Starting phenix.real_space_refine on Thu Jul 2 07:00:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8aw5_15691/07_2026/8aw5_15691.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aw5_15691/07_2026/8aw5_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 { model { file = "/net/cci-nas-00/data/ceres_data/8aw5_15691/07_2026/8aw5_15691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aw5_15691/07_2026/8aw5_15691.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8aw5_15691/07_2026/8aw5_15691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aw5_15691/07_2026/8aw5_15691.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8aw5_15691/07_2026/8aw5_15691.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8aw5_15691/07_2026/8aw5_15691.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 1.60, per 1000 atoms: 0.23 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: 0.67 Conformation dependent library (CDL) restraints added in 336.9 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: 0.16 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: 1.12 Time building geometry restraints manager: 0.87 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: 3942 28.36 - 56.72: 117 56.72 - 85.07: 33 85.07 - 113.43: 18 113.43 - 141.79: 6 Dihedral angle restraints: 4116 sinusoidal: 1773 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 4113 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.930 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 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 : 0.018 0.351 7224 Z= 0.925 Angle : 1.758 17.246 9792 Z= 0.905 Chirality : 0.070 0.309 1101 Planarity : 0.036 0.272 1095 Dihedral : 17.384 141.787 2622 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.08 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG A 137 TYR 0.010 0.001 TYR B 164 PHE 0.014 0.002 PHE A 272 TRP 0.007 0.002 TRP B 276 HIS 0.002 0.001 HIS C 81 Details of bonding type rmsd/Z covalent geometry : bond 0.01662 / 0.92 ( 7221) covalent geometry : angle 1.75754 / 0.90 ( 9792) hydrogen bonds : bond 0.12127 / 8.69 ( 523) hydrogen bonds : angle 5.69009 / 4.21 ( 1551) Misc. bond : bond 0.35008 / 21.97 ( 3) *********************** 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 : 0.261 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: 0.5197 time to fit residues: 97.9286 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 : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3523 r_free = 0.3523 target = 0.133340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.096183 restraints weight = 8115.758| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.57 r_work: 0.2792 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 7224 Z= 0.170 Angle : 0.670 13.184 9792 Z= 0.317 Chirality : 0.041 0.185 1101 Planarity : 0.004 0.045 1095 Dihedral : 18.022 133.585 1224 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 : 3.61 % Allowed : 14.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.30), residues: 786 helix: 2.46 (0.20), residues: 627 sheet: None (None), residues: 0 loop : -2.81 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 127 TYR 0.015 0.001 TYR C 199 PHE 0.016 0.002 PHE B 272 TRP 0.011 0.001 TRP A 44 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.17 ( 7221) covalent geometry : angle 0.67044 / 0.32 ( 9792) hydrogen bonds : bond 0.05006 / 3.43 ( 523) hydrogen bonds : angle 3.85676 / 2.81 ( 1551) Misc. bond : bond 0.07667 / 4.38 ( 3) *********************** 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 126 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.286 Fit side-chains REVERT: A 14 LEU cc_start: 0.8838 (mt) cc_final: 0.8488 (mt) REVERT: A 78 GLU cc_start: 0.8011 (tp30) cc_final: 0.7718 (tp30) REVERT: A 171 GLU cc_start: 0.8420 (mp0) cc_final: 0.7976 (mp0) REVERT: A 172 ARG cc_start: 0.6736 (tpm170) cc_final: 0.6314 (tpp-160) REVERT: A 201 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8049 (mmtp) REVERT: B 171 GLU cc_start: 0.8004 (mp0) cc_final: 0.7765 (mp0) REVERT: B 172 ARG cc_start: 0.6762 (tpm170) cc_final: 0.6423 (tpp-160) REVERT: C 243 MET cc_start: 0.9210 (mmt) cc_final: 0.8872 (mmt) outliers start: 25 outliers final: 7 residues processed: 117 average time/residue: 0.6904 time to fit residues: 84.3614 Evaluate side-chains 95 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 255 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 56 optimal weight: 0.0770 chunk 44 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3506 r_free = 0.3506 target = 0.132029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.094592 restraints weight = 8080.280| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.56 r_work: 0.2787 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 7224 Z= 0.148 Angle : 0.610 13.448 9792 Z= 0.292 Chirality : 0.039 0.203 1101 Planarity : 0.004 0.042 1095 Dihedral : 17.380 127.478 1224 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.90 % Allowed : 14.57 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.30), residues: 786 helix: 2.85 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.63 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.013 0.001 TYR C 199 PHE 0.015 0.002 PHE C 272 TRP 0.008 0.001 TRP A 44 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.15 ( 7221) covalent geometry : angle 0.60955 / 0.29 ( 9792) hydrogen bonds : bond 0.04638 / 3.19 ( 523) hydrogen bonds : angle 3.74046 / 2.72 ( 1551) Misc. bond : bond 0.08825 / 5.39 ( 3) *********************** 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 128 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.255 Fit side-chains REVERT: A 14 LEU cc_start: 0.8847 (mt) cc_final: 0.8496 (mt) REVERT: A 78 GLU cc_start: 0.8115 (tp30) cc_final: 0.7722 (tp30) REVERT: A 171 GLU cc_start: 0.8450 (mp0) cc_final: 0.8007 (mp0) REVERT: A 172 ARG cc_start: 0.6928 (tpm170) cc_final: 0.6530 (tpp-160) REVERT: A 201 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7889 (mmtm) REVERT: A 258 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.7105 (t80) REVERT: B 78 GLU cc_start: 0.7825 (tp30) cc_final: 0.7550 (tp30) REVERT: B 143 VAL cc_start: 0.9048 (t) cc_final: 0.8811 (t) REVERT: B 172 ARG cc_start: 0.6938 (tpm170) cc_final: 0.6672 (tpp-160) REVERT: C 243 MET cc_start: 0.9192 (mmt) cc_final: 0.8895 (mmt) REVERT: C 258 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.6982 (t80) outliers start: 27 outliers final: 10 residues processed: 116 average time/residue: 0.6610 time to fit residues: 80.2201 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 : 0.192 ------------------------------------------------------------------------------- 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 174 LYS Chi-restraints excluded: chain B residue 181 ASP 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 3 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 HIS B 141 HIS B 246 GLN 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 = 0.3508 r_free = 0.3508 target = 0.132161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.096306 restraints weight = 8148.280| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.49 r_work: 0.2787 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 7224 Z= 0.144 Angle : 0.586 6.727 9792 Z= 0.285 Chirality : 0.038 0.135 1101 Planarity : 0.004 0.040 1095 Dihedral : 17.006 124.055 1224 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.32 % Allowed : 15.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.30), residues: 786 helix: 2.91 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.55 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 137 TYR 0.012 0.001 TYR C 199 PHE 0.015 0.002 PHE C 272 TRP 0.007 0.001 TRP A 276 HIS 0.003 0.001 HIS C 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.14 ( 7221) covalent geometry : angle 0.58643 / 0.29 ( 9792) hydrogen bonds : bond 0.04486 / 3.08 ( 523) hydrogen bonds : angle 3.71384 / 2.69 ( 1551) Misc. bond : bond 0.10275 / 6.43 ( 3) *********************** 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 119 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.256 Fit side-chains REVERT: A 14 LEU cc_start: 0.8869 (mt) cc_final: 0.8533 (mt) REVERT: A 78 GLU cc_start: 0.8199 (tp30) cc_final: 0.7788 (tp30) REVERT: A 171 GLU cc_start: 0.8531 (mp0) cc_final: 0.8285 (mp0) REVERT: A 201 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8318 (mmtp) REVERT: A 258 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7093 (t80) REVERT: B 78 GLU cc_start: 0.7842 (tp30) cc_final: 0.7541 (tp30) REVERT: B 143 VAL cc_start: 0.9045 (t) cc_final: 0.8804 (t) REVERT: B 172 ARG cc_start: 0.6852 (tpm170) cc_final: 0.6224 (mmp80) REVERT: B 234 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8463 (ptmm) REVERT: C 78 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7675 (tp30) REVERT: C 243 MET cc_start: 0.9206 (mmt) cc_final: 0.8946 (mmt) REVERT: C 258 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.6936 (t80) outliers start: 23 outliers final: 6 residues processed: 108 average time/residue: 0.6963 time to fit residues: 78.5357 Evaluate side-chains 105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 136 LEU 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 20 optimal weight: 0.9980 chunk 56 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3501 r_free = 0.3501 target = 0.131405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.095733 restraints weight = 8134.123| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.48 r_work: 0.2786 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 7224 Z= 0.143 Angle : 0.586 6.536 9792 Z= 0.284 Chirality : 0.038 0.133 1101 Planarity : 0.004 0.041 1095 Dihedral : 16.829 125.323 1224 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.30), residues: 786 helix: 2.91 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.54 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 137 TYR 0.013 0.001 TYR C 199 PHE 0.015 0.002 PHE C 272 TRP 0.007 0.001 TRP B 276 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.14 ( 7221) covalent geometry : angle 0.58602 / 0.28 ( 9792) hydrogen bonds : bond 0.04451 / 3.06 ( 523) hydrogen bonds : angle 3.69503 / 2.67 ( 1551) Misc. bond : bond 0.10554 / 6.66 ( 3) *********************** 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 : 0.252 Fit side-chains REVERT: A 14 LEU cc_start: 0.8887 (mt) cc_final: 0.8553 (mt) REVERT: A 78 GLU cc_start: 0.8201 (tp30) cc_final: 0.7855 (tp30) REVERT: A 171 GLU cc_start: 0.8546 (mp0) cc_final: 0.8210 (mp0) REVERT: A 258 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.7051 (t80) REVERT: B 78 GLU cc_start: 0.7845 (tp30) cc_final: 0.7538 (tp30) REVERT: B 143 VAL cc_start: 0.9042 (t) cc_final: 0.8812 (t) REVERT: B 172 ARG cc_start: 0.6878 (tpm170) cc_final: 0.6283 (mmp80) REVERT: B 234 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8470 (ptmm) REVERT: C 78 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7571 (tp30) REVERT: C 243 MET cc_start: 0.9169 (mmt) cc_final: 0.8949 (mmt) REVERT: C 258 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.6899 (t80) outliers start: 24 outliers final: 11 residues processed: 114 average time/residue: 0.6713 time to fit residues: 80.1370 Evaluate side-chains 105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 70 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 76 optimal weight: 0.0570 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 45 optimal weight: 0.0970 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN A 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 = 0.3515 r_free = 0.3515 target = 0.132663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.095253 restraints weight = 8225.255| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.57 r_work: 0.2799 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 7224 Z= 0.126 Angle : 0.565 6.463 9792 Z= 0.275 Chirality : 0.037 0.129 1101 Planarity : 0.004 0.040 1095 Dihedral : 16.348 118.577 1224 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.42 % Favored : 97.20 % Rotamer: Outliers : 3.17 % Allowed : 15.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.30), residues: 786 helix: 2.98 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.55 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 137 TYR 0.012 0.001 TYR C 199 PHE 0.013 0.001 PHE C 272 TRP 0.007 0.001 TRP A 276 HIS 0.003 0.001 HIS C 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 ( 7221) covalent geometry : angle 0.56550 / 0.28 ( 9792) hydrogen bonds : bond 0.04220 / 2.90 ( 523) hydrogen bonds : angle 3.64580 / 2.64 ( 1551) Misc. bond : bond 0.09663 / 6.07 ( 3) *********************** 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 122 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.270 Fit side-chains REVERT: A 14 LEU cc_start: 0.8854 (mt) cc_final: 0.8523 (mt) REVERT: A 78 GLU cc_start: 0.8217 (tp30) cc_final: 0.7797 (tp30) REVERT: A 171 GLU cc_start: 0.8556 (mp0) cc_final: 0.8329 (mp0) REVERT: A 172 ARG cc_start: 0.7560 (mmp-170) cc_final: 0.7013 (mmp80) REVERT: A 258 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.6842 (t80) REVERT: B 78 GLU cc_start: 0.7815 (tp30) cc_final: 0.7509 (tp30) REVERT: B 143 VAL cc_start: 0.8986 (t) cc_final: 0.8758 (t) REVERT: B 172 ARG cc_start: 0.6945 (tpm170) cc_final: 0.6356 (mmp80) REVERT: C 78 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7389 (tp30) REVERT: C 82 ARG cc_start: 0.8217 (mtp180) cc_final: 0.7449 (mmm-85) REVERT: C 243 MET cc_start: 0.9164 (mmt) cc_final: 0.8934 (mmt) REVERT: C 258 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.6953 (t80) outliers start: 22 outliers final: 6 residues processed: 113 average time/residue: 0.6689 time to fit residues: 79.0397 Evaluate side-chains 101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.0010 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN A 141 HIS B 141 HIS C 141 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.131899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.094639 restraints weight = 8158.608| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.57 r_work: 0.2793 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 7224 Z= 0.135 Angle : 0.590 6.517 9792 Z= 0.287 Chirality : 0.038 0.130 1101 Planarity : 0.004 0.041 1095 Dihedral : 16.260 114.869 1224 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.80 % Favored : 96.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.30), residues: 786 helix: 2.95 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.61 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.013 0.001 TYR C 199 PHE 0.014 0.001 PHE C 272 TRP 0.006 0.001 TRP B 276 HIS 0.003 0.001 HIS C 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.13 ( 7221) covalent geometry : angle 0.58974 / 0.29 ( 9792) hydrogen bonds : bond 0.04301 / 2.96 ( 523) hydrogen bonds : angle 3.68270 / 2.65 ( 1551) Misc. bond : bond 0.10334 / 6.50 ( 3) *********************** 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 112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.199 Fit side-chains REVERT: A 14 LEU cc_start: 0.8868 (mt) cc_final: 0.8540 (mt) REVERT: A 78 GLU cc_start: 0.8235 (tp30) cc_final: 0.7807 (tp30) REVERT: A 171 GLU cc_start: 0.8552 (mp0) cc_final: 0.8267 (mp0) REVERT: A 258 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.6818 (t80) REVERT: B 78 GLU cc_start: 0.7769 (tp30) cc_final: 0.7478 (tp30) REVERT: B 143 VAL cc_start: 0.9014 (t) cc_final: 0.8781 (t) REVERT: B 172 ARG cc_start: 0.6942 (tpm170) cc_final: 0.6361 (mmp80) REVERT: C 78 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7570 (tp30) REVERT: C 243 MET cc_start: 0.9135 (mmt) cc_final: 0.8899 (mmt) REVERT: C 258 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.6946 (t80) outliers start: 17 outliers final: 7 residues processed: 104 average time/residue: 0.7061 time to fit residues: 76.6184 Evaluate side-chains 101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 181 ASP Chi-restraints excluded: chain C residue 203 LEU 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 20 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 40 optimal weight: 0.0470 chunk 64 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3517 r_free = 0.3517 target = 0.132647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.095902 restraints weight = 8180.372| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.54 r_work: 0.2822 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 7224 Z= 0.136 Angle : 0.588 6.475 9792 Z= 0.286 Chirality : 0.038 0.131 1101 Planarity : 0.004 0.038 1095 Dihedral : 15.911 111.508 1224 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.67 % Favored : 96.95 % Rotamer: Outliers : 2.60 % Allowed : 16.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.29), residues: 786 helix: 2.95 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.65 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 137 TYR 0.012 0.001 TYR C 199 PHE 0.014 0.001 PHE C 272 TRP 0.006 0.001 TRP B 276 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.14 ( 7221) covalent geometry : angle 0.58833 / 0.29 ( 9792) hydrogen bonds : bond 0.04309 / 2.96 ( 523) hydrogen bonds : angle 3.66831 / 2.65 ( 1551) Misc. bond : bond 0.09650 / 6.25 ( 3) *********************** 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 111 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.248 Fit side-chains REVERT: A 14 LEU cc_start: 0.8875 (mt) cc_final: 0.8549 (mt) REVERT: A 78 GLU cc_start: 0.8204 (tp30) cc_final: 0.7780 (tp30) REVERT: A 171 GLU cc_start: 0.8556 (mp0) cc_final: 0.8283 (mp0) REVERT: A 247 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.9095 (mt) REVERT: A 258 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.6809 (t80) REVERT: B 78 GLU cc_start: 0.7759 (tp30) cc_final: 0.7476 (tp30) REVERT: B 143 VAL cc_start: 0.9014 (t) cc_final: 0.8786 (t) REVERT: B 172 ARG cc_start: 0.6939 (tpm170) cc_final: 0.6384 (mmp80) REVERT: C 78 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7580 (tp30) REVERT: C 243 MET cc_start: 0.9131 (mmt) cc_final: 0.8923 (mmt) REVERT: C 258 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.6835 (t80) outliers start: 18 outliers final: 11 residues processed: 104 average time/residue: 0.6439 time to fit residues: 69.8918 Evaluate side-chains 106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 204 GLU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 51 LEU 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 181 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 258 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 0.0770 chunk 39 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 52 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3497 r_free = 0.3497 target = 0.131118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.093758 restraints weight = 8262.688| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.57 r_work: 0.2790 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 7224 Z= 0.143 Angle : 0.593 6.471 9792 Z= 0.286 Chirality : 0.038 0.132 1101 Planarity : 0.004 0.039 1095 Dihedral : 15.945 111.530 1224 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.44 % Favored : 96.18 % Rotamer: Outliers : 2.02 % Allowed : 17.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.29), residues: 786 helix: 2.91 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.59 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.013 0.001 TYR C 199 PHE 0.015 0.002 PHE C 272 TRP 0.006 0.001 TRP B 276 HIS 0.003 0.001 HIS C 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.14 ( 7221) covalent geometry : angle 0.59264 / 0.29 ( 9792) hydrogen bonds : bond 0.04406 / 3.03 ( 523) hydrogen bonds : angle 3.69179 / 2.66 ( 1551) Misc. bond : bond 0.10578 / 6.77 ( 3) *********************** 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 108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.199 Fit side-chains REVERT: A 14 LEU cc_start: 0.8877 (mt) cc_final: 0.8546 (mt) REVERT: A 78 GLU cc_start: 0.8248 (tp30) cc_final: 0.7845 (tp30) REVERT: A 171 GLU cc_start: 0.8582 (mp0) cc_final: 0.8321 (mp0) REVERT: A 247 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9137 (mt) REVERT: A 258 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.6846 (t80) REVERT: B 78 GLU cc_start: 0.7757 (tp30) cc_final: 0.7460 (tp30) REVERT: B 143 VAL cc_start: 0.9035 (t) cc_final: 0.8810 (t) REVERT: B 172 ARG cc_start: 0.6943 (tpm170) cc_final: 0.6505 (mmp80) REVERT: C 78 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7581 (tp30) REVERT: C 243 MET cc_start: 0.9163 (mmt) cc_final: 0.8890 (mmt) REVERT: C 258 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.6810 (t80) outliers start: 14 outliers final: 9 residues processed: 104 average time/residue: 0.6345 time to fit residues: 68.7723 Evaluate side-chains 103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TRP 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3488 r_free = 0.3488 target = 0.130392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.093359 restraints weight = 8160.891| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.56 r_work: 0.2759 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 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 : 0.005 0.121 7224 Z= 0.162 Angle : 0.618 6.492 9792 Z= 0.298 Chirality : 0.039 0.146 1101 Planarity : 0.004 0.040 1095 Dihedral : 16.321 115.127 1224 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.80 % Favored : 96.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.29), residues: 786 helix: 2.85 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.58 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 198 TYR 0.016 0.001 TYR C 199 PHE 0.016 0.002 PHE B 272 TRP 0.007 0.001 TRP C 76 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.16 ( 7221) covalent geometry : angle 0.61790 / 0.30 ( 9792) hydrogen bonds : bond 0.04586 / 3.15 ( 523) hydrogen bonds : angle 3.73633 / 2.69 ( 1551) Misc. bond : bond 0.11487 / 7.24 ( 3) ********************** 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 106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.228 Fit side-chains REVERT: A 14 LEU cc_start: 0.8908 (mt) cc_final: 0.8552 (mt) REVERT: A 78 GLU cc_start: 0.8215 (tp30) cc_final: 0.7852 (tp30) REVERT: A 171 GLU cc_start: 0.8606 (mp0) cc_final: 0.8332 (mp0) REVERT: A 258 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.6924 (t80) REVERT: B 78 GLU cc_start: 0.7749 (tp30) cc_final: 0.7459 (tp30) REVERT: B 143 VAL cc_start: 0.9048 (t) cc_final: 0.8810 (t) REVERT: B 172 ARG cc_start: 0.6958 (tpm170) cc_final: 0.6394 (mmp80) REVERT: C 78 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7575 (tp30) REVERT: C 243 MET cc_start: 0.9201 (mmt) cc_final: 0.8897 (mmt) REVERT: C 258 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.6693 (t80) outliers start: 13 outliers final: 8 residues processed: 101 average time/residue: 0.6554 time to fit residues: 68.9473 Evaluate side-chains 103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 0.0870 chunk 74 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 3 optimal weight: 0.0670 chunk 58 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3523 r_free = 0.3523 target = 0.133316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.097088 restraints weight = 8168.389| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.53 r_work: 0.2800 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 7224 Z= 0.128 Angle : 0.575 6.409 9792 Z= 0.280 Chirality : 0.037 0.138 1101 Planarity : 0.004 0.038 1095 Dihedral : 15.926 108.158 1224 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.80 % Favored : 96.82 % Rotamer: Outliers : 1.73 % Allowed : 17.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.29), residues: 786 helix: 2.95 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.56 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.011 0.001 TYR C 199 PHE 0.013 0.001 PHE C 272 TRP 0.007 0.001 TRP C 76 HIS 0.003 0.001 HIS C 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 ( 7221) covalent geometry : angle 0.57487 / 0.28 ( 9792) hydrogen bonds : bond 0.04250 / 2.92 ( 523) hydrogen bonds : angle 3.66778 / 2.64 ( 1551) Misc. bond : bond 0.09451 / 6.06 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2736.31 seconds wall clock time: 47 minutes 27.24 seconds (2847.24 seconds total)