Starting phenix.real_space_refine on Tue Feb 3 16:18:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yac_39095/02_2026/8yac_39095.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yac_39095/02_2026/8yac_39095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yac_39095/02_2026/8yac_39095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yac_39095/02_2026/8yac_39095.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yac_39095/02_2026/8yac_39095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yac_39095/02_2026/8yac_39095.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 C 1467 2.51 5 N 585 2.21 5 O 477 1.98 5 H 2214 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4743 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 527 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "B" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 527 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "C" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 527 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "D" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 527 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "E" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 527 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "F" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 527 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "G" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 527 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "H" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 527 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "I" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 527 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Time building chain proxies: 0.70, per 1000 atoms: 0.15 Number of scatterers: 4743 At special positions: 0 Unit cell: (89.972, 86.72, 31.436, 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) O 477 8.00 N 585 7.00 C 1467 6.00 H 2214 1.00 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: 0.25 Conformation dependent library (CDL) restraints added in 88.7 milliseconds 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 558 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 50.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 180 through 186 removed outlier: 6.338A pdb=" N LEU A 177 " --> pdb=" O HIS G 178 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N GLN G 180 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLN A 179 " --> pdb=" O GLN G 180 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N HIS G 182 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLN A 181 " --> pdb=" O HIS G 182 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N GLN G 184 " --> pdb=" O GLN A 181 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN A 183 " --> pdb=" O GLN G 184 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N HIS G 186 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLN A 185 " --> pdb=" O HIS G 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 197 through 204 Processing sheet with id=AA3, first strand: chain 'F' and resid 197 through 204 removed outlier: 7.822A pdb=" N HIS G 201 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLN A 200 " --> pdb=" O HIS G 201 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N GLN G 203 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLN A 202 " --> pdb=" O GLN G 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 180 through 186 removed outlier: 6.383A pdb=" N GLN B 181 " --> pdb=" O HIS E 182 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLN E 184 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN B 183 " --> pdb=" O GLN E 184 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N HIS E 186 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLN B 185 " --> pdb=" O HIS E 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 197 through 204 removed outlier: 6.371A pdb=" N LEU B 198 " --> pdb=" O HIS E 199 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N HIS E 201 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN B 200 " --> pdb=" O HIS E 201 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N GLN E 203 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN B 202 " --> pdb=" O GLN E 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 180 through 186 removed outlier: 6.324A pdb=" N LEU C 177 " --> pdb=" O HIS I 178 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLN I 180 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLN C 179 " --> pdb=" O GLN I 180 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N HIS I 182 " --> pdb=" O GLN C 179 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN C 181 " --> pdb=" O HIS I 182 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N GLN I 184 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLN C 183 " --> pdb=" O GLN I 184 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N HIS I 186 " --> pdb=" O GLN C 183 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLN C 185 " --> pdb=" O HIS I 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 197 through 204 removed outlier: 6.330A pdb=" N LEU C 198 " --> pdb=" O HIS I 199 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N HIS I 201 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN C 200 " --> pdb=" O HIS I 201 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N GLN I 203 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN C 202 " --> pdb=" O GLN I 203 " (cutoff:3.500A) 47 hydrogen bonds defined for protein. 141 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: 1.06 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 0.98: 2214 0.98 - 1.12: 0 1.12 - 1.26: 468 1.26 - 1.40: 765 1.40 - 1.54: 1350 Bond restraints: 4797 Sorted by residual: bond pdb=" C GLN G 195 " pdb=" N GLN G 196 " ideal model delta sigma weight residual 1.329 1.383 -0.054 1.36e-02 5.41e+03 1.57e+01 bond pdb=" C GLN I 195 " pdb=" N GLN I 196 " ideal model delta sigma weight residual 1.329 1.383 -0.054 1.36e-02 5.41e+03 1.57e+01 bond pdb=" C GLN E 195 " pdb=" N GLN E 196 " ideal model delta sigma weight residual 1.329 1.383 -0.054 1.36e-02 5.41e+03 1.56e+01 bond pdb=" C GLN H 195 " pdb=" N GLN H 196 " ideal model delta sigma weight residual 1.329 1.383 -0.054 1.36e-02 5.41e+03 1.56e+01 bond pdb=" C GLN A 195 " pdb=" N GLN A 196 " ideal model delta sigma weight residual 1.329 1.383 -0.053 1.36e-02 5.41e+03 1.53e+01 ... (remaining 4792 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 6445 1.97 - 3.93: 1647 3.93 - 5.90: 345 5.90 - 7.86: 20 7.86 - 9.83: 12 Bond angle restraints: 8469 Sorted by residual: angle pdb=" CA GLN H 196 " pdb=" C GLN H 196 " pdb=" O GLN H 196 " ideal model delta sigma weight residual 121.47 116.37 5.10 1.15e+00 7.56e-01 1.96e+01 angle pdb=" CA GLN D 196 " pdb=" C GLN D 196 " pdb=" O GLN D 196 " ideal model delta sigma weight residual 121.47 116.42 5.05 1.15e+00 7.56e-01 1.93e+01 angle pdb=" CA HIS B 192 " pdb=" C HIS B 192 " pdb=" O HIS B 192 " ideal model delta sigma weight residual 121.84 116.78 5.06 1.16e+00 7.43e-01 1.90e+01 angle pdb=" CA GLN I 196 " pdb=" C GLN I 196 " pdb=" O GLN I 196 " ideal model delta sigma weight residual 121.47 116.46 5.01 1.15e+00 7.56e-01 1.90e+01 angle pdb=" CA GLN G 196 " pdb=" C GLN G 196 " pdb=" O GLN G 196 " ideal model delta sigma weight residual 121.47 116.47 5.00 1.15e+00 7.56e-01 1.89e+01 ... (remaining 8464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 1967 17.05 - 34.11: 189 34.11 - 51.16: 79 51.16 - 68.22: 6 68.22 - 85.27: 27 Dihedral angle restraints: 2268 sinusoidal: 1251 harmonic: 1017 Sorted by residual: dihedral pdb=" C GLN B 193 " pdb=" N GLN B 193 " pdb=" CA GLN B 193 " pdb=" CB GLN B 193 " ideal model delta harmonic sigma weight residual -122.60 -130.39 7.79 0 2.50e+00 1.60e-01 9.72e+00 dihedral pdb=" C GLN A 193 " pdb=" N GLN A 193 " pdb=" CA GLN A 193 " pdb=" CB GLN A 193 " ideal model delta harmonic sigma weight residual -122.60 -130.37 7.77 0 2.50e+00 1.60e-01 9.66e+00 dihedral pdb=" C GLN I 193 " pdb=" N GLN I 193 " pdb=" CA GLN I 193 " pdb=" CB GLN I 193 " ideal model delta harmonic sigma weight residual -122.60 -130.36 7.76 0 2.50e+00 1.60e-01 9.64e+00 ... (remaining 2265 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.041: 78 0.041 - 0.078: 62 0.078 - 0.116: 80 0.116 - 0.153: 41 0.153 - 0.190: 45 Chirality restraints: 306 Sorted by residual: chirality pdb=" CA GLN B 193 " pdb=" N GLN B 193 " pdb=" C GLN B 193 " pdb=" CB GLN B 193 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.06e-01 chirality pdb=" CA GLN F 193 " pdb=" N GLN F 193 " pdb=" C GLN F 193 " pdb=" CB GLN F 193 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CA GLN A 193 " pdb=" N GLN A 193 " pdb=" C GLN A 193 " pdb=" CB GLN A 193 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.75e-01 ... (remaining 303 not shown) Planarity restraints: 792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 196 " -0.012 2.00e-02 2.50e+03 2.55e-02 6.49e+00 pdb=" C GLN F 196 " 0.044 2.00e-02 2.50e+03 pdb=" O GLN F 196 " -0.016 2.00e-02 2.50e+03 pdb=" N GLN F 197 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 196 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C GLN B 196 " 0.044 2.00e-02 2.50e+03 pdb=" O GLN B 196 " -0.016 2.00e-02 2.50e+03 pdb=" N GLN B 197 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 196 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C GLN D 196 " 0.043 2.00e-02 2.50e+03 pdb=" O GLN D 196 " -0.016 2.00e-02 2.50e+03 pdb=" N GLN D 197 " -0.015 2.00e-02 2.50e+03 ... (remaining 789 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.28: 581 2.28 - 2.83: 9690 2.83 - 3.39: 11487 3.39 - 3.94: 15804 3.94 - 4.50: 22318 Nonbonded interactions: 59880 Sorted by model distance: nonbonded pdb="HD22 LEU B 205 " pdb="HD12 LEU E 205 " model vdw 1.725 2.440 nonbonded pdb="HE22 GLN C 193 " pdb=" HG3 GLN H 193 " model vdw 1.728 2.270 nonbonded pdb="HE22 GLN A 193 " pdb=" HG3 GLN F 193 " model vdw 1.733 2.270 nonbonded pdb="HD22 LEU C 205 " pdb="HD12 LEU I 205 " model vdw 1.742 2.440 nonbonded pdb=" HG3 GLN C 193 " pdb="HE22 GLN I 193 " model vdw 1.744 2.270 ... (remaining 59875 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 0.970 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: 0.030 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.290 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 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 : 0.012 0.054 2583 Z= 0.892 Angle : 2.089 6.616 3465 Z= 1.448 Chirality : 0.100 0.190 306 Planarity : 0.008 0.025 522 Dihedral : 21.346 85.274 1008 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.17), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.13), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.01214 ( 2583) covalent geometry : angle 2.08890 ( 3465) hydrogen bonds : bond 0.15046 ( 40) hydrogen bonds : angle 7.49665 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.117 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 181 GLN cc_start: 0.8290 (mt0) cc_final: 0.8088 (mt0) REVERT: B 184 GLN cc_start: 0.8009 (mt0) cc_final: 0.7532 (tt0) REVERT: C 184 GLN cc_start: 0.7772 (mt0) cc_final: 0.7199 (tt0) REVERT: E 181 GLN cc_start: 0.8326 (mt0) cc_final: 0.8092 (mt0) REVERT: E 184 GLN cc_start: 0.8086 (mt0) cc_final: 0.7709 (tt0) REVERT: H 184 GLN cc_start: 0.8056 (mt0) cc_final: 0.7817 (tt0) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.0677 time to fit residues: 9.2823 Evaluate side-chains 42 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS A 184 GLN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN C 202 GLN D 183 GLN D 193 GLN ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 GLN D 203 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 GLN F 193 GLN ** F 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 HIS G 184 GLN ** G 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 GLN ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 197 GLN ** H 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 GLN ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5499 r_free = 0.5499 target = 0.426553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.6112 r_free = 0.6112 target = 0.375694 restraints weight = 7910.835| |-----------------------------------------------------------------------------| r_work (start): 0.5171 rms_B_bonded: 0.60 r_work: 0.5124 rms_B_bonded: 0.65 restraints_weight: 0.5000 r_work: 0.5067 rms_B_bonded: 1.18 restraints_weight: 0.2500 r_work: 0.4890 rms_B_bonded: 3.62 restraints_weight: 0.1250 r_work (final): 0.4890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2583 Z= 0.118 Angle : 0.470 4.643 3465 Z= 0.265 Chirality : 0.031 0.070 306 Planarity : 0.002 0.011 522 Dihedral : 5.668 18.050 279 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.36 % Allowed : 7.17 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.18), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.14), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS H 178 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 2583) covalent geometry : angle 0.46952 ( 3465) hydrogen bonds : bond 0.01965 ( 40) hydrogen bonds : angle 4.18841 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.096 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: symmetry clash REVERT: B 194 GLN cc_start: 0.8634 (mp10) cc_final: 0.8386 (mp10) REVERT: C 179 GLN cc_start: 0.8829 (mt0) cc_final: 0.8487 (mt0) REVERT: C 188 GLN cc_start: 0.8211 (mt0) cc_final: 0.7732 (mp10) REVERT: E 184 GLN cc_start: 0.8192 (mt0) cc_final: 0.7701 (tt0) REVERT: F 194 GLN cc_start: 0.8295 (pm20) cc_final: 0.7847 (mp10) REVERT: G 205 LEU cc_start: 0.8709 (mt) cc_final: 0.8498 (tt) REVERT: I 182 HIS cc_start: 0.7522 (t-170) cc_final: 0.7210 (t-170) outliers start: 1 outliers final: 0 residues processed: 67 average time/residue: 0.0717 time to fit residues: 6.2286 Evaluate side-chains 48 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN B 182 HIS ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.159620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.134662 restraints weight = 7448.543| |-----------------------------------------------------------------------------| r_work (start): 0.4721 rms_B_bonded: 2.92 r_work: 0.4578 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.4456 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.4456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2583 Z= 0.143 Angle : 0.442 3.984 3465 Z= 0.252 Chirality : 0.030 0.075 306 Planarity : 0.002 0.011 522 Dihedral : 5.015 15.834 279 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.36 % Allowed : 7.17 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.87 (0.19), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.15), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS I 178 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 2583) covalent geometry : angle 0.44170 ( 3465) hydrogen bonds : bond 0.01848 ( 40) hydrogen bonds : angle 3.76180 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.107 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLN cc_start: 0.9137 (mt0) cc_final: 0.8488 (mt0) REVERT: B 200 GLN cc_start: 0.8749 (mt0) cc_final: 0.7889 (mt0) REVERT: B 202 GLN cc_start: 0.9037 (mt0) cc_final: 0.8769 (mt0) REVERT: C 194 GLN cc_start: 0.8472 (mp10) cc_final: 0.8230 (mp10) REVERT: D 181 GLN cc_start: 0.7941 (mt0) cc_final: 0.7602 (mt0) REVERT: E 184 GLN cc_start: 0.8314 (mt0) cc_final: 0.7679 (mt0) REVERT: F 195 GLN cc_start: 0.7496 (tt0) cc_final: 0.7263 (tt0) REVERT: G 200 GLN cc_start: 0.9079 (mt0) cc_final: 0.8791 (mt0) REVERT: H 179 GLN cc_start: 0.8032 (mt0) cc_final: 0.7772 (mt0) outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 0.0670 time to fit residues: 4.9372 Evaluate side-chains 52 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 GLN I 182 HIS ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.158414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.134187 restraints weight = 7572.957| |-----------------------------------------------------------------------------| r_work (start): 0.4686 rms_B_bonded: 2.87 r_work: 0.4563 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4444 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2583 Z= 0.116 Angle : 0.394 3.681 3465 Z= 0.223 Chirality : 0.029 0.061 306 Planarity : 0.001 0.010 522 Dihedral : 4.673 13.759 279 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.36 % Allowed : 6.09 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.85 (0.20), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.15), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS I 178 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 2583) covalent geometry : angle 0.39419 ( 3465) hydrogen bonds : bond 0.01365 ( 40) hydrogen bonds : angle 3.65678 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.103 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 GLN cc_start: 0.9065 (mt0) cc_final: 0.8337 (mt0) REVERT: E 189 HIS cc_start: 0.7326 (t-90) cc_final: 0.7049 (m90) REVERT: F 181 GLN cc_start: 0.8338 (mt0) cc_final: 0.7890 (mt0) REVERT: F 195 GLN cc_start: 0.7670 (tt0) cc_final: 0.7326 (mt0) REVERT: G 195 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8116 (mm110) REVERT: H 179 GLN cc_start: 0.8335 (mt0) cc_final: 0.8100 (mt0) REVERT: H 189 HIS cc_start: 0.7400 (t70) cc_final: 0.7125 (m90) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.0566 time to fit residues: 4.1363 Evaluate side-chains 49 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 23 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 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 = 0.4843 r_free = 0.4843 target = 0.151780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.127169 restraints weight = 7926.449| |-----------------------------------------------------------------------------| r_work (start): 0.4616 rms_B_bonded: 2.93 r_work: 0.4491 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4373 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2583 Z= 0.175 Angle : 0.426 3.650 3465 Z= 0.243 Chirality : 0.029 0.087 306 Planarity : 0.002 0.010 522 Dihedral : 4.926 16.768 279 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.22), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.16), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS I 182 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 2583) covalent geometry : angle 0.42598 ( 3465) hydrogen bonds : bond 0.01538 ( 40) hydrogen bonds : angle 3.72110 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.131 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: symmetry clash REVERT: E 189 HIS cc_start: 0.7434 (t-90) cc_final: 0.7072 (m90) REVERT: F 181 GLN cc_start: 0.8252 (mt0) cc_final: 0.7725 (mt0) REVERT: F 195 GLN cc_start: 0.7883 (tt0) cc_final: 0.7419 (mt0) REVERT: F 200 GLN cc_start: 0.8818 (mt0) cc_final: 0.8479 (mt0) REVERT: G 195 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8155 (mm110) REVERT: H 189 HIS cc_start: 0.7481 (t70) cc_final: 0.7061 (m90) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0628 time to fit residues: 4.2268 Evaluate side-chains 46 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 HIS ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.158084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.133818 restraints weight = 7810.398| |-----------------------------------------------------------------------------| r_work (start): 0.4714 rms_B_bonded: 2.90 r_work: 0.4593 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.4471 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.4471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2583 Z= 0.082 Angle : 0.379 3.443 3465 Z= 0.214 Chirality : 0.029 0.077 306 Planarity : 0.001 0.009 522 Dihedral : 4.312 13.013 279 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.22), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.17), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS I 182 Details of bonding type rmsd covalent geometry : bond 0.00171 ( 2583) covalent geometry : angle 0.37887 ( 3465) hydrogen bonds : bond 0.01222 ( 40) hydrogen bonds : angle 3.54271 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.133 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: symmetry clash revert: symmetry clash REVERT: B 200 GLN cc_start: 0.9056 (mt0) cc_final: 0.8344 (mt0) REVERT: C 179 GLN cc_start: 0.8871 (mt0) cc_final: 0.8641 (mt0) REVERT: C 195 GLN cc_start: 0.8700 (mt0) cc_final: 0.8485 (mt0) REVERT: E 189 HIS cc_start: 0.7419 (t-90) cc_final: 0.7077 (m90) REVERT: G 195 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7981 (mt0) REVERT: G 204 GLN cc_start: 0.8818 (mt0) cc_final: 0.8618 (mt0) REVERT: H 179 GLN cc_start: 0.8437 (mt0) cc_final: 0.7995 (mt0) REVERT: H 189 HIS cc_start: 0.7488 (t70) cc_final: 0.7113 (m90) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0575 time to fit residues: 3.8538 Evaluate side-chains 48 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.153662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.129332 restraints weight = 7968.717| |-----------------------------------------------------------------------------| r_work (start): 0.4661 rms_B_bonded: 2.96 r_work: 0.4538 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.4421 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2583 Z= 0.109 Angle : 0.366 3.128 3465 Z= 0.209 Chirality : 0.028 0.068 306 Planarity : 0.001 0.006 522 Dihedral : 4.229 12.473 279 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.72 % Allowed : 7.89 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.79 (0.24), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.18), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS I 182 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 2583) covalent geometry : angle 0.36580 ( 3465) hydrogen bonds : bond 0.01230 ( 40) hydrogen bonds : angle 3.52425 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.131 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: symmetry clash revert: symmetry clash REVERT: B 200 GLN cc_start: 0.9065 (mt0) cc_final: 0.8316 (mt0) REVERT: C 179 GLN cc_start: 0.8892 (mt0) cc_final: 0.8647 (mt0) REVERT: D 181 GLN cc_start: 0.8370 (mt0) cc_final: 0.7768 (mt0) REVERT: E 189 HIS cc_start: 0.7484 (t-90) cc_final: 0.7082 (m90) REVERT: G 195 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8018 (mt0) REVERT: H 179 GLN cc_start: 0.8405 (mt0) cc_final: 0.7979 (mt0) REVERT: H 189 HIS cc_start: 0.7491 (t70) cc_final: 0.7059 (m90) outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.0641 time to fit residues: 4.0393 Evaluate side-chains 46 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 206 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 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 = 0.4863 r_free = 0.4863 target = 0.152933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.128729 restraints weight = 8221.757| |-----------------------------------------------------------------------------| r_work (start): 0.4663 rms_B_bonded: 2.99 r_work: 0.4530 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.4413 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.6442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2583 Z= 0.120 Angle : 0.373 3.127 3465 Z= 0.215 Chirality : 0.028 0.062 306 Planarity : 0.001 0.006 522 Dihedral : 4.248 13.680 279 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.36 % Allowed : 8.60 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.25), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.19), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 182 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 2583) covalent geometry : angle 0.37311 ( 3465) hydrogen bonds : bond 0.01325 ( 40) hydrogen bonds : angle 3.59051 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.108 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 195 GLN cc_start: 0.8992 (mt0) cc_final: 0.8789 (mt0) REVERT: B 200 GLN cc_start: 0.9059 (mt0) cc_final: 0.8316 (mt0) REVERT: C 179 GLN cc_start: 0.8900 (mt0) cc_final: 0.8675 (mt0) REVERT: E 189 HIS cc_start: 0.7524 (t-90) cc_final: 0.7095 (m90) REVERT: F 200 GLN cc_start: 0.8687 (mt0) cc_final: 0.8368 (mt0) REVERT: H 179 GLN cc_start: 0.8323 (mt0) cc_final: 0.7907 (mt0) REVERT: H 181 GLN cc_start: 0.8156 (mt0) cc_final: 0.7912 (mt0) REVERT: H 189 HIS cc_start: 0.7517 (t70) cc_final: 0.7083 (m90) outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.0589 time to fit residues: 3.7084 Evaluate side-chains 48 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 206 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5107 r_free = 0.5107 target = 0.174446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.148860 restraints weight = 7567.496| |-----------------------------------------------------------------------------| r_work (start): 0.4888 rms_B_bonded: 3.02 r_work: 0.4699 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.6572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2583 Z= 0.099 Angle : 0.359 2.945 3465 Z= 0.206 Chirality : 0.028 0.060 306 Planarity : 0.001 0.005 522 Dihedral : 3.978 12.737 279 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.36 % Allowed : 8.60 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.26), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.19), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 182 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 2583) covalent geometry : angle 0.35862 ( 3465) hydrogen bonds : bond 0.01263 ( 40) hydrogen bonds : angle 3.51204 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.101 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLN cc_start: 0.9258 (mt0) cc_final: 0.8875 (mt0) REVERT: B 200 GLN cc_start: 0.8956 (mt0) cc_final: 0.8507 (mt0) REVERT: E 189 HIS cc_start: 0.7485 (t-90) cc_final: 0.7130 (m90) REVERT: F 200 GLN cc_start: 0.8589 (mt0) cc_final: 0.8277 (mt0) REVERT: G 189 HIS cc_start: 0.7474 (t-90) cc_final: 0.7206 (m90) REVERT: H 179 GLN cc_start: 0.8529 (mt0) cc_final: 0.8026 (mt0) REVERT: H 189 HIS cc_start: 0.7473 (t70) cc_final: 0.7137 (m90) REVERT: I 189 HIS cc_start: 0.7386 (t-90) cc_final: 0.7163 (m90) outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 0.0667 time to fit residues: 4.4093 Evaluate side-chains 51 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 0.2980 chunk 16 optimal weight: 6.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 193 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 = 0.5130 r_free = 0.5130 target = 0.177444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.151724 restraints weight = 7444.562| |-----------------------------------------------------------------------------| r_work (start): 0.4934 rms_B_bonded: 3.02 r_work: 0.4801 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.4670 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.6653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2583 Z= 0.080 Angle : 0.357 3.353 3465 Z= 0.205 Chirality : 0.029 0.059 306 Planarity : 0.001 0.006 522 Dihedral : 3.728 12.127 279 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.36 % Allowed : 8.96 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (0.26), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.20), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 182 Details of bonding type rmsd covalent geometry : bond 0.00173 ( 2583) covalent geometry : angle 0.35721 ( 3465) hydrogen bonds : bond 0.01319 ( 40) hydrogen bonds : angle 3.50761 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.080 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLN cc_start: 0.9232 (mt0) cc_final: 0.8791 (mt0) REVERT: C 179 GLN cc_start: 0.8893 (mt0) cc_final: 0.8579 (mt0) REVERT: E 189 HIS cc_start: 0.7494 (t-90) cc_final: 0.7047 (m90) REVERT: F 200 GLN cc_start: 0.8707 (mt0) cc_final: 0.8384 (mt0) REVERT: G 189 HIS cc_start: 0.7537 (t-90) cc_final: 0.7168 (m90) REVERT: H 181 GLN cc_start: 0.8375 (mt0) cc_final: 0.8113 (mt0) REVERT: H 189 HIS cc_start: 0.7525 (t70) cc_final: 0.7140 (m90) REVERT: I 189 HIS cc_start: 0.7468 (t-90) cc_final: 0.7148 (m90) outliers start: 1 outliers final: 1 residues processed: 55 average time/residue: 0.0510 time to fit residues: 3.7572 Evaluate side-chains 50 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 20 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 HIS C 184 GLN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5077 r_free = 0.5077 target = 0.171751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.146027 restraints weight = 7739.462| |-----------------------------------------------------------------------------| r_work (start): 0.4851 rms_B_bonded: 3.02 r_work: 0.4666 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.6784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2583 Z= 0.137 Angle : 0.379 3.147 3465 Z= 0.219 Chirality : 0.027 0.058 306 Planarity : 0.001 0.011 522 Dihedral : 4.031 12.415 279 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.36 % Allowed : 8.96 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (0.27), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.21), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 182 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 2583) covalent geometry : angle 0.37942 ( 3465) hydrogen bonds : bond 0.01424 ( 40) hydrogen bonds : angle 3.60902 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1458.38 seconds wall clock time: 25 minutes 19.95 seconds (1519.95 seconds total)