8131 (mp0) REVERT: A 258 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.6945 (t80) REVERT: B 78 GLU cc_start: 0.7816 (tp30) cc_final: 0.7533 (tp30) REVERT: B 143 VAL cc_start: 0.8956 (t) cc_final: 0.8735 (t) REVERT: B 172 ARG cc_start: 0.6897 (tpm170) cc_final: 0.6331 (mmp80) REVERT: B 260 LEU cc_start: 0.8946 (mt) cc_final: 0.8657 (mp) REVERT: C 78 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7547 (tp30) REVERT: C 243 MET cc_start: 0.9148 (mmt) cc_final: 0.8918 (mmt) REVERT: C 258 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.6858 (t80) outliers start: 17 outliers final: 5 residues processed: 108 average time/residue: 1.3943 time to fit residues: 157.6699 Evaluate side-chains 102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 258 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 3 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 141 HIS C 141 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.132593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.096065 restraints weight = 8177.939| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.54 r_work: 0.2789 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7221 Z= 0.241 Angle : 0.604 6.477 9792 Z= 0.293 Chirality : 0.038 0.132 1101 Planarity : 0.004 0.038 1095 Dihedral : 16.829 112.417 1278 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.67 % Favored : 96.95 % Rotamer: Outliers : 2.60 % Allowed : 16.59 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.30), residues: 786 helix: 2.92 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.58 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 276 HIS 0.003 0.001 HIS C 266 PHE 0.015 0.002 PHE B 272 TYR 0.013 0.001 TYR C 199 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.736 Fit side-chains REVERT: A 14 LEU cc_start: 0.8866 (mt) cc_final: 0.8538 (mt) REVERT: A 78 GLU cc_start: 0.8218 (tp30) cc_final: 0.7797 (tp30) REVERT: A 171 GLU cc_start: 0.8521 (mp0) cc_final: 0.8154 (mp0) REVERT: A 247 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9110 (mt) REVERT: A 258 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.6869 (t80) REVERT: B 78 GLU cc_start: 0.7785 (tp30) cc_final: 0.7494 (tp30) REVERT: B 143 VAL cc_start: 0.9025 (t) cc_final: 0.8792 (t) REVERT: B 172 ARG cc_start: 0.6927 (tpm170) cc_final: 0.6370 (mmp80) REVERT: B 201 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8169 (mmtm) REVERT: C 78 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7417 (tp30) REVERT: C 82 ARG cc_start: 0.8228 (mtp180) cc_final: 0.7477 (mmm-85) REVERT: C 243 MET cc_start: 0.9147 (mmt) cc_final: 0.8910 (mmt) REVERT: C 258 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.6788 (t80) outliers start: 18 outliers final: 9 residues processed: 103 average time/residue: 1.5091 time to fit residues: 162.3799 Evaluate side-chains 105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 260 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 70 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.0470 chunk 14 optimal weight: 0.3980 chunk 33 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 141 HIS C 141 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.134397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.097786 restraints weight = 8196.306| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.55 r_work: 0.2832 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7221 Z= 0.208 Angle : 0.571 6.392 9792 Z= 0.278 Chirality : 0.037 0.126 1101 Planarity : 0.004 0.037 1095 Dihedral : 16.402 107.415 1278 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.80 % Favored : 96.82 % Rotamer: Outliers : 2.16 % Allowed : 16.88 % Favored : 80.95 % 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: 2.98 (0.30), residues: 786 helix: 2.98 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.57 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.003 0.001 HIS C 213 PHE 0.013 0.001 PHE C 272 TYR 0.012 0.001 TYR C 164 ARG 0.001 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8861 (mt) cc_final: 0.8528 (mt) REVERT: A 78 GLU cc_start: 0.8201 (tp30) cc_final: 0.7763 (tp30) REVERT: A 171 GLU cc_start: 0.8487 (mp0) cc_final: 0.8141 (mp0) REVERT: A 247 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.9051 (mt) REVERT: A 258 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.6755 (t80) REVERT: B 78 GLU cc_start: 0.7774 (tp30) cc_final: 0.7488 (tp30) REVERT: B 143 VAL cc_start: 0.8991 (t) cc_final: 0.8773 (t) REVERT: B 172 ARG cc_start: 0.6904 (tpm170) cc_final: 0.6360 (mmp80) REVERT: C 78 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7543 (tp30) REVERT: C 258 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.6835 (t80) outliers start: 15 outliers final: 8 residues processed: 102 average time/residue: 1.4360 time to fit residues: 153.1039 Evaluate side-chains 105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TRP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 56 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 141 HIS C 141 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.129518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.093642 restraints weight = 8303.920| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.51 r_work: 0.2776 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7221 Z= 0.279 Angle : 0.627 6.478 9792 Z= 0.302 Chirality : 0.039 0.138 1101 Planarity : 0.004 0.039 1095 Dihedral : 16.869 111.754 1278 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.18 % Favored : 96.44 % Rotamer: Outliers : 1.88 % Allowed : 17.03 % Favored : 81.10 % 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: 2.80 (0.29), residues: 786 helix: 2.84 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.54 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 276 HIS 0.003 0.001 HIS B 266 PHE 0.016 0.002 PHE C 272 TYR 0.014 0.001 TYR C 199 ARG 0.002 0.000 ARG B 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.671 Fit side-chains REVERT: A 14 LEU cc_start: 0.8899 (mt) cc_final: 0.8541 (mt) REVERT: A 78 GLU cc_start: 0.8220 (tp30) cc_final: 0.7793 (tp30) REVERT: A 171 GLU cc_start: 0.8550 (mp0) cc_final: 0.8278 (mp0) REVERT: A 247 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9063 (mt) REVERT: A 258 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.6937 (t80) REVERT: B 78 GLU cc_start: 0.7755 (tp30) cc_final: 0.7472 (tp30) REVERT: B 143 VAL cc_start: 0.9039 (t) cc_final: 0.8804 (t) REVERT: B 172 ARG cc_start: 0.6934 (tpm170) cc_final: 0.6388 (mmp80) REVERT: C 78 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7567 (tp30) REVERT: C 258 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.6760 (t80) outliers start: 13 outliers final: 10 residues processed: 102 average time/residue: 1.5526 time to fit residues: 165.2663 Evaluate side-chains 104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 56 optimal weight: 0.0020 chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 44 optimal weight: 0.5980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 141 HIS C 141 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.133072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.099461 restraints weight = 8214.957| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.57 r_work: 0.2834 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7221 Z= 0.214 Angle : 0.579 6.375 9792 Z= 0.280 Chirality : 0.037 0.128 1101 Planarity : 0.004 0.037 1095 Dihedral : 16.519 104.767 1278 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.93 % Favored : 96.69 % Rotamer: Outliers : 2.31 % Allowed : 16.59 % Favored : 81.10 % 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: 2.93 (0.29), residues: 786 helix: 2.94 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.56 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 76 HIS 0.003 0.001 HIS C 213 PHE 0.013 0.001 PHE B 272 TYR 0.013 0.001 TYR C 199 ARG 0.002 0.000 ARG B 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5615.72 seconds wall clock time: 96 minutes 40.21 seconds (5800.21 seconds total)