Starting phenix.real_space_refine on Tue Feb 11 23:19:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u15_26278/02_2025/7u15_26278.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u15_26278/02_2025/7u15_26278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u15_26278/02_2025/7u15_26278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u15_26278/02_2025/7u15_26278.map" model { file = "/net/cci-nas-00/data/ceres_data/7u15_26278/02_2025/7u15_26278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u15_26278/02_2025/7u15_26278.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 21 5.16 5 C 2178 2.51 5 N 531 2.21 5 O 699 1.98 5 H 3255 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6684 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2172 Classifications: {'peptide': 135} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: C, B Time building chain proxies: 3.70, per 1000 atoms: 0.55 Number of scatterers: 6684 At special positions: 0 Unit cell: (93.183, 114.123, 39.786, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 O 699 8.00 N 531 7.00 C 2178 6.00 H 3255 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.03 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=0, symmetry=0 Links applied NAG-ASN " NAG A 301 " - " ASN A 183 " " NAG A 302 " - " ASN A 145 " " NAG A 303 " - " ASN A 151 " " NAG A 304 " - " ASN A 164 " " NAG B 301 " - " ASN B 183 " " NAG B 302 " - " ASN B 145 " " NAG B 303 " - " ASN B 151 " " NAG B 304 " - " ASN B 164 " " NAG C 301 " - " ASN C 183 " " NAG C 302 " - " ASN C 145 " " NAG C 303 " - " ASN C 151 " " NAG C 304 " - " ASN C 164 " Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 644.2 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 123 removed outlier: 6.773A pdb=" N ASP B 122 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130 removed outlier: 6.649A pdb=" N LYS B 129 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.475A pdb=" N VAL B 133 " --> pdb=" O SER A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 144 removed outlier: 6.827A pdb=" N TYR B 143 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.076A pdb=" N LEU B 150 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 156 through 158 removed outlier: 6.608A pdb=" N ASN B 156 " --> pdb=" O TYR A 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 169 through 171 removed outlier: 6.542A pdb=" N VAL B 169 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLN B 170 " --> pdb=" O PHE C 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 186 removed outlier: 6.623A pdb=" N THR B 185 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 190 through 191 removed outlier: 6.467A pdb=" N LEU B 190 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 195 through 196 removed outlier: 6.381A pdb=" N ILE B 195 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 206 through 207 removed outlier: 7.009A pdb=" N GLU B 206 " --> pdb=" O MET A 207 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 210 through 212 removed outlier: 6.784A pdb=" N TYR B 211 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 217 through 219 removed outlier: 6.077A pdb=" N SER B 218 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 224 through 231 removed outlier: 6.833A pdb=" N THR A 231 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL B 225 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET C 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N MET B 227 " --> pdb=" O MET C 228 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL C 230 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N GLN B 229 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 235 through 236 removed outlier: 6.851A pdb=" N THR B 235 " --> pdb=" O TYR A 236 " (cutoff:3.500A) 24 hydrogen bonds defined for protein. 72 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3255 1.03 - 1.23: 37 1.23 - 1.42: 1399 1.42 - 1.62: 2011 1.62 - 1.81: 36 Bond restraints: 6738 Sorted by residual: bond pdb=" C1 NAG B 302 " pdb=" O5 NAG B 302 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 8.94e+00 bond pdb=" C1 NAG A 302 " pdb=" O5 NAG A 302 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.85e+00 bond pdb=" C1 NAG C 302 " pdb=" O5 NAG C 302 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.78e+00 bond pdb=" CB ASP A 191 " pdb=" CG ASP A 191 " ideal model delta sigma weight residual 1.516 1.471 0.045 2.50e-02 1.60e+03 3.18e+00 bond pdb=" CB ASP C 191 " pdb=" CG ASP C 191 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.16e+00 ... (remaining 6733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.38: 12030 5.38 - 10.76: 27 10.76 - 16.15: 3 16.15 - 21.53: 0 21.53 - 26.91: 9 Bond angle restraints: 12069 Sorted by residual: angle pdb=" CG2 THR A 235 " pdb=" CB THR A 235 " pdb=" HB THR A 235 " ideal model delta sigma weight residual 108.00 81.09 26.91 3.00e+00 1.11e-01 8.05e+01 angle pdb=" CG2 THR B 235 " pdb=" CB THR B 235 " pdb=" HB THR B 235 " ideal model delta sigma weight residual 108.00 81.14 26.86 3.00e+00 1.11e-01 8.02e+01 angle pdb=" CG2 THR C 235 " pdb=" CB THR C 235 " pdb=" HB THR C 235 " ideal model delta sigma weight residual 108.00 81.16 26.84 3.00e+00 1.11e-01 8.00e+01 angle pdb=" OG1 THR B 235 " pdb=" CB THR B 235 " pdb=" HB THR B 235 " ideal model delta sigma weight residual 109.00 82.96 26.04 3.00e+00 1.11e-01 7.53e+01 angle pdb=" OG1 THR C 235 " pdb=" CB THR C 235 " pdb=" HB THR C 235 " ideal model delta sigma weight residual 109.00 83.02 25.98 3.00e+00 1.11e-01 7.50e+01 ... (remaining 12064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 2811 16.15 - 32.31: 408 32.31 - 48.46: 66 48.46 - 64.61: 54 64.61 - 80.77: 15 Dihedral angle restraints: 3354 sinusoidal: 1923 harmonic: 1431 Sorted by residual: dihedral pdb=" CA ALA A 204 " pdb=" C ALA A 204 " pdb=" N GLU A 205 " pdb=" CA GLU A 205 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ALA C 204 " pdb=" C ALA C 204 " pdb=" N GLU C 205 " pdb=" CA GLU C 205 " ideal model delta harmonic sigma weight residual 180.00 150.56 29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ALA B 204 " pdb=" C ALA B 204 " pdb=" N GLU B 205 " pdb=" CA GLU B 205 " ideal model delta harmonic sigma weight residual 180.00 150.60 29.40 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 3351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.293: 597 0.293 - 0.585: 3 0.585 - 0.878: 0 0.878 - 1.170: 0 1.170 - 1.463: 3 Chirality restraints: 603 Sorted by residual: chirality pdb=" CB THR A 235 " pdb=" CA THR A 235 " pdb=" OG1 THR A 235 " pdb=" CG2 THR A 235 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.35e+01 chirality pdb=" CB THR B 235 " pdb=" CA THR B 235 " pdb=" OG1 THR B 235 " pdb=" CG2 THR B 235 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.34e+01 chirality pdb=" CB THR C 235 " pdb=" CA THR C 235 " pdb=" OG1 THR C 235 " pdb=" CG2 THR C 235 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.34e+01 ... (remaining 600 not shown) Planarity restraints: 981 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 145 " -0.037 2.00e-02 2.50e+03 2.83e-02 1.20e+01 pdb=" CG ASN A 145 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 145 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 145 " 0.028 2.00e-02 2.50e+03 pdb="HD21 ASN A 145 " 0.010 2.00e-02 2.50e+03 pdb=" C1 NAG A 302 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 145 " -0.037 2.00e-02 2.50e+03 2.82e-02 1.19e+01 pdb=" CG ASN C 145 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN C 145 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 145 " 0.028 2.00e-02 2.50e+03 pdb="HD21 ASN C 145 " 0.010 2.00e-02 2.50e+03 pdb=" C1 NAG C 302 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 145 " -0.037 2.00e-02 2.50e+03 2.81e-02 1.19e+01 pdb=" CG ASN B 145 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN B 145 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 145 " 0.028 2.00e-02 2.50e+03 pdb="HD21 ASN B 145 " 0.010 2.00e-02 2.50e+03 pdb=" C1 NAG B 302 " -0.037 2.00e-02 2.50e+03 ... (remaining 978 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 485 2.19 - 2.79: 13507 2.79 - 3.40: 17853 3.40 - 4.00: 24411 4.00 - 4.60: 34874 Nonbonded interactions: 91130 Sorted by model distance: nonbonded pdb=" H VAL B 128 " pdb=" O VAL C 128 " model vdw 1.591 2.450 nonbonded pdb=" O VAL B 128 " pdb=" H VAL A 128 " model vdw 1.612 2.450 nonbonded pdb=" OG SER B 240 " pdb=" HH TYR C 236 " model vdw 1.663 2.450 nonbonded pdb=" HH TYR B 236 " pdb=" OG SER A 240 " model vdw 1.680 2.450 nonbonded pdb=" O GLU B 205 " pdb=" H GLU C 206 " model vdw 1.745 2.450 ... (remaining 91125 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.110 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.610 Find NCS groups from input model: 0.090 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:17.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 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 : 0.006 0.060 3483 Z= 0.395 Angle : 1.217 11.646 4737 Z= 0.678 Chirality : 0.124 1.463 603 Planarity : 0.009 0.056 573 Dihedral : 17.227 69.314 1461 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.44 % Allowed : 33.86 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.51 (0.28), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.96 (0.21), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.004 HIS C 239 PHE 0.006 0.001 PHE B 237 TYR 0.028 0.003 TYR A 250 ARG 0.007 0.002 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 ARG cc_start: 0.7214 (ptp90) cc_final: 0.6847 (ttp-110) REVERT: B 207 MET cc_start: 0.5623 (tmt) cc_final: 0.5314 (tmm) REVERT: A 124 LYS cc_start: 0.8111 (tppt) cc_final: 0.6240 (pptt) REVERT: A 180 ARG cc_start: 0.7229 (ptp90) cc_final: 0.6625 (mmm160) REVERT: A 207 MET cc_start: 0.5681 (tmt) cc_final: 0.5338 (tmm) REVERT: C 155 ASN cc_start: 0.7116 (m-40) cc_final: 0.6287 (p0) REVERT: C 180 ARG cc_start: 0.7526 (ptp90) cc_final: 0.6348 (ptp90) REVERT: C 207 MET cc_start: 0.6443 (tmt) cc_final: 0.6016 (tmm) REVERT: C 227 MET cc_start: 0.8210 (mtm) cc_final: 0.7970 (mtm) outliers start: 13 outliers final: 10 residues processed: 93 average time/residue: 1.4399 time to fit residues: 140.2522 Evaluate side-chains 78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.0870 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN B 155 ASN B 242 GLN A 154 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN C 154 ASN C 155 ASN C 242 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5157 r_free = 0.5157 target = 0.239973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.222178 restraints weight = 12591.334| |-----------------------------------------------------------------------------| r_work (start): 0.5039 rms_B_bonded: 2.16 r_work: 0.4988 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4923 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.4923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3483 Z= 0.214 Angle : 0.747 11.746 4737 Z= 0.413 Chirality : 0.112 1.528 603 Planarity : 0.005 0.049 573 Dihedral : 9.136 59.768 719 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.79 % Favored : 82.21 % Rotamer: Outliers : 6.61 % Allowed : 29.10 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.17 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.70 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 239 PHE 0.013 0.002 PHE C 213 TYR 0.024 0.002 TYR B 250 ARG 0.004 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.5973 (tmt) cc_final: 0.5409 (tmm) REVERT: A 124 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.6072 (pptt) REVERT: A 140 ARG cc_start: 0.5568 (OUTLIER) cc_final: 0.2814 (tpp-160) REVERT: A 168 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7748 (tp-100) REVERT: A 178 LYS cc_start: 0.7435 (ptmm) cc_final: 0.5146 (mmmt) REVERT: A 180 ARG cc_start: 0.7474 (ptp90) cc_final: 0.6620 (mmm160) REVERT: A 207 MET cc_start: 0.5665 (tmt) cc_final: 0.5166 (tmm) REVERT: A 247 ARG cc_start: 0.7649 (mtm-85) cc_final: 0.6005 (mtp85) REVERT: C 150 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7300 (mt) REVERT: C 180 ARG cc_start: 0.7776 (ptp90) cc_final: 0.6495 (ptt90) REVERT: C 207 MET cc_start: 0.6537 (tmt) cc_final: 0.6028 (tmm) REVERT: C 227 MET cc_start: 0.8493 (mtm) cc_final: 0.8205 (mtm) outliers start: 25 outliers final: 5 residues processed: 101 average time/residue: 1.6938 time to fit residues: 177.9911 Evaluate side-chains 90 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 192 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5146 r_free = 0.5146 target = 0.237618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5015 r_free = 0.5015 target = 0.219400 restraints weight = 12286.524| |-----------------------------------------------------------------------------| r_work (start): 0.5026 rms_B_bonded: 2.08 r_work: 0.4979 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4913 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3483 Z= 0.186 Angle : 0.689 11.451 4737 Z= 0.386 Chirality : 0.112 1.439 603 Planarity : 0.004 0.043 573 Dihedral : 7.371 52.154 703 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 5.56 % Allowed : 29.37 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.95 (0.29), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.53 (0.22), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 239 PHE 0.006 0.001 PHE C 171 TYR 0.014 0.001 TYR C 250 ARG 0.006 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 202 VAL cc_start: 0.6643 (OUTLIER) cc_final: 0.6237 (m) REVERT: B 241 GLU cc_start: 0.7939 (tt0) cc_final: 0.7727 (tt0) REVERT: A 124 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.5505 (pptt) REVERT: A 178 LYS cc_start: 0.7330 (ptmm) cc_final: 0.5083 (mmmt) REVERT: A 180 ARG cc_start: 0.7373 (ptp90) cc_final: 0.6512 (mmm160) REVERT: A 207 MET cc_start: 0.5758 (tmt) cc_final: 0.5446 (tmt) REVERT: A 239 HIS cc_start: 0.7914 (OUTLIER) cc_final: 0.7609 (p-80) REVERT: A 247 ARG cc_start: 0.7658 (mtm-85) cc_final: 0.5935 (mtp85) REVERT: C 150 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7557 (mt) REVERT: C 180 ARG cc_start: 0.7863 (ptp90) cc_final: 0.6757 (ptt90) REVERT: C 207 MET cc_start: 0.6475 (tmt) cc_final: 0.6145 (tmm) REVERT: C 227 MET cc_start: 0.8458 (mtm) cc_final: 0.8074 (mtm) outliers start: 21 outliers final: 4 residues processed: 93 average time/residue: 1.5736 time to fit residues: 152.6536 Evaluate side-chains 79 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5101 r_free = 0.5101 target = 0.231389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.213208 restraints weight = 12540.695| |-----------------------------------------------------------------------------| r_work (start): 0.5005 rms_B_bonded: 2.14 r_work: 0.4948 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4874 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.4874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3483 Z= 0.179 Angle : 0.654 11.452 4737 Z= 0.367 Chirality : 0.111 1.430 603 Planarity : 0.004 0.036 573 Dihedral : 6.016 33.947 703 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.54 % Favored : 82.46 % Rotamer: Outliers : 5.29 % Allowed : 30.69 % Favored : 64.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.66 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.31 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 239 PHE 0.007 0.001 PHE B 213 TYR 0.013 0.001 TYR C 143 ARG 0.006 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: B 207 MET cc_start: 0.5905 (tpt) cc_final: 0.5321 (tmm) REVERT: B 213 PHE cc_start: 0.6519 (t80) cc_final: 0.6141 (t80) REVERT: A 124 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.5810 (pptt) REVERT: A 180 ARG cc_start: 0.7503 (ptp90) cc_final: 0.6408 (mmm160) REVERT: A 207 MET cc_start: 0.5915 (tmt) cc_final: 0.5703 (tmm) REVERT: A 239 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.7567 (p-80) REVERT: A 247 ARG cc_start: 0.7775 (mtm-85) cc_final: 0.6226 (mtp85) REVERT: C 144 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7575 (pt) REVERT: C 150 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7728 (mt) REVERT: C 178 LYS cc_start: 0.7142 (ptmm) cc_final: 0.6775 (mtmm) REVERT: C 180 ARG cc_start: 0.7955 (ptp90) cc_final: 0.6832 (ptt90) REVERT: C 207 MET cc_start: 0.6599 (tmt) cc_final: 0.6169 (tmm) REVERT: C 227 MET cc_start: 0.8558 (mtm) cc_final: 0.8259 (mtm) REVERT: C 250 TYR cc_start: 0.7560 (p90) cc_final: 0.5219 (t80) outliers start: 20 outliers final: 8 residues processed: 104 average time/residue: 1.5618 time to fit residues: 169.5177 Evaluate side-chains 95 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 192 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 21 optimal weight: 0.3980 chunk 9 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5039 r_free = 0.5039 target = 0.222205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.203669 restraints weight = 12628.115| |-----------------------------------------------------------------------------| r_work (start): 0.4912 rms_B_bonded: 2.10 r_work: 0.4858 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4786 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.4786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3483 Z= 0.196 Angle : 0.654 11.417 4737 Z= 0.367 Chirality : 0.111 1.427 603 Planarity : 0.003 0.039 573 Dihedral : 5.903 32.780 703 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.54 % Favored : 83.46 % Rotamer: Outliers : 6.35 % Allowed : 31.22 % Favored : 62.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.58 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.25 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 239 PHE 0.007 0.001 PHE A 213 TYR 0.013 0.001 TYR A 211 ARG 0.005 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.549 Fit side-chains REVERT: B 163 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: B 207 MET cc_start: 0.5649 (tpt) cc_final: 0.5428 (tpt) REVERT: A 124 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.5652 (pptt) REVERT: A 163 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: A 180 ARG cc_start: 0.7498 (ptp90) cc_final: 0.6269 (mmm160) REVERT: A 207 MET cc_start: 0.5875 (tmt) cc_final: 0.5560 (tmt) REVERT: A 241 GLU cc_start: 0.7958 (tt0) cc_final: 0.7736 (tt0) REVERT: A 247 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.5987 (mtp85) REVERT: C 124 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7226 (mmtt) REVERT: C 150 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8022 (mt) REVERT: C 163 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: C 178 LYS cc_start: 0.7096 (ptmm) cc_final: 0.6445 (pttt) REVERT: C 180 ARG cc_start: 0.8098 (ptp90) cc_final: 0.6747 (ptt90) REVERT: C 207 MET cc_start: 0.6860 (tmt) cc_final: 0.6319 (tmm) REVERT: C 227 MET cc_start: 0.8775 (mtm) cc_final: 0.8334 (mtm) REVERT: C 250 TYR cc_start: 0.7693 (p90) cc_final: 0.5007 (t80) outliers start: 24 outliers final: 11 residues processed: 102 average time/residue: 1.4130 time to fit residues: 151.1472 Evaluate side-chains 99 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 240 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN A 148 ASN A 154 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4997 r_free = 0.4997 target = 0.217496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.199043 restraints weight = 12371.551| |-----------------------------------------------------------------------------| r_work (start): 0.4875 rms_B_bonded: 2.05 r_work: 0.4820 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4747 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.4747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3483 Z= 0.217 Angle : 0.661 11.407 4737 Z= 0.372 Chirality : 0.111 1.431 603 Planarity : 0.004 0.038 573 Dihedral : 5.841 32.571 703 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.30 % Favored : 81.70 % Rotamer: Outliers : 6.08 % Allowed : 30.95 % Favored : 62.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.45 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.15 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 239 PHE 0.007 0.001 PHE C 171 TYR 0.015 0.001 TYR C 143 ARG 0.006 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: B 239 HIS cc_start: 0.8002 (OUTLIER) cc_final: 0.7256 (p-80) REVERT: A 207 MET cc_start: 0.5913 (OUTLIER) cc_final: 0.5553 (tmt) REVERT: A 239 HIS cc_start: 0.7704 (OUTLIER) cc_final: 0.7419 (p-80) REVERT: A 247 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.5929 (mtp85) REVERT: C 124 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7270 (mmtt) REVERT: C 150 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8186 (mt) REVERT: C 163 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: C 178 LYS cc_start: 0.7532 (ptmm) cc_final: 0.6622 (pttt) REVERT: C 180 ARG cc_start: 0.8057 (ptp90) cc_final: 0.6133 (pmt-80) REVERT: C 207 MET cc_start: 0.6919 (tmt) cc_final: 0.6355 (tmm) REVERT: C 250 TYR cc_start: 0.8005 (p90) cc_final: 0.4901 (t80) outliers start: 23 outliers final: 11 residues processed: 106 average time/residue: 1.4406 time to fit residues: 159.9246 Evaluate side-chains 108 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 192 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 0 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4976 r_free = 0.4976 target = 0.214654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.196242 restraints weight = 12332.096| |-----------------------------------------------------------------------------| r_work (start): 0.4847 rms_B_bonded: 2.05 r_work: 0.4793 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4721 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.4721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.6564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3483 Z= 0.211 Angle : 0.657 11.388 4737 Z= 0.371 Chirality : 0.111 1.425 603 Planarity : 0.004 0.050 573 Dihedral : 5.798 32.540 703 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.30 % Favored : 81.70 % Rotamer: Outliers : 5.03 % Allowed : 34.39 % Favored : 60.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.41 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.12 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 239 PHE 0.007 0.001 PHE C 171 TYR 0.014 0.001 TYR C 143 ARG 0.009 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: B 207 MET cc_start: 0.5661 (tpt) cc_final: 0.5280 (tmm) REVERT: B 239 HIS cc_start: 0.7888 (OUTLIER) cc_final: 0.7212 (p-80) REVERT: A 132 TYR cc_start: 0.8659 (t80) cc_final: 0.8262 (t80) REVERT: A 168 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8265 (tm-30) REVERT: A 207 MET cc_start: 0.6146 (tmt) cc_final: 0.5840 (tmm) REVERT: A 239 HIS cc_start: 0.7694 (OUTLIER) cc_final: 0.7414 (p-80) REVERT: A 247 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.5966 (mtp85) REVERT: C 124 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7321 (mmtt) REVERT: C 156 ASN cc_start: 0.8612 (m110) cc_final: 0.8319 (m110) REVERT: C 163 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: C 178 LYS cc_start: 0.7704 (ptmm) cc_final: 0.7009 (pttt) REVERT: C 207 MET cc_start: 0.7053 (tmt) cc_final: 0.6402 (tmm) REVERT: C 250 TYR cc_start: 0.8219 (p90) cc_final: 0.4742 (t80) outliers start: 19 outliers final: 9 residues processed: 105 average time/residue: 1.4889 time to fit residues: 163.4856 Evaluate side-chains 102 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 240 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.214926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.196424 restraints weight = 12070.942| |-----------------------------------------------------------------------------| r_work (start): 0.4853 rms_B_bonded: 2.06 r_work: 0.4799 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4724 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.4724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.6861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3483 Z= 0.178 Angle : 0.627 11.386 4737 Z= 0.355 Chirality : 0.110 1.421 603 Planarity : 0.004 0.049 573 Dihedral : 5.581 33.895 703 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.29 % Favored : 82.71 % Rotamer: Outliers : 4.76 % Allowed : 32.54 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.35 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 239 PHE 0.005 0.001 PHE C 171 TYR 0.012 0.001 TYR C 211 ARG 0.008 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.5652 (tpt) cc_final: 0.5096 (tmm) REVERT: A 132 TYR cc_start: 0.8649 (t80) cc_final: 0.8321 (t80) REVERT: A 180 ARG cc_start: 0.7444 (ptp90) cc_final: 0.7042 (pmm-80) REVERT: A 207 MET cc_start: 0.6083 (OUTLIER) cc_final: 0.5771 (tmm) REVERT: A 247 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.5935 (mtp85) REVERT: C 124 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7279 (mmtt) REVERT: C 156 ASN cc_start: 0.8656 (m110) cc_final: 0.8312 (m-40) REVERT: C 163 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: C 178 LYS cc_start: 0.7685 (ptmm) cc_final: 0.6994 (pttt) REVERT: C 207 MET cc_start: 0.7053 (tmt) cc_final: 0.6493 (tmm) REVERT: C 250 TYR cc_start: 0.8145 (p90) cc_final: 0.4734 (t80) outliers start: 18 outliers final: 9 residues processed: 100 average time/residue: 1.5228 time to fit residues: 159.3696 Evaluate side-chains 92 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 192 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.211793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.193201 restraints weight = 12113.865| |-----------------------------------------------------------------------------| r_work (start): 0.4840 rms_B_bonded: 2.07 r_work: 0.4784 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4712 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.4712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.7101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3483 Z= 0.204 Angle : 0.642 11.429 4737 Z= 0.364 Chirality : 0.111 1.432 603 Planarity : 0.004 0.044 573 Dihedral : 5.637 32.978 703 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.30 % Favored : 81.70 % Rotamer: Outliers : 4.50 % Allowed : 34.13 % Favored : 61.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.32 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 239 PHE 0.007 0.001 PHE C 171 TYR 0.014 0.001 TYR C 143 ARG 0.006 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.6040 (tpt) cc_final: 0.5583 (tmm) REVERT: B 239 HIS cc_start: 0.7864 (OUTLIER) cc_final: 0.7527 (p-80) REVERT: A 132 TYR cc_start: 0.8577 (t80) cc_final: 0.8248 (t80) REVERT: A 180 ARG cc_start: 0.7456 (ptp90) cc_final: 0.7203 (pmm-80) REVERT: A 207 MET cc_start: 0.6150 (OUTLIER) cc_final: 0.5824 (tmm) REVERT: A 247 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.5968 (mtp85) REVERT: C 124 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7339 (mmtt) REVERT: C 156 ASN cc_start: 0.8665 (m110) cc_final: 0.8345 (m-40) REVERT: C 163 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: C 178 LYS cc_start: 0.7745 (ptmm) cc_final: 0.7053 (pttt) REVERT: C 207 MET cc_start: 0.7107 (tmt) cc_final: 0.6536 (tmm) REVERT: C 250 TYR cc_start: 0.8305 (p90) cc_final: 0.4752 (t80) outliers start: 17 outliers final: 8 residues processed: 99 average time/residue: 1.3842 time to fit residues: 144.0415 Evaluate side-chains 94 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 240 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.213533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.195338 restraints weight = 12181.832| |-----------------------------------------------------------------------------| r_work (start): 0.4863 rms_B_bonded: 2.10 r_work: 0.4806 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4732 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.4732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.7282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3483 Z= 0.176 Angle : 0.627 11.413 4737 Z= 0.356 Chirality : 0.110 1.427 603 Planarity : 0.004 0.044 573 Dihedral : 5.501 33.642 703 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.29 % Favored : 82.71 % Rotamer: Outliers : 4.23 % Allowed : 32.80 % Favored : 62.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.28 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 239 PHE 0.006 0.001 PHE C 171 TYR 0.013 0.001 TYR C 143 ARG 0.006 0.001 ARG A 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.6051 (tpt) cc_final: 0.5655 (tmm) REVERT: B 239 HIS cc_start: 0.7821 (OUTLIER) cc_final: 0.7561 (p-80) REVERT: A 180 ARG cc_start: 0.7473 (ptp90) cc_final: 0.7039 (pmm-80) REVERT: A 207 MET cc_start: 0.6163 (OUTLIER) cc_final: 0.5850 (tmm) REVERT: A 247 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.5964 (mtp85) REVERT: C 124 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7347 (mmtt) REVERT: C 156 ASN cc_start: 0.8651 (m110) cc_final: 0.8312 (m-40) REVERT: C 163 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: C 178 LYS cc_start: 0.7814 (ptmm) cc_final: 0.7093 (pttt) REVERT: C 207 MET cc_start: 0.7098 (tmt) cc_final: 0.6546 (tmm) REVERT: C 239 HIS cc_start: 0.6974 (OUTLIER) cc_final: 0.6733 (p90) REVERT: C 250 TYR cc_start: 0.8228 (p90) cc_final: 0.4730 (t80) outliers start: 16 outliers final: 9 residues processed: 91 average time/residue: 1.4397 time to fit residues: 137.3538 Evaluate side-chains 94 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 240 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5013 r_free = 0.5013 target = 0.217327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.199363 restraints weight = 12107.129| |-----------------------------------------------------------------------------| r_work (start): 0.4899 rms_B_bonded: 2.09 r_work: 0.4843 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4771 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.4771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.7392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3483 Z= 0.157 Angle : 0.613 11.389 4737 Z= 0.348 Chirality : 0.110 1.425 603 Planarity : 0.004 0.043 573 Dihedral : 5.333 33.750 703 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 4.23 % Allowed : 32.80 % Favored : 62.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.26 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 222 PHE 0.004 0.001 PHE C 171 TYR 0.013 0.001 TYR B 211 ARG 0.006 0.001 ARG A 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5705.28 seconds wall clock time: 100 minutes 53.09 seconds (6053.09 seconds total)