Starting phenix.real_space_refine on Tue Mar 11 22:50:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u15_26278/03_2025/7u15_26278.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u15_26278/03_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_26278/03_2025/7u15_26278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u15_26278/03_2025/7u15_26278.map" model { file = "/net/cci-nas-00/data/ceres_data/7u15_26278/03_2025/7u15_26278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u15_26278/03_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-5624/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: 3.92, per 1000 atoms: 0.59 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: 1.76 Conformation dependent library (CDL) restraints added in 634.7 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: 0.69 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: 2.02 Time building geometry restraints manager: 2.16 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: 0.830 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.840 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:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.540 ------------------------------------------------------------------------------- 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 : 0.544 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: 1.4126 time to fit residues: 137.9221 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 : 0.511 ------------------------------------------------------------------------------- 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: 2.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- 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 = 0.5100 r_free = 0.5100 target = 0.233821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.215524 restraints weight = 12455.827| |-----------------------------------------------------------------------------| r_work (start): 0.4977 rms_B_bonded: 2.12 r_work: 0.4924 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.4854 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3483 Z= 0.243 Angle : 0.769 11.546 4737 Z= 0.425 Chirality : 0.112 1.500 603 Planarity : 0.005 0.050 573 Dihedral : 8.536 48.424 719 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.79 % Favored : 82.21 % Rotamer: Outliers : 7.41 % Allowed : 27.25 % Favored : 65.34 % 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: -6.18 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.71 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 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 120 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 LYS cc_start: 0.6939 (ptmm) cc_final: 0.5779 (pttt) REVERT: B 202 VAL cc_start: 0.6588 (OUTLIER) cc_final: 0.6292 (m) REVERT: B 207 MET cc_start: 0.5943 (tmt) cc_final: 0.5351 (tmm) REVERT: B 241 GLU cc_start: 0.8153 (tt0) cc_final: 0.7915 (tt0) REVERT: A 124 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.5927 (pptt) REVERT: A 157 TYR cc_start: 0.8757 (m-80) cc_final: 0.8537 (m-80) REVERT: A 178 LYS cc_start: 0.7450 (ptmm) cc_final: 0.5192 (mmpt) REVERT: A 180 ARG cc_start: 0.7494 (ptp90) cc_final: 0.6659 (mmp-170) REVERT: A 207 MET cc_start: 0.5721 (tmt) cc_final: 0.5216 (tmm) REVERT: A 239 HIS cc_start: 0.7790 (OUTLIER) cc_final: 0.7497 (p-80) REVERT: A 247 ARG cc_start: 0.7746 (mtm-85) cc_final: 0.5993 (mtp85) REVERT: C 150 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7438 (mt) REVERT: C 178 LYS cc_start: 0.6851 (ptmm) cc_final: 0.6602 (mtmm) REVERT: C 180 ARG cc_start: 0.7816 (ptp90) cc_final: 0.6458 (ptt90) REVERT: C 207 MET cc_start: 0.6575 (tmt) cc_final: 0.6019 (tmm) REVERT: C 227 MET cc_start: 0.8546 (mtm) cc_final: 0.8264 (mtm) outliers start: 28 outliers final: 7 residues processed: 110 average time/residue: 1.6463 time to fit residues: 188.4709 Evaluate side-chains 96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 170 GLN 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 130 SER Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 240 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** 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 = 0.5047 r_free = 0.5047 target = 0.223674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.205300 restraints weight = 12485.884| |-----------------------------------------------------------------------------| r_work (start): 0.4912 rms_B_bonded: 2.11 r_work: 0.4861 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4795 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.4795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3483 Z= 0.238 Angle : 0.735 11.450 4737 Z= 0.411 Chirality : 0.113 1.450 603 Planarity : 0.004 0.046 573 Dihedral : 6.656 34.335 703 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.54 % Favored : 84.46 % Rotamer: Outliers : 6.88 % Allowed : 27.51 % Favored : 65.61 % 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: -5.87 (0.29), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.47 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 239 PHE 0.008 0.001 PHE B 213 TYR 0.013 0.001 TYR C 143 ARG 0.007 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 123 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: B 178 LYS cc_start: 0.7137 (ptmm) cc_final: 0.6922 (ptmt) REVERT: B 207 MET cc_start: 0.5941 (tmt) cc_final: 0.5700 (tpt) REVERT: B 241 GLU cc_start: 0.8049 (tt0) cc_final: 0.7830 (tt0) REVERT: A 124 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.5959 (pptt) REVERT: A 163 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: A 168 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: A 180 ARG cc_start: 0.7565 (ptp90) cc_final: 0.6376 (mmm160) REVERT: A 207 MET cc_start: 0.6187 (tmt) cc_final: 0.5717 (tmt) REVERT: A 247 ARG cc_start: 0.7864 (mtm-85) cc_final: 0.5968 (mtp85) REVERT: C 150 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7883 (mt) REVERT: C 163 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: C 178 LYS cc_start: 0.6975 (ptmm) cc_final: 0.6673 (mtmm) REVERT: C 180 ARG cc_start: 0.7972 (ptp90) cc_final: 0.6775 (ptt90) REVERT: C 207 MET cc_start: 0.6652 (tmt) cc_final: 0.6288 (tmm) REVERT: C 250 TYR cc_start: 0.7553 (p90) cc_final: 0.5091 (t80) outliers start: 26 outliers final: 9 residues processed: 115 average time/residue: 1.4176 time to fit residues: 170.5150 Evaluate side-chains 101 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 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 168 GLN Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 144 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 21 optimal weight: 0.0870 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 GLN ** 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 = 0.5075 r_free = 0.5075 target = 0.228731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.210928 restraints weight = 12525.599| |-----------------------------------------------------------------------------| r_work (start): 0.4975 rms_B_bonded: 2.12 r_work: 0.4912 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4835 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.4835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3483 Z= 0.165 Angle : 0.643 11.319 4737 Z= 0.362 Chirality : 0.110 1.417 603 Planarity : 0.003 0.040 573 Dihedral : 6.002 35.278 703 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.04 % Favored : 83.96 % Rotamer: Outliers : 5.82 % Allowed : 29.89 % 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: -5.65 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.30 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 239 PHE 0.011 0.001 PHE A 213 TYR 0.011 0.001 TYR C 143 ARG 0.004 0.000 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 108 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: B 178 LYS cc_start: 0.7226 (ptmm) cc_final: 0.7002 (ptmt) REVERT: B 207 MET cc_start: 0.6216 (tmt) cc_final: 0.5972 (tpt) REVERT: B 239 HIS cc_start: 0.8128 (OUTLIER) cc_final: 0.7512 (p-80) REVERT: A 124 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.5717 (pptt) REVERT: A 168 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: A 180 ARG cc_start: 0.7531 (ptp90) cc_final: 0.6481 (mmm160) REVERT: A 207 MET cc_start: 0.6193 (tmt) cc_final: 0.5852 (tmt) REVERT: A 239 HIS cc_start: 0.7743 (OUTLIER) cc_final: 0.7364 (p-80) REVERT: A 247 ARG cc_start: 0.7775 (mtm-85) cc_final: 0.6221 (mtp85) REVERT: C 150 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7672 (mt) REVERT: C 163 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: C 178 LYS cc_start: 0.7240 (ptmm) cc_final: 0.6904 (mtmm) REVERT: C 180 ARG cc_start: 0.7991 (ptp90) cc_final: 0.6830 (ptt90) REVERT: C 207 MET cc_start: 0.6742 (tmt) cc_final: 0.6359 (tmm) REVERT: C 215 THR cc_start: 0.7755 (p) cc_final: 0.7507 (t) REVERT: C 227 MET cc_start: 0.8833 (mtm) cc_final: 0.8463 (mtm) REVERT: C 250 TYR cc_start: 0.7676 (p90) cc_final: 0.5175 (t80) outliers start: 22 outliers final: 9 residues processed: 101 average time/residue: 1.3139 time to fit residues: 139.3268 Evaluate side-chains 97 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 215 THR Chi-restraints excluded: chain B residue 239 HIS 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 168 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 170 GLN 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: 3.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 0.0070 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.5094 r_free = 0.5094 target = 0.230298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.212415 restraints weight = 12163.569| |-----------------------------------------------------------------------------| r_work (start): 0.4972 rms_B_bonded: 2.01 r_work: 0.4923 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4857 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.4857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3483 Z= 0.156 Angle : 0.628 11.342 4737 Z= 0.354 Chirality : 0.109 1.406 603 Planarity : 0.003 0.038 573 Dihedral : 5.709 35.457 703 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.54 % Favored : 83.46 % Rotamer: Outliers : 3.97 % Allowed : 32.01 % 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: -5.50 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.19 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 239 PHE 0.005 0.001 PHE C 171 TYR 0.011 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 103 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.542 Fit side-chains REVERT: B 178 LYS cc_start: 0.7297 (ptmm) cc_final: 0.7095 (ptmt) REVERT: B 207 MET cc_start: 0.6000 (tmt) cc_final: 0.5706 (tpt) REVERT: B 239 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7430 (p-80) REVERT: A 124 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.5305 (pptt) REVERT: A 168 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: A 180 ARG cc_start: 0.7521 (ptp90) cc_final: 0.6388 (mmm160) REVERT: A 207 MET cc_start: 0.6028 (tmt) cc_final: 0.5606 (tmt) REVERT: A 227 MET cc_start: 0.8366 (mtp) cc_final: 0.8125 (mtm) REVERT: A 239 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.7374 (p-80) REVERT: A 247 ARG cc_start: 0.7563 (mtm-85) cc_final: 0.6004 (mtp85) REVERT: C 132 TYR cc_start: 0.7659 (t80) cc_final: 0.7438 (t80) REVERT: C 150 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7763 (mt) REVERT: C 168 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.6826 (tm-30) REVERT: C 178 LYS cc_start: 0.7121 (ptmm) cc_final: 0.6729 (mtmm) REVERT: C 180 ARG cc_start: 0.8009 (ptp90) cc_final: 0.6771 (ptt90) REVERT: C 207 MET cc_start: 0.6642 (tmt) cc_final: 0.6207 (tmm) REVERT: C 215 THR cc_start: 0.7279 (p) cc_final: 0.6962 (t) REVERT: C 250 TYR cc_start: 0.7660 (p90) cc_final: 0.5062 (t80) outliers start: 15 outliers final: 6 residues processed: 98 average time/residue: 1.4101 time to fit residues: 144.7974 Evaluate side-chains 93 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 210 MET 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 124 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 168 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN A 154 ASN ** A 155 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.224642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.206449 restraints weight = 12237.637| |-----------------------------------------------------------------------------| r_work (start): 0.4916 rms_B_bonded: 2.11 r_work: 0.4862 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4790 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.4790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.5673 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= 0.186 Angle : 0.635 11.399 4737 Z= 0.358 Chirality : 0.110 1.424 603 Planarity : 0.004 0.038 573 Dihedral : 5.647 34.420 703 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.29 % Favored : 82.71 % Rotamer: Outliers : 5.29 % Allowed : 30.95 % Favored : 63.76 % 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: -5.40 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 222 PHE 0.004 0.001 PHE C 171 TYR 0.013 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 114 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: B 207 MET cc_start: 0.5895 (tmt) cc_final: 0.5493 (tpt) REVERT: B 239 HIS cc_start: 0.7995 (OUTLIER) cc_final: 0.7333 (p-80) REVERT: A 124 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.5431 (pptt) REVERT: A 168 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: A 180 ARG cc_start: 0.7528 (ptp90) cc_final: 0.6399 (mmm160) REVERT: A 207 MET cc_start: 0.6097 (tmt) cc_final: 0.5590 (tmt) REVERT: A 239 HIS cc_start: 0.7657 (OUTLIER) cc_final: 0.7367 (p-80) REVERT: A 247 ARG cc_start: 0.7697 (mtm-85) cc_final: 0.5916 (mtp85) REVERT: C 124 LYS cc_start: 0.8483 (mmtp) cc_final: 0.7410 (mmtt) REVERT: C 150 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7990 (mt) REVERT: C 168 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.6874 (tm-30) REVERT: C 171 PHE cc_start: 0.5500 (m-10) cc_final: 0.5091 (m-80) REVERT: C 178 LYS cc_start: 0.7486 (ptmm) cc_final: 0.6623 (pttt) REVERT: C 180 ARG cc_start: 0.8105 (ptp90) cc_final: 0.6792 (ptt90) REVERT: C 207 MET cc_start: 0.6781 (tmt) cc_final: 0.6259 (tmm) REVERT: C 215 THR cc_start: 0.7260 (p) cc_final: 0.6871 (t) REVERT: C 250 TYR cc_start: 0.7800 (p90) cc_final: 0.4907 (t80) outliers start: 20 outliers final: 9 residues processed: 107 average time/residue: 1.3871 time to fit residues: 155.4627 Evaluate side-chains 102 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 215 THR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 239 HIS 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 168 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 170 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 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 A 148 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4992 r_free = 0.4992 target = 0.217014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.198352 restraints weight = 12304.604| |-----------------------------------------------------------------------------| r_work (start): 0.4861 rms_B_bonded: 2.04 r_work: 0.4808 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4738 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.4738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.6230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3483 Z= 0.214 Angle : 0.647 11.384 4737 Z= 0.366 Chirality : 0.109 1.417 603 Planarity : 0.004 0.040 573 Dihedral : 5.645 34.045 703 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.29 % Favored : 82.71 % Rotamer: Outliers : 5.03 % Allowed : 31.22 % Favored : 63.76 % 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: -5.37 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 239 PHE 0.005 0.001 PHE B 213 TYR 0.014 0.001 TYR A 211 ARG 0.006 0.001 ARG B 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 118 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.6127 (OUTLIER) cc_final: 0.5743 (tpt) REVERT: B 239 HIS cc_start: 0.7947 (OUTLIER) cc_final: 0.7183 (p-80) REVERT: A 132 TYR cc_start: 0.8537 (t80) cc_final: 0.8232 (t80) REVERT: A 207 MET cc_start: 0.6276 (OUTLIER) cc_final: 0.5703 (tmt) REVERT: A 239 HIS cc_start: 0.8084 (OUTLIER) cc_final: 0.7798 (p-80) REVERT: A 247 ARG cc_start: 0.7776 (mtm-85) cc_final: 0.6006 (mtp85) REVERT: C 124 LYS cc_start: 0.8564 (mmtp) cc_final: 0.7554 (mmtt) REVERT: C 132 TYR cc_start: 0.7788 (t80) cc_final: 0.7518 (t80) REVERT: C 150 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8175 (mt) REVERT: C 163 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: C 168 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7052 (tm-30) REVERT: C 171 PHE cc_start: 0.5594 (m-10) cc_final: 0.5237 (m-10) REVERT: C 178 LYS cc_start: 0.7645 (ptmm) cc_final: 0.6802 (pttt) REVERT: C 180 ARG cc_start: 0.8095 (ptp90) cc_final: 0.6147 (pmt-80) REVERT: C 207 MET cc_start: 0.6854 (tmt) cc_final: 0.6273 (tmm) REVERT: C 215 THR cc_start: 0.7539 (p) cc_final: 0.7081 (t) REVERT: C 250 TYR cc_start: 0.8031 (p90) cc_final: 0.4799 (t80) outliers start: 19 outliers final: 9 residues processed: 111 average time/residue: 1.3843 time to fit residues: 161.2654 Evaluate side-chains 107 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 218 SER 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 168 GLN Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 170 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN B 156 ASN A 148 ASN A 155 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4966 r_free = 0.4966 target = 0.213762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.194943 restraints weight = 12295.864| |-----------------------------------------------------------------------------| r_work (start): 0.4834 rms_B_bonded: 2.03 r_work: 0.4778 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4705 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.4705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.6568 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 : 0.654 11.471 4737 Z= 0.369 Chirality : 0.111 1.432 603 Planarity : 0.004 0.039 573 Dihedral : 5.693 34.024 703 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.79 % Favored : 83.21 % Rotamer: Outliers : 5.82 % Allowed : 30.95 % Favored : 63.23 % 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 (0.33), 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 0.003 0.001 HIS C 239 PHE 0.004 0.001 PHE B 171 TYR 0.014 0.001 TYR C 143 ARG 0.006 0.001 ARG B 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 112 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ILE cc_start: 0.8098 (mp) cc_final: 0.7897 (mm) REVERT: B 207 MET cc_start: 0.6240 (OUTLIER) cc_final: 0.5657 (tmm) REVERT: B 239 HIS cc_start: 0.7842 (OUTLIER) cc_final: 0.7173 (p-80) REVERT: A 207 MET cc_start: 0.6310 (OUTLIER) cc_final: 0.5841 (tmm) REVERT: A 239 HIS cc_start: 0.7627 (OUTLIER) cc_final: 0.7371 (p-80) REVERT: A 247 ARG cc_start: 0.7792 (mtm-85) cc_final: 0.5968 (mtp85) REVERT: C 124 LYS cc_start: 0.8519 (mmtp) cc_final: 0.7483 (mmtt) REVERT: C 132 TYR cc_start: 0.7779 (t80) cc_final: 0.7494 (t80) REVERT: C 150 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8353 (mt) REVERT: C 163 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: C 168 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: C 178 LYS cc_start: 0.7667 (ptmm) cc_final: 0.6869 (pttt) REVERT: C 180 ARG cc_start: 0.8077 (ptp90) cc_final: 0.6221 (pmt-80) REVERT: C 207 MET cc_start: 0.6908 (tmt) cc_final: 0.6375 (tmm) REVERT: C 215 THR cc_start: 0.7518 (p) cc_final: 0.7014 (t) REVERT: C 239 HIS cc_start: 0.7221 (OUTLIER) cc_final: 0.6697 (p-80) REVERT: C 250 TYR cc_start: 0.8182 (p90) cc_final: 0.4722 (t80) outliers start: 22 outliers final: 12 residues processed: 105 average time/residue: 1.3523 time to fit residues: 149.0001 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 : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 218 SER 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 168 GLN Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 239 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN B 242 GLN A 148 ASN A 155 ASN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN C 148 ASN C 242 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.214431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.195707 restraints weight = 12337.398| |-----------------------------------------------------------------------------| r_work (start): 0.4855 rms_B_bonded: 2.10 r_work: 0.4798 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4725 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.4725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.6789 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= 0.188 Angle : 0.638 11.392 4737 Z= 0.361 Chirality : 0.110 1.420 603 Planarity : 0.003 0.040 573 Dihedral : 5.583 34.969 703 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.04 % Favored : 82.96 % Rotamer: Outliers : 4.50 % Allowed : 33.33 % Favored : 62.17 % 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: -5.27 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 222 PHE 0.004 0.001 PHE C 171 TYR 0.014 0.001 TYR A 211 ARG 0.007 0.001 ARG B 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 111 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ILE cc_start: 0.8185 (mp) cc_final: 0.7921 (mm) REVERT: B 207 MET cc_start: 0.6467 (OUTLIER) cc_final: 0.5859 (tmm) REVERT: A 207 MET cc_start: 0.6399 (tmt) cc_final: 0.5824 (tmm) REVERT: A 239 HIS cc_start: 0.7629 (OUTLIER) cc_final: 0.7318 (p-80) REVERT: A 247 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.5921 (mtp85) REVERT: C 124 LYS cc_start: 0.8497 (mmtp) cc_final: 0.7451 (mmtt) REVERT: C 132 TYR cc_start: 0.7783 (t80) cc_final: 0.7556 (t80) REVERT: C 150 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8441 (mt) REVERT: C 168 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.6969 (tm-30) REVERT: C 171 PHE cc_start: 0.5794 (m-10) cc_final: 0.5433 (m-80) REVERT: C 178 LYS cc_start: 0.7711 (ptmm) cc_final: 0.6938 (pttt) REVERT: C 180 ARG cc_start: 0.8031 (ptp90) cc_final: 0.6184 (pmt-80) REVERT: C 207 MET cc_start: 0.6925 (tmt) cc_final: 0.6243 (tmm) REVERT: C 215 THR cc_start: 0.7445 (p) cc_final: 0.6921 (t) REVERT: C 250 TYR cc_start: 0.8126 (p90) cc_final: 0.4705 (t80) outliers start: 17 outliers final: 9 residues processed: 105 average time/residue: 1.3384 time to fit residues: 147.8197 Evaluate side-chains 103 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 170 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.0980 chunk 32 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN A 148 ASN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN C 148 ASN C 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.217293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.198831 restraints weight = 12247.969| |-----------------------------------------------------------------------------| r_work (start): 0.4887 rms_B_bonded: 2.13 r_work: 0.4833 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.4759 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.4759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.6950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3483 Z= 0.164 Angle : 0.624 11.375 4737 Z= 0.353 Chirality : 0.110 1.421 603 Planarity : 0.003 0.038 573 Dihedral : 5.452 35.982 703 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.54 % Favored : 83.46 % 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: -5.21 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (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 0.014 0.001 TYR B 211 ARG 0.004 0.001 ARG B 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 107 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ILE cc_start: 0.8292 (mp) cc_final: 0.8006 (mm) REVERT: B 207 MET cc_start: 0.6569 (OUTLIER) cc_final: 0.5943 (tmm) REVERT: A 207 MET cc_start: 0.6383 (tmt) cc_final: 0.5824 (tmm) REVERT: A 239 HIS cc_start: 0.7788 (OUTLIER) cc_final: 0.7467 (p-80) REVERT: A 247 ARG cc_start: 0.7639 (mtm-85) cc_final: 0.5864 (mtp85) REVERT: C 124 LYS cc_start: 0.8473 (mmtp) cc_final: 0.7249 (mmtt) REVERT: C 132 TYR cc_start: 0.7737 (t80) cc_final: 0.7525 (t80) REVERT: C 150 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8432 (mt) REVERT: C 171 PHE cc_start: 0.5769 (m-10) cc_final: 0.5336 (m-80) REVERT: C 178 LYS cc_start: 0.7687 (ptmm) cc_final: 0.6947 (pttt) REVERT: C 180 ARG cc_start: 0.7972 (ptp90) cc_final: 0.6183 (pmt-80) REVERT: C 207 MET cc_start: 0.6933 (tmt) cc_final: 0.6383 (tmm) REVERT: C 215 THR cc_start: 0.7074 (p) cc_final: 0.6574 (t) REVERT: C 250 TYR cc_start: 0.8119 (p90) cc_final: 0.4680 (t80) outliers start: 16 outliers final: 10 residues processed: 101 average time/residue: 1.4439 time to fit residues: 152.7946 Evaluate side-chains 100 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 218 SER 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 168 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 170 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN A 242 GLN C 148 ASN C 154 ASN C 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5006 r_free = 0.5006 target = 0.217235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.198820 restraints weight = 12149.378| |-----------------------------------------------------------------------------| r_work (start): 0.4886 rms_B_bonded: 2.11 r_work: 0.4833 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4760 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.4760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.7021 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= 0.171 Angle : 0.623 11.389 4737 Z= 0.353 Chirality : 0.110 1.425 603 Planarity : 0.003 0.038 573 Dihedral : 5.327 34.778 703 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.04 % Favored : 83.96 % Rotamer: Outliers : 3.97 % Allowed : 32.80 % Favored : 63.23 % 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: -5.17 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 239 PHE 0.004 0.001 PHE C 171 TYR 0.015 0.001 TYR A 211 ARG 0.012 0.001 ARG B 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5816.39 seconds wall clock time: 99 minutes 1.99 seconds (5941.99 seconds total)