Starting phenix.real_space_refine on Tue Feb 3 22:04:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aw5_15691/02_2026/8aw5_15691.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aw5_15691/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8aw5_15691/02_2026/8aw5_15691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aw5_15691/02_2026/8aw5_15691.map" model { file = "/net/cci-nas-00/data/ceres_data/8aw5_15691/02_2026/8aw5_15691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aw5_15691/02_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-2.0-5952/lib/python3.9/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: 1.36, per 1000 atoms: 0.19 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: 0.68 Conformation dependent library (CDL) restraints added in 208.1 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: 0.15 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: 0.99 Time building geometry restraints manager: 0.84 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: 0.02 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: 0.910 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.990 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:8.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.400 ------------------------------------------------------------------------------- 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 : 0.018 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 : 18.375 141.787 2676 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 covalent geometry : bond 0.01662 ( 7221) covalent geometry : angle 1.75754 ( 9792) hydrogen bonds : bond 0.12127 ( 523) hydrogen bonds : angle 5.69009 ( 1551) Misc. bond : bond 0.35008 ( 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 : 0.237 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: 0.4671 time to fit residues: 87.7430 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 : 0.154 ------------------------------------------------------------------------------- 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... 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 = 41)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.096068 restraints weight = 8124.901| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.58 r_work: 0.2784 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 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 : 0.005 0.107 7224 Z= 0.175 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 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: 2.23 (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 ARG 0.001 0.000 ARG B 82 TYR 0.015 0.001 TYR C 199 PHE 0.016 0.002 PHE B 272 TRP 0.012 0.002 TRP A 44 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 7221) covalent geometry : angle 0.67184 ( 9792) hydrogen bonds : bond 0.04998 ( 523) hydrogen bonds : angle 3.85906 ( 1551) Misc. bond : bond 0.07844 ( 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 125 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.178 Fit side-chains REVERT: A 14 LEU cc_start: 0.8840 (mt) cc_final: 0.8487 (mt) REVERT: A 78 GLU cc_start: 0.8019 (tp30) cc_final: 0.7725 (tp30) REVERT: A 171 GLU cc_start: 0.8427 (mp0) cc_final: 0.7982 (mp0) REVERT: A 172 ARG cc_start: 0.6738 (tpm170) cc_final: 0.6315 (tpp-160) REVERT: A 201 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8086 (mmtp) REVERT: B 171 GLU cc_start: 0.7999 (mp0) cc_final: 0.7763 (mp0) REVERT: B 172 ARG cc_start: 0.6760 (tpm170) cc_final: 0.6422 (tpp-160) REVERT: C 243 MET cc_start: 0.9215 (mmt) cc_final: 0.8873 (mmt) outliers start: 24 outliers final: 6 residues processed: 116 average time/residue: 0.5663 time to fit residues: 68.6441 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 : 0.247 ------------------------------------------------------------------------------- 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 45 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 56 optimal weight: 0.0970 chunk 44 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.132171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.096146 restraints weight = 8056.661| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.52 r_work: 0.2788 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 7224 Z= 0.150 Angle : 0.614 13.326 9792 Z= 0.294 Chirality : 0.039 0.198 1101 Planarity : 0.004 0.042 1095 Dihedral : 18.584 128.110 1278 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.19 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 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: 2.76 (0.30), residues: 786 helix: 2.83 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.65 (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 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 7221) covalent geometry : angle 0.61410 ( 9792) hydrogen bonds : bond 0.04666 ( 523) hydrogen bonds : angle 3.74188 ( 1551) Misc. bond : bond 0.09175 ( 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 129 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.245 Fit side-chains REVERT: A 14 LEU cc_start: 0.8810 (mt) cc_final: 0.8444 (mt) REVERT: A 78 GLU cc_start: 0.8096 (tp30) cc_final: 0.7682 (tp30) REVERT: A 171 GLU cc_start: 0.8418 (mp0) cc_final: 0.7949 (mp0) REVERT: A 172 ARG cc_start: 0.6906 (tpm170) cc_final: 0.6509 (tpp-160) REVERT: A 201 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7837 (mmtm) REVERT: A 258 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.7073 (t80) REVERT: B 78 GLU cc_start: 0.7797 (tp30) cc_final: 0.7505 (tp30) REVERT: B 143 VAL cc_start: 0.8988 (t) cc_final: 0.8739 (t) REVERT: B 171 GLU cc_start: 0.8042 (mp0) cc_final: 0.7840 (mp0) REVERT: B 172 ARG cc_start: 0.6899 (tpm170) cc_final: 0.6633 (tpp-160) REVERT: B 234 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8380 (ptmm) REVERT: C 243 MET cc_start: 0.9185 (mmt) cc_final: 0.8919 (mmt) REVERT: C 258 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.6921 (t80) outliers start: 29 outliers final: 10 residues processed: 115 average time/residue: 0.6143 time to fit residues: 73.8372 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 : 0.258 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 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: 0.5980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.131345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.095252 restraints weight = 8156.589| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.49 r_work: 0.2781 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2861 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= 0.149 Angle : 0.592 6.874 9792 Z= 0.286 Chirality : 0.038 0.136 1101 Planarity : 0.004 0.040 1095 Dihedral : 17.970 126.139 1278 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.61 % Allowed : 14.43 % Favored : 81.96 % 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: 2.87 (0.30), residues: 786 helix: 2.89 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.56 (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 164 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 covalent geometry : bond 0.00387 ( 7221) covalent geometry : angle 0.59176 ( 9792) hydrogen bonds : bond 0.04537 ( 523) hydrogen bonds : angle 3.73174 ( 1551) Misc. bond : bond 0.10732 ( 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 122 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.156 Fit side-chains REVERT: A 14 LEU cc_start: 0.8872 (mt) cc_final: 0.8540 (mt) REVERT: A 78 GLU cc_start: 0.8203 (tp30) cc_final: 0.7793 (tp30) REVERT: A 171 GLU cc_start: 0.8539 (mp0) cc_final: 0.8284 (mp0) REVERT: A 201 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8260 (mmtp) REVERT: A 258 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.7124 (t80) REVERT: B 78 GLU cc_start: 0.7843 (tp30) cc_final: 0.7545 (tp30) REVERT: B 143 VAL cc_start: 0.9035 (t) cc_final: 0.8792 (t) REVERT: B 172 ARG cc_start: 0.6847 (tpm170) cc_final: 0.6211 (mmp80) REVERT: B 234 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8371 (ptmm) REVERT: C 78 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7718 (tp30) REVERT: C 243 MET cc_start: 0.9209 (mmt) cc_final: 0.8938 (mmt) REVERT: C 258 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.6929 (t80) outliers start: 25 outliers final: 10 residues processed: 109 average time/residue: 0.5656 time to fit residues: 64.4567 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 : 0.173 ------------------------------------------------------------------------------- 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 149 LEU Chi-restraints excluded: chain B residue 174 LYS 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: 1.9990 chunk 56 optimal weight: 0.0370 chunk 24 optimal weight: 3.9990 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: 0.5980 chunk 33 optimal weight: 0.0000 chunk 54 optimal weight: 0.0370 chunk 68 optimal weight: 0.5980 overall best weight: 0.2540 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.134187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.098200 restraints weight = 8148.627| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.51 r_work: 0.2844 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 7224 Z= 0.114 Angle : 0.553 6.476 9792 Z= 0.269 Chirality : 0.037 0.126 1101 Planarity : 0.004 0.038 1095 Dihedral : 17.074 115.978 1278 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.17 % Allowed : 15.73 % 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: 3.07 (0.30), residues: 786 helix: 3.04 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.51 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.010 0.001 TYR C 164 PHE 0.011 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 covalent geometry : bond 0.00283 ( 7221) covalent geometry : angle 0.55345 ( 9792) hydrogen bonds : bond 0.04038 ( 523) hydrogen bonds : angle 3.61673 ( 1551) Misc. bond : bond 0.08375 ( 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 124 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8828 (mt) cc_final: 0.8484 (mt) REVERT: A 78 GLU cc_start: 0.8191 (tp30) cc_final: 0.7765 (tp30) REVERT: A 171 GLU cc_start: 0.8442 (mp0) cc_final: 0.7836 (mp0) REVERT: A 247 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.8966 (mt) REVERT: A 258 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.6736 (t80) REVERT: B 78 GLU cc_start: 0.7845 (tp30) cc_final: 0.7531 (tp30) REVERT: B 143 VAL cc_start: 0.8845 (t) cc_final: 0.8611 (t) REVERT: B 172 ARG cc_start: 0.6809 (tpm170) cc_final: 0.6210 (mmp80) REVERT: B 201 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8212 (mmtt) REVERT: C 78 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7628 (tp30) REVERT: C 258 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.6870 (t80) outliers start: 22 outliers final: 5 residues processed: 117 average time/residue: 0.6118 time to fit residues: 74.7320 Evaluate side-chains 104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 181 ASP Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 136 LEU 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: 0.7980 chunk 70 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 0.0570 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 66 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 141 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.131652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.095007 restraints weight = 8224.252| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.53 r_work: 0.2796 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 7224 Z= 0.133 Angle : 0.583 6.460 9792 Z= 0.282 Chirality : 0.038 0.132 1101 Planarity : 0.004 0.040 1095 Dihedral : 17.022 112.911 1278 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.54 % Favored : 97.07 % Rotamer: Outliers : 3.03 % Allowed : 16.31 % 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: 2.98 (0.30), residues: 786 helix: 2.98 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.53 (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 0.014 0.002 PHE B 272 TRP 0.006 0.001 TRP B 276 HIS 0.002 0.001 HIS C 213 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7221) covalent geometry : angle 0.58302 ( 9792) hydrogen bonds : bond 0.04312 ( 523) hydrogen bonds : angle 3.65909 ( 1551) Misc. bond : bond 0.10301 ( 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 120 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.203 Fit side-chains REVERT: A 14 LEU cc_start: 0.8843 (mt) cc_final: 0.8500 (mt) REVERT: A 78 GLU cc_start: 0.8201 (tp30) cc_final: 0.7840 (tp30) REVERT: A 171 GLU cc_start: 0.8489 (mp0) cc_final: 0.8206 (mp0) REVERT: A 258 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7010 (t80) REVERT: B 78 GLU cc_start: 0.7814 (tp30) cc_final: 0.7502 (tp30) REVERT: B 143 VAL cc_start: 0.8958 (t) cc_final: 0.8730 (t) REVERT: B 172 ARG cc_start: 0.6923 (tpm170) cc_final: 0.6320 (mmp80) REVERT: B 201 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8230 (mmtt) REVERT: C 78 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7597 (tp30) REVERT: C 82 ARG cc_start: 0.8214 (mtp180) cc_final: 0.7544 (mmm-85) REVERT: C 258 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.6842 (t80) outliers start: 21 outliers final: 8 residues processed: 112 average time/residue: 0.5314 time to fit residues: 62.3042 Evaluate side-chains 104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 149 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 136 LEU 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 66 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 51 optimal weight: 0.0970 chunk 59 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 141 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.131826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.094379 restraints weight = 8181.498| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.57 r_work: 0.2788 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 7224 Z= 0.139 Angle : 0.604 8.343 9792 Z= 0.292 Chirality : 0.038 0.132 1101 Planarity : 0.004 0.041 1095 Dihedral : 17.002 112.174 1278 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.67 % Favored : 96.95 % Rotamer: Outliers : 2.89 % Allowed : 16.31 % 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: 2.91 (0.30), residues: 786 helix: 2.92 (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 0.002 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 A 276 HIS 0.003 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 7221) covalent geometry : angle 0.60449 ( 9792) hydrogen bonds : bond 0.04326 ( 523) hydrogen bonds : angle 3.68290 ( 1551) Misc. bond : bond 0.09556 ( 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 117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.208 Fit side-chains REVERT: A 14 LEU cc_start: 0.8858 (mt) cc_final: 0.8527 (mt) REVERT: A 78 GLU cc_start: 0.8255 (tp30) cc_final: 0.7815 (tp30) REVERT: A 171 GLU cc_start: 0.8522 (mp0) cc_final: 0.8255 (mp0) REVERT: A 237 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.8966 (tp) REVERT: A 258 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.6833 (t80) REVERT: B 78 GLU cc_start: 0.7807 (tp30) cc_final: 0.7515 (tp30) REVERT: B 143 VAL cc_start: 0.8997 (t) cc_final: 0.8761 (t) REVERT: B 172 ARG cc_start: 0.6954 (tpm170) cc_final: 0.6378 (mmp80) REVERT: B 201 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8144 (mmtm) REVERT: C 78 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7563 (tp30) REVERT: C 258 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.6853 (t80) outliers start: 20 outliers final: 10 residues processed: 110 average time/residue: 0.5708 time to fit residues: 65.6766 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 : 0.247 ------------------------------------------------------------------------------- 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 237 LEU 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 201 LYS Chi-restraints excluded: chain B residue 284 SER 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 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: 0.8980 chunk 25 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 0.0570 chunk 40 optimal weight: 0.0070 chunk 64 optimal weight: 0.6980 overall best weight: 0.3516 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.134516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.098002 restraints weight = 8218.808| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.54 r_work: 0.2828 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 7224 Z= 0.122 Angle : 0.577 8.075 9792 Z= 0.278 Chirality : 0.037 0.126 1101 Planarity : 0.004 0.037 1095 Dihedral : 16.397 106.870 1278 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.93 % Favored : 96.69 % Rotamer: Outliers : 2.16 % Allowed : 17.32 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.97 (0.30), residues: 786 helix: 2.98 (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 B 137 TYR 0.011 0.001 TYR C 164 PHE 0.013 0.001 PHE C 115 TRP 0.006 0.001 TRP A 276 HIS 0.003 0.001 HIS C 213 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7221) covalent geometry : angle 0.57663 ( 9792) hydrogen bonds : bond 0.04112 ( 523) hydrogen bonds : angle 3.62834 ( 1551) Misc. bond : bond 0.09092 ( 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 112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.167 Fit side-chains REVERT: A 14 LEU cc_start: 0.8862 (mt) cc_final: 0.8527 (mt) REVERT: A 78 GLU cc_start: 0.8243 (tp30) cc_final: 0.7839 (tp30) REVERT: A 171 GLU cc_start: 0.8487 (mp0) cc_final: 0.8140 (mp0) REVERT: A 237 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.8941 (tp) REVERT: A 258 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.6615 (t80) REVERT: B 78 GLU cc_start: 0.7840 (tp30) cc_final: 0.7548 (tp30) REVERT: B 143 VAL cc_start: 0.8927 (t) cc_final: 0.8707 (t) REVERT: B 172 ARG cc_start: 0.6926 (tpm170) cc_final: 0.6365 (mmp80) REVERT: B 201 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8237 (mmtt) REVERT: B 260 LEU cc_start: 0.8969 (mt) cc_final: 0.8664 (mp) REVERT: C 78 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7585 (tp30) REVERT: C 258 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.6838 (t80) outliers start: 15 outliers final: 6 residues processed: 105 average time/residue: 0.5939 time to fit residues: 65.0732 Evaluate side-chains 108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 237 LEU Chi-restraints excluded: chain A residue 258 PHE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 59 optimal weight: 0.0670 chunk 39 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.132051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.095040 restraints weight = 8269.506| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.56 r_work: 0.2792 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 7224 Z= 0.139 Angle : 0.602 8.201 9792 Z= 0.289 Chirality : 0.038 0.132 1101 Planarity : 0.004 0.038 1095 Dihedral : 16.479 106.258 1278 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.05 % Favored : 96.56 % Rotamer: Outliers : 1.73 % Allowed : 17.75 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.92 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.54 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.012 0.001 TYR C 199 PHE 0.015 0.002 PHE C 115 TRP 0.006 0.001 TRP B 276 HIS 0.003 0.001 HIS C 213 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7221) covalent geometry : angle 0.60163 ( 9792) hydrogen bonds : bond 0.04329 ( 523) hydrogen bonds : angle 3.67147 ( 1551) Misc. bond : bond 0.10215 ( 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 105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.160 Fit side-chains REVERT: A 14 LEU cc_start: 0.8868 (mt) cc_final: 0.8537 (mt) REVERT: A 78 GLU cc_start: 0.8231 (tp30) cc_final: 0.7809 (tp30) REVERT: A 171 GLU cc_start: 0.8506 (mp0) cc_final: 0.8256 (mp0) REVERT: A 237 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.8962 (tp) REVERT: A 258 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.6845 (t80) REVERT: B 78 GLU cc_start: 0.7763 (tp30) cc_final: 0.7468 (tp30) REVERT: B 143 VAL cc_start: 0.9006 (t) cc_final: 0.8771 (t) REVERT: B 172 ARG cc_start: 0.6921 (tpm170) cc_final: 0.6365 (mmp80) REVERT: B 201 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8242 (mmtt) REVERT: C 78 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7570 (tp30) REVERT: C 258 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.6892 (t80) outliers start: 12 outliers final: 9 residues processed: 100 average time/residue: 0.6612 time to fit residues: 68.8956 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 : 0.257 ------------------------------------------------------------------------------- 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 237 LEU 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 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 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: 0.9980 chunk 36 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 75 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.130477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.093221 restraints weight = 8194.783| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.58 r_work: 0.2773 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 7224 Z= 0.154 Angle : 0.615 8.215 9792 Z= 0.294 Chirality : 0.039 0.135 1101 Planarity : 0.004 0.039 1095 Dihedral : 16.795 108.193 1278 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.05 % Favored : 96.56 % 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: 2.84 (0.29), residues: 786 helix: 2.87 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.57 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 127 TYR 0.013 0.001 TYR C 199 PHE 0.016 0.002 PHE C 115 TRP 0.008 0.001 TRP C 76 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 7221) covalent geometry : angle 0.61507 ( 9792) hydrogen bonds : bond 0.04493 ( 523) hydrogen bonds : angle 3.72650 ( 1551) Misc. bond : bond 0.11311 ( 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 108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.286 Fit side-chains REVERT: A 14 LEU cc_start: 0.8867 (mt) cc_final: 0.8516 (mt) REVERT: A 78 GLU cc_start: 0.8223 (tp30) cc_final: 0.7783 (tp30) REVERT: A 171 GLU cc_start: 0.8568 (mp0) cc_final: 0.8313 (mp0) REVERT: A 237 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.8991 (tp) REVERT: A 258 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.6881 (t80) REVERT: B 78 GLU cc_start: 0.7753 (tp30) cc_final: 0.7461 (tp30) REVERT: B 143 VAL cc_start: 0.9051 (t) cc_final: 0.8826 (t) REVERT: B 172 ARG cc_start: 0.6951 (tpm170) cc_final: 0.6502 (mmp80) REVERT: B 201 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8125 (mmmm) REVERT: C 78 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7570 (tp30) REVERT: C 258 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.6857 (t80) outliers start: 12 outliers final: 7 residues processed: 103 average time/residue: 0.6782 time to fit residues: 72.7352 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 : 0.236 ------------------------------------------------------------------------------- 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 237 LEU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 chunk 74 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 0.0070 chunk 58 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 HIS C 141 HIS 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 = 0.133506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.098496 restraints weight = 8167.813| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.60 r_work: 0.2810 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 7224 Z= 0.130 Angle : 0.591 8.192 9792 Z= 0.285 Chirality : 0.038 0.126 1101 Planarity : 0.004 0.037 1095 Dihedral : 16.516 101.949 1278 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.67 % Favored : 96.95 % Rotamer: Outliers : 1.59 % Allowed : 17.46 % 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: 2.93 (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 ARG 0.001 0.000 ARG B 127 TYR 0.013 0.001 TYR C 199 PHE 0.014 0.001 PHE C 115 TRP 0.007 0.001 TRP C 76 HIS 0.003 0.001 HIS C 213 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 7221) covalent geometry : angle 0.59126 ( 9792) hydrogen bonds : bond 0.04230 ( 523) hydrogen bonds : angle 3.65811 ( 1551) Misc. bond : bond 0.09417 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2397.56 seconds wall clock time: 41 minutes 26.37 seconds (2486.37 seconds total)