Starting phenix.real_space_refine on Fri Sep 11 00:16:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25ve_80402/09_2026/25ve_80402.cif Found real_map, /net/cci-nas-00/data/ceres_data/25ve_80402/09_2026/25ve_80402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25ve_80402/09_2026/25ve_80402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25ve_80402/09_2026/25ve_80402.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25ve_80402/09_2026/25ve_80402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25ve_80402/09_2026/25ve_80402.map" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.118 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 3603 2.51 5 N 1002 2.21 5 O 1095 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5736 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1912 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 241} Chain: "B" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1912 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 241} Chain: "C" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1912 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 241} Time building chain proxies: 1.49, per 1000 atoms: 0.26 Number of scatterers: 5736 At special positions: 0 Unit cell: (60.19, 61.116, 145.382, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1095 8.00 N 1002 7.00 C 3603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 238.9 milliseconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 15 sheets defined 12.8% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 109 through 117 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 139 Processing helix chain 'A' and resid 157 through 161 removed outlier: 4.040A pdb=" N LEU A 161 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 117 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.634A pdb=" N LEU B 161 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 117 Processing helix chain 'C' and resid 119 through 128 Processing helix chain 'C' and resid 130 through 139 Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.560A pdb=" N SER C 160 " --> pdb=" O ASP C 157 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU C 161 " --> pdb=" O LEU C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 157 through 161' Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 154 removed outlier: 5.810A pdb=" N MET A 153 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 252 removed outlier: 3.854A pdb=" N THR A 265 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 292 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 292 removed outlier: 6.992A pdb=" N LEU A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL A 333 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER A 339 " --> pdb=" O MET A 331 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 329 " --> pdb=" O TYR A 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 153 through 155 removed outlier: 5.660A pdb=" N MET B 153 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 182 " --> pdb=" O HIS B 169 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 214 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN B 217 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 153 through 155 removed outlier: 5.660A pdb=" N MET B 153 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 182 " --> pdb=" O HIS B 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 247 through 252 removed outlier: 3.759A pdb=" N THR B 265 " --> pdb=" O TYR B 261 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG B 361 " --> pdb=" O PRO B 308 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 291 through 292 Processing sheet with id=AA9, first strand: chain 'B' and resid 291 through 292 removed outlier: 6.695A pdb=" N LEU B 337 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N VAL B 333 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER B 339 " --> pdb=" O MET B 331 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 316 through 317 Processing sheet with id=AB2, first strand: chain 'C' and resid 153 through 155 removed outlier: 5.757A pdb=" N MET C 153 " --> pdb=" O ALA C 168 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY C 182 " --> pdb=" O HIS C 169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 247 through 252 removed outlier: 3.827A pdb=" N THR C 265 " --> pdb=" O TYR C 261 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 291 through 292 Processing sheet with id=AB5, first strand: chain 'C' and resid 291 through 292 removed outlier: 6.645A pdb=" N LEU C 337 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL C 333 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N SER C 339 " --> pdb=" O MET C 331 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 316 through 317 229 hydrogen bonds defined for protein. 594 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1892 1.34 - 1.46: 1261 1.46 - 1.57: 2679 1.57 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 5901 Sorted by residual: bond pdb=" CB VAL A 196 " pdb=" CG2 VAL A 196 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.91e+00 bond pdb=" CG1 ILE B 212 " pdb=" CD1 ILE B 212 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.71e+00 bond pdb=" CB TRP A 148 " pdb=" CG TRP A 148 " ideal model delta sigma weight residual 1.498 1.459 0.039 3.10e-02 1.04e+03 1.58e+00 bond pdb=" CB ILE C 246 " pdb=" CG2 ILE C 246 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.49e+00 bond pdb=" CZ2 TRP A 148 " pdb=" CH2 TRP A 148 " ideal model delta sigma weight residual 1.368 1.345 0.023 1.90e-02 2.77e+03 1.42e+00 ... (remaining 5896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 7997 2.99 - 5.99: 70 5.99 - 8.98: 4 8.98 - 11.97: 0 11.97 - 14.96: 2 Bond angle restraints: 8073 Sorted by residual: angle pdb=" CA LEU A 202 " pdb=" CB LEU A 202 " pdb=" CG LEU A 202 " ideal model delta sigma weight residual 116.30 131.26 -14.96 3.50e+00 8.16e-02 1.83e+01 angle pdb=" C ASN B 314 " pdb=" CA ASN B 314 " pdb=" CB ASN B 314 " ideal model delta sigma weight residual 110.16 115.52 -5.36 1.33e+00 5.65e-01 1.62e+01 angle pdb=" CA LEU B 202 " pdb=" CB LEU B 202 " pdb=" CG LEU B 202 " ideal model delta sigma weight residual 116.30 128.45 -12.15 3.50e+00 8.16e-02 1.21e+01 angle pdb=" CA ASN B 314 " pdb=" CB ASN B 314 " pdb=" CG ASN B 314 " ideal model delta sigma weight residual 112.60 115.25 -2.65 1.00e+00 1.00e+00 7.02e+00 angle pdb=" C ALA A 319 " pdb=" CA ALA A 319 " pdb=" CB ALA A 319 " ideal model delta sigma weight residual 110.42 115.41 -4.99 1.99e+00 2.53e-01 6.29e+00 ... (remaining 8068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.90: 2847 15.90 - 31.79: 344 31.79 - 47.69: 99 47.69 - 63.58: 52 63.58 - 79.48: 6 Dihedral angle restraints: 3348 sinusoidal: 1188 harmonic: 2160 Sorted by residual: dihedral pdb=" CA ASN A 144 " pdb=" C ASN A 144 " pdb=" N GLN A 145 " pdb=" CA GLN A 145 " ideal model delta harmonic sigma weight residual 180.00 161.59 18.41 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ASN B 144 " pdb=" C ASN B 144 " pdb=" N GLN B 145 " pdb=" CA GLN B 145 " ideal model delta harmonic sigma weight residual 180.00 161.77 18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA VAL B 313 " pdb=" C VAL B 313 " pdb=" N ASN B 314 " pdb=" CA ASN B 314 " ideal model delta harmonic sigma weight residual 180.00 163.01 16.99 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 3345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 557 0.045 - 0.090: 214 0.090 - 0.135: 67 0.135 - 0.180: 3 0.180 - 0.226: 2 Chirality restraints: 843 Sorted by residual: chirality pdb=" CG LEU A 125 " pdb=" CB LEU A 125 " pdb=" CD1 LEU A 125 " pdb=" CD2 LEU A 125 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE C 246 " pdb=" CA ILE C 246 " pdb=" CG1 ILE C 246 " pdb=" CG2 ILE C 246 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CA ASN B 314 " pdb=" N ASN B 314 " pdb=" C ASN B 314 " pdb=" CB ASN B 314 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 840 not shown) Planarity restraints: 1068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 175 " -0.042 5.00e-02 4.00e+02 6.38e-02 6.50e+00 pdb=" N PRO A 176 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 175 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO C 176 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 176 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 176 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 314 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C ASN B 314 " -0.030 2.00e-02 2.50e+03 pdb=" O ASN B 314 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO B 315 " 0.010 2.00e-02 2.50e+03 ... (remaining 1065 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1133 2.77 - 3.30: 4984 3.30 - 3.83: 10276 3.83 - 4.37: 12722 4.37 - 4.90: 22118 Nonbonded interactions: 51233 Sorted by model distance: nonbonded pdb=" OD1 ASN C 256 " pdb=" OH TYR C 356 " model vdw 2.232 3.040 nonbonded pdb=" O THR A 273 " pdb=" OG1 THR A 273 " model vdw 2.239 3.040 nonbonded pdb=" OD1 ASN A 256 " pdb=" OH TYR A 356 " model vdw 2.256 3.040 nonbonded pdb=" OD1 ASN B 256 " pdb=" OH TYR B 356 " model vdw 2.260 3.040 nonbonded pdb=" O GLN A 145 " pdb=" N GLY A 147 " model vdw 2.267 3.120 ... (remaining 51228 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.620 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 0.056 5901 Z= 0.250 Angle : 0.746 14.964 8073 Z= 0.385 Chirality : 0.050 0.226 843 Planarity : 0.005 0.064 1068 Dihedral : 16.968 79.475 1992 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.84 % Allowed : 26.25 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.30), residues: 759 helix: 2.41 (0.56), residues: 84 sheet: 0.07 (0.32), residues: 264 loop : -1.34 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 361 TYR 0.022 0.002 TYR A 343 PHE 0.010 0.002 PHE B 290 TRP 0.024 0.003 TRP C 221 HIS 0.005 0.002 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.25 ( 5901) covalent geometry : angle 0.74562 / 0.39 ( 8073) hydrogen bonds : bond 0.14028 / 10.09 ( 206) hydrogen bonds : angle 6.46886 / 4.78 ( 594) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.138 Fit side-chains REVERT: C 148 TRP cc_start: 0.6675 (m-90) cc_final: 0.5847 (m-90) REVERT: C 341 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.7971 (p90) outliers start: 28 outliers final: 20 residues processed: 102 average time/residue: 0.3683 time to fit residues: 40.0829 Evaluate side-chains 97 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 341 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.0060 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.0000 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 ASN B 133 ASN C 113 GLN C 208 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.135921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.108606 restraints weight = 6687.591| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.80 r_work: 0.3116 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5901 Z= 0.104 Angle : 0.582 9.387 8073 Z= 0.303 Chirality : 0.044 0.127 843 Planarity : 0.004 0.058 1068 Dihedral : 7.401 64.074 867 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.84 % Allowed : 25.04 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.30), residues: 759 helix: 2.81 (0.58), residues: 84 sheet: 0.01 (0.31), residues: 264 loop : -1.18 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 123 TYR 0.014 0.001 TYR B 341 PHE 0.007 0.001 PHE C 338 TRP 0.014 0.001 TRP B 327 HIS 0.001 0.000 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 5901) covalent geometry : angle 0.58233 / 0.30 ( 8073) hydrogen bonds : bond 0.03433 / 2.47 ( 206) hydrogen bonds : angle 5.62830 / 4.11 ( 594) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.127 Fit side-chains REVERT: A 341 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: C 343 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.7661 (m-80) outliers start: 28 outliers final: 13 residues processed: 98 average time/residue: 0.3695 time to fit residues: 38.4974 Evaluate side-chains 91 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 343 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 48 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.105108 restraints weight = 6650.421| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.80 r_work: 0.3052 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5901 Z= 0.164 Angle : 0.635 11.357 8073 Z= 0.325 Chirality : 0.045 0.135 843 Planarity : 0.005 0.062 1068 Dihedral : 6.605 58.703 847 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 5.53 % Allowed : 23.66 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.31), residues: 759 helix: 2.78 (0.58), residues: 84 sheet: -0.09 (0.31), residues: 270 loop : -1.17 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 361 TYR 0.020 0.002 TYR A 343 PHE 0.012 0.001 PHE C 338 TRP 0.019 0.002 TRP C 221 HIS 0.003 0.001 HIS B 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 ( 5901) covalent geometry : angle 0.63520 / 0.32 ( 8073) hydrogen bonds : bond 0.03811 / 2.76 ( 206) hydrogen bonds : angle 5.58667 / 4.08 ( 594) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 0.181 Fit side-chains REVERT: A 341 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.7839 (m-80) REVERT: B 191 ASN cc_start: 0.7571 (OUTLIER) cc_final: 0.7263 (t0) REVERT: B 233 LEU cc_start: 0.8228 (tp) cc_final: 0.7899 (mt) REVERT: C 255 PHE cc_start: 0.7803 (m-10) cc_final: 0.7476 (m-80) REVERT: C 341 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.7717 (p90) REVERT: C 343 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.7645 (m-80) outliers start: 32 outliers final: 15 residues processed: 101 average time/residue: 0.3601 time to fit residues: 38.7330 Evaluate side-chains 96 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain C residue 343 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 33 optimal weight: 0.0470 chunk 9 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN A 203 ASN B 126 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.135841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.108585 restraints weight = 6650.528| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.79 r_work: 0.3125 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5901 Z= 0.102 Angle : 0.569 8.737 8073 Z= 0.295 Chirality : 0.044 0.128 843 Planarity : 0.004 0.058 1068 Dihedral : 6.110 59.504 845 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.84 % Allowed : 25.73 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.30), residues: 759 helix: 2.78 (0.59), residues: 84 sheet: -0.11 (0.31), residues: 270 loop : -1.10 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 317 TYR 0.016 0.001 TYR B 341 PHE 0.008 0.001 PHE C 338 TRP 0.012 0.001 TRP B 327 HIS 0.002 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 5901) covalent geometry : angle 0.56925 / 0.29 ( 8073) hydrogen bonds : bond 0.03190 / 2.32 ( 206) hydrogen bonds : angle 5.39951 / 3.92 ( 594) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 341 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: B 123 ARG cc_start: 0.5766 (OUTLIER) cc_final: 0.5526 (mpp-170) REVERT: B 233 LEU cc_start: 0.8174 (tp) cc_final: 0.7808 (mt) REVERT: C 255 PHE cc_start: 0.7733 (m-10) cc_final: 0.7474 (m-80) REVERT: C 341 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.7623 (p90) REVERT: C 343 TYR cc_start: 0.8906 (OUTLIER) cc_final: 0.7630 (m-80) outliers start: 28 outliers final: 12 residues processed: 102 average time/residue: 0.4125 time to fit residues: 44.6762 Evaluate side-chains 94 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain C residue 343 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 69 optimal weight: 0.0170 chunk 67 optimal weight: 6.9990 chunk 3 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 ASN B 133 ASN C 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.135288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107636 restraints weight = 6693.580| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.80 r_work: 0.3116 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5901 Z= 0.108 Angle : 0.572 8.445 8073 Z= 0.294 Chirality : 0.044 0.127 843 Planarity : 0.004 0.059 1068 Dihedral : 5.957 59.656 845 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 6.22 % Allowed : 23.83 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.31), residues: 759 helix: 2.82 (0.59), residues: 84 sheet: -0.13 (0.31), residues: 270 loop : -1.05 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 317 TYR 0.014 0.001 TYR A 343 PHE 0.009 0.001 PHE C 338 TRP 0.012 0.001 TRP C 221 HIS 0.002 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 5901) covalent geometry : angle 0.57160 / 0.29 ( 8073) hydrogen bonds : bond 0.03162 / 2.30 ( 206) hydrogen bonds : angle 5.33698 / 3.88 ( 594) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 82 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 341 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: B 191 ASN cc_start: 0.7619 (OUTLIER) cc_final: 0.7284 (t0) REVERT: B 233 LEU cc_start: 0.8189 (tp) cc_final: 0.7835 (mt) REVERT: C 255 PHE cc_start: 0.7804 (m-10) cc_final: 0.7544 (m-80) REVERT: C 307 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7283 (mtm-85) REVERT: C 341 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.7642 (p90) REVERT: C 343 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.7606 (m-80) outliers start: 36 outliers final: 17 residues processed: 107 average time/residue: 0.4074 time to fit residues: 46.2887 Evaluate side-chains 102 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain C residue 343 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 25 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 ASN C 181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.132305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.104569 restraints weight = 6748.660| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.83 r_work: 0.3049 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5901 Z= 0.185 Angle : 0.652 10.920 8073 Z= 0.331 Chirality : 0.046 0.136 843 Planarity : 0.005 0.062 1068 Dihedral : 6.224 59.355 845 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 6.22 % Allowed : 23.83 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.31), residues: 759 helix: 2.75 (0.59), residues: 84 sheet: -0.20 (0.31), residues: 270 loop : -1.09 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 361 TYR 0.024 0.002 TYR A 343 PHE 0.012 0.002 PHE C 338 TRP 0.020 0.002 TRP C 221 HIS 0.003 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.18 ( 5901) covalent geometry : angle 0.65174 / 0.33 ( 8073) hydrogen bonds : bond 0.03716 / 2.70 ( 206) hydrogen bonds : angle 5.49397 / 3.99 ( 594) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 341 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.7792 (m-80) REVERT: B 233 LEU cc_start: 0.8183 (tp) cc_final: 0.7780 (mt) REVERT: C 341 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.7890 (p90) REVERT: C 343 TYR cc_start: 0.8942 (OUTLIER) cc_final: 0.7613 (m-80) REVERT: C 344 ASP cc_start: 0.8396 (t0) cc_final: 0.8039 (t0) outliers start: 36 outliers final: 18 residues processed: 105 average time/residue: 0.4206 time to fit residues: 46.8828 Evaluate side-chains 98 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain C residue 343 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.134472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.106859 restraints weight = 6723.283| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.82 r_work: 0.3095 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5901 Z= 0.118 Angle : 0.599 9.841 8073 Z= 0.305 Chirality : 0.044 0.148 843 Planarity : 0.004 0.059 1068 Dihedral : 6.040 59.472 845 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.66 % Allowed : 26.60 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.30), residues: 759 helix: 2.76 (0.59), residues: 84 sheet: -0.28 (0.31), residues: 270 loop : -1.03 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 317 TYR 0.016 0.001 TYR A 343 PHE 0.009 0.001 PHE C 338 TRP 0.011 0.001 TRP B 221 HIS 0.002 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 5901) covalent geometry : angle 0.59936 / 0.31 ( 8073) hydrogen bonds : bond 0.03305 / 2.40 ( 206) hydrogen bonds : angle 5.42071 / 3.93 ( 594) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: A 341 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.7885 (m-80) REVERT: B 123 ARG cc_start: 0.5541 (OUTLIER) cc_final: 0.5241 (mpp-170) REVERT: B 233 LEU cc_start: 0.8193 (tp) cc_final: 0.7858 (mt) REVERT: C 341 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.7897 (p90) REVERT: C 343 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.7712 (m-80) outliers start: 27 outliers final: 15 residues processed: 97 average time/residue: 0.4244 time to fit residues: 43.7062 Evaluate side-chains 97 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain C residue 343 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 59 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.132139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.104418 restraints weight = 6745.354| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.82 r_work: 0.3039 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5901 Z= 0.171 Angle : 0.652 11.022 8073 Z= 0.329 Chirality : 0.046 0.164 843 Planarity : 0.005 0.061 1068 Dihedral : 6.268 59.238 845 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 4.66 % Allowed : 26.25 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.31), residues: 759 helix: 2.78 (0.58), residues: 84 sheet: -0.55 (0.29), residues: 291 loop : -1.04 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 361 TYR 0.022 0.002 TYR A 343 PHE 0.011 0.001 PHE C 338 TRP 0.018 0.002 TRP C 221 HIS 0.003 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 ( 5901) covalent geometry : angle 0.65203 / 0.33 ( 8073) hydrogen bonds : bond 0.03672 / 2.67 ( 206) hydrogen bonds : angle 5.51801 / 4.00 ( 594) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 341 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7897 (m-80) REVERT: B 123 ARG cc_start: 0.5669 (OUTLIER) cc_final: 0.5427 (mpp-170) REVERT: B 233 LEU cc_start: 0.8244 (tp) cc_final: 0.7872 (mt) REVERT: C 341 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.7945 (p90) REVERT: C 343 TYR cc_start: 0.8968 (OUTLIER) cc_final: 0.7667 (m-80) outliers start: 27 outliers final: 18 residues processed: 98 average time/residue: 0.4368 time to fit residues: 45.4180 Evaluate side-chains 100 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain C residue 343 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 42 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.134023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.106240 restraints weight = 6678.334| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.82 r_work: 0.3081 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5901 Z= 0.136 Angle : 0.619 10.014 8073 Z= 0.314 Chirality : 0.045 0.188 843 Planarity : 0.004 0.060 1068 Dihedral : 6.241 59.832 845 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.84 % Allowed : 25.91 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.31), residues: 759 helix: 2.68 (0.58), residues: 84 sheet: -0.57 (0.29), residues: 291 loop : -0.99 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 317 TYR 0.018 0.002 TYR A 343 PHE 0.009 0.001 PHE C 338 TRP 0.013 0.002 TRP C 221 HIS 0.002 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 5901) covalent geometry : angle 0.61919 / 0.31 ( 8073) hydrogen bonds : bond 0.03427 / 2.50 ( 206) hydrogen bonds : angle 5.48174 / 3.98 ( 594) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 341 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7893 (m-80) REVERT: B 233 LEU cc_start: 0.8211 (tp) cc_final: 0.7818 (mt) REVERT: C 257 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: C 341 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.7912 (p90) REVERT: C 343 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: C 344 ASP cc_start: 0.8371 (t0) cc_final: 0.8006 (t0) outliers start: 28 outliers final: 19 residues processed: 101 average time/residue: 0.4184 time to fit residues: 44.9125 Evaluate side-chains 102 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain C residue 343 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 58 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.134902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.107013 restraints weight = 6785.907| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.83 r_work: 0.3076 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5901 Z= 0.119 Angle : 0.589 8.995 8073 Z= 0.303 Chirality : 0.045 0.193 843 Planarity : 0.004 0.059 1068 Dihedral : 6.117 59.863 845 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.66 % Allowed : 25.91 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.31), residues: 759 helix: 2.41 (0.58), residues: 84 sheet: -0.54 (0.29), residues: 291 loop : -0.94 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 317 TYR 0.016 0.002 TYR B 341 PHE 0.008 0.001 PHE C 338 TRP 0.012 0.002 TRP C 221 HIS 0.003 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 5901) covalent geometry : angle 0.58869 / 0.30 ( 8073) hydrogen bonds : bond 0.03309 / 2.42 ( 206) hydrogen bonds : angle 5.49611 / 4.01 ( 594) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 341 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: B 233 LEU cc_start: 0.8208 (tp) cc_final: 0.7821 (mt) REVERT: C 133 ASN cc_start: 0.7450 (OUTLIER) cc_final: 0.7231 (m-40) REVERT: C 257 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: C 341 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.7850 (p90) REVERT: C 343 TYR cc_start: 0.8959 (OUTLIER) cc_final: 0.7671 (m-80) REVERT: C 344 ASP cc_start: 0.8365 (t0) cc_final: 0.8070 (t0) outliers start: 27 outliers final: 19 residues processed: 97 average time/residue: 0.4015 time to fit residues: 41.3705 Evaluate side-chains 103 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain C residue 343 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 0.0770 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 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 = 0.3525 r_free = 0.3525 target = 0.135681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.108009 restraints weight = 6598.171| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.81 r_work: 0.3106 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5901 Z= 0.113 Angle : 0.587 8.534 8073 Z= 0.302 Chirality : 0.044 0.190 843 Planarity : 0.004 0.059 1068 Dihedral : 5.842 59.665 843 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.32 % Allowed : 26.25 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.31), residues: 759 helix: 2.31 (0.59), residues: 84 sheet: -0.55 (0.29), residues: 291 loop : -0.89 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 123 TYR 0.016 0.002 TYR B 341 PHE 0.007 0.001 PHE A 255 TRP 0.011 0.001 TRP B 221 HIS 0.002 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 5901) covalent geometry : angle 0.58740 / 0.30 ( 8073) hydrogen bonds : bond 0.03251 / 2.37 ( 206) hydrogen bonds : angle 5.50017 / 4.02 ( 594) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2020.07 seconds wall clock time: 35 minutes 15.03 seconds (2115.03 seconds total)