Starting phenix.real_space_refine on Wed Mar 12 22:32:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ot9_13057/03_2025/7ot9_13057.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ot9_13057/03_2025/7ot9_13057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ot9_13057/03_2025/7ot9_13057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ot9_13057/03_2025/7ot9_13057.map" model { file = "/net/cci-nas-00/data/ceres_data/7ot9_13057/03_2025/7ot9_13057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ot9_13057/03_2025/7ot9_13057.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 S 55 5.16 5 C 5650 2.51 5 N 1395 2.21 5 O 1310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8410 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1682 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain breaks: 2 Restraints were copied for chains: C, B, E, D Time building chain proxies: 3.73, per 1000 atoms: 0.44 Number of scatterers: 8410 At special positions: 0 Unit cell: (126.312, 125.204, 60.94, 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 55 16.00 O 1310 8.00 N 1395 7.00 C 5650 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: 2.34 Conformation dependent library (CDL) restraints added in 1.2 seconds 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 9 through 48 Proline residue: A 33 - end of helix removed outlier: 4.468A pdb=" N LEU A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLY A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 59 Processing helix chain 'A' and resid 62 through 79 Processing helix chain 'A' and resid 167 through 180 Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 198 through 230 removed outlier: 3.997A pdb=" N GLY A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 3.749A pdb=" N LEU A 281 " --> pdb=" O TRP A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 307 through 322 Processing helix chain 'A' and resid 325 through 346 Proline residue: A 331 - end of helix Processing helix chain 'E' and resid 9 through 48 Proline residue: E 33 - end of helix removed outlier: 4.468A pdb=" N LEU E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLY E 37 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY E 42 " --> pdb=" O PHE E 38 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 59 Processing helix chain 'E' and resid 62 through 79 Processing helix chain 'E' and resid 167 through 180 Processing helix chain 'E' and resid 180 through 196 Processing helix chain 'E' and resid 198 through 230 removed outlier: 3.996A pdb=" N GLY E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 289 removed outlier: 3.749A pdb=" N LEU E 281 " --> pdb=" O TRP E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 Processing helix chain 'E' and resid 307 through 322 Processing helix chain 'E' and resid 325 through 346 Proline residue: E 331 - end of helix Processing helix chain 'D' and resid 9 through 48 Proline residue: D 33 - end of helix removed outlier: 4.468A pdb=" N LEU D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLY D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY D 42 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 59 Processing helix chain 'D' and resid 62 through 79 Processing helix chain 'D' and resid 167 through 180 Processing helix chain 'D' and resid 180 through 196 Processing helix chain 'D' and resid 198 through 230 removed outlier: 3.997A pdb=" N GLY D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 289 removed outlier: 3.748A pdb=" N LEU D 281 " --> pdb=" O TRP D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 Processing helix chain 'D' and resid 307 through 322 Processing helix chain 'D' and resid 325 through 346 Proline residue: D 331 - end of helix Processing helix chain 'C' and resid 9 through 48 Proline residue: C 33 - end of helix removed outlier: 4.468A pdb=" N LEU C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLY C 37 " --> pdb=" O PRO C 33 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 59 Processing helix chain 'C' and resid 62 through 79 Processing helix chain 'C' and resid 167 through 180 Processing helix chain 'C' and resid 180 through 196 Processing helix chain 'C' and resid 198 through 230 removed outlier: 3.997A pdb=" N GLY C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 289 removed outlier: 3.749A pdb=" N LEU C 281 " --> pdb=" O TRP C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 Processing helix chain 'C' and resid 307 through 322 Processing helix chain 'C' and resid 325 through 346 Proline residue: C 331 - end of helix Processing helix chain 'B' and resid 9 through 48 Proline residue: B 33 - end of helix removed outlier: 4.468A pdb=" N LEU B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLY B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 59 Processing helix chain 'B' and resid 62 through 79 Processing helix chain 'B' and resid 167 through 180 Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 198 through 230 removed outlier: 3.997A pdb=" N GLY B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 289 removed outlier: 3.749A pdb=" N LEU B 281 " --> pdb=" O TRP B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 307 through 322 Processing helix chain 'B' and resid 325 through 346 Proline residue: B 331 - end of helix 695 hydrogen bonds defined for protein. 2055 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 2.77 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: 2565 1.34 - 1.46: 1319 1.46 - 1.57: 4606 1.57 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 8590 Sorted by residual: bond pdb=" C ALA C 41 " pdb=" N GLY C 42 " ideal model delta sigma weight residual 1.331 1.316 0.015 1.46e-02 4.69e+03 1.01e+00 bond pdb=" C ALA D 41 " pdb=" N GLY D 42 " ideal model delta sigma weight residual 1.331 1.316 0.014 1.46e-02 4.69e+03 9.84e-01 bond pdb=" C ALA A 41 " pdb=" N GLY A 42 " ideal model delta sigma weight residual 1.331 1.316 0.014 1.46e-02 4.69e+03 9.59e-01 bond pdb=" C ALA B 41 " pdb=" N GLY B 42 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.46e-02 4.69e+03 9.11e-01 bond pdb=" C ALA E 41 " pdb=" N GLY E 42 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.46e-02 4.69e+03 9.03e-01 ... (remaining 8585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 11006 1.20 - 2.40: 569 2.40 - 3.60: 85 3.60 - 4.80: 50 4.80 - 6.00: 20 Bond angle restraints: 11730 Sorted by residual: angle pdb=" N VAL E 198 " pdb=" CA VAL E 198 " pdb=" C VAL E 198 " ideal model delta sigma weight residual 113.53 108.12 5.41 9.80e-01 1.04e+00 3.05e+01 angle pdb=" N VAL B 198 " pdb=" CA VAL B 198 " pdb=" C VAL B 198 " ideal model delta sigma weight residual 113.53 108.15 5.38 9.80e-01 1.04e+00 3.01e+01 angle pdb=" N VAL C 198 " pdb=" CA VAL C 198 " pdb=" C VAL C 198 " ideal model delta sigma weight residual 113.53 108.16 5.37 9.80e-01 1.04e+00 3.01e+01 angle pdb=" N VAL A 198 " pdb=" CA VAL A 198 " pdb=" C VAL A 198 " ideal model delta sigma weight residual 113.53 108.16 5.37 9.80e-01 1.04e+00 3.00e+01 angle pdb=" N VAL D 198 " pdb=" CA VAL D 198 " pdb=" C VAL D 198 " ideal model delta sigma weight residual 113.53 108.16 5.37 9.80e-01 1.04e+00 3.00e+01 ... (remaining 11725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 4470 17.70 - 35.40: 410 35.40 - 53.10: 45 53.10 - 70.80: 10 70.80 - 88.49: 15 Dihedral angle restraints: 4950 sinusoidal: 1845 harmonic: 3105 Sorted by residual: dihedral pdb=" CA ASN A 293 " pdb=" C ASN A 293 " pdb=" N VAL A 294 " pdb=" CA VAL A 294 " ideal model delta harmonic sigma weight residual -180.00 -160.95 -19.05 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASN C 293 " pdb=" C ASN C 293 " pdb=" N VAL C 294 " pdb=" CA VAL C 294 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASN D 293 " pdb=" C ASN D 293 " pdb=" N VAL D 294 " pdb=" CA VAL D 294 " ideal model delta harmonic sigma weight residual 180.00 -160.99 -19.01 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 4947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 840 0.031 - 0.062: 479 0.062 - 0.092: 124 0.092 - 0.123: 37 0.123 - 0.154: 10 Chirality restraints: 1490 Sorted by residual: chirality pdb=" CB ILE E 300 " pdb=" CA ILE E 300 " pdb=" CG1 ILE E 300 " pdb=" CG2 ILE E 300 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CB ILE A 300 " pdb=" CA ILE A 300 " pdb=" CG1 ILE A 300 " pdb=" CG2 ILE A 300 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CB ILE B 300 " pdb=" CA ILE B 300 " pdb=" CG1 ILE B 300 " pdb=" CG2 ILE B 300 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.84e-01 ... (remaining 1487 not shown) Planarity restraints: 1385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 42 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C GLY C 42 " 0.040 2.00e-02 2.50e+03 pdb=" O GLY C 42 " -0.015 2.00e-02 2.50e+03 pdb=" N THR C 43 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 42 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" C GLY B 42 " -0.040 2.00e-02 2.50e+03 pdb=" O GLY B 42 " 0.015 2.00e-02 2.50e+03 pdb=" N THR B 43 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 42 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C GLY D 42 " 0.040 2.00e-02 2.50e+03 pdb=" O GLY D 42 " -0.015 2.00e-02 2.50e+03 pdb=" N THR D 43 " -0.014 2.00e-02 2.50e+03 ... (remaining 1382 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 103 2.69 - 3.24: 8869 3.24 - 3.80: 13722 3.80 - 4.35: 15471 4.35 - 4.90: 27598 Nonbonded interactions: 65763 Sorted by model distance: nonbonded pdb=" O TRP D 344 " pdb=" NH1 ARG C 194 " model vdw 2.138 3.120 nonbonded pdb=" OG1 THR C 48 " pdb=" OH TYR C 178 " model vdw 2.140 3.040 nonbonded pdb=" OG1 THR E 48 " pdb=" OH TYR E 178 " model vdw 2.140 3.040 nonbonded pdb=" OG1 THR D 48 " pdb=" OH TYR D 178 " model vdw 2.141 3.040 nonbonded pdb=" OG1 THR A 48 " pdb=" OH TYR A 178 " model vdw 2.141 3.040 ... (remaining 65758 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.560 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.010 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:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 : 0.005 0.030 8590 Z= 0.319 Angle : 0.667 6.000 11730 Z= 0.365 Chirality : 0.040 0.154 1490 Planarity : 0.004 0.023 1385 Dihedral : 14.505 88.495 2940 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.25), residues: 1075 helix: 2.27 (0.17), residues: 905 sheet: None (None), residues: 0 loop : -2.04 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 344 HIS 0.019 0.007 HIS B 190 PHE 0.011 0.001 PHE C 163 TYR 0.003 0.001 TYR B 178 ARG 0.004 0.000 ARG C 301 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.855 Fit side-chains REVERT: A 170 MET cc_start: 0.6257 (ttm) cc_final: 0.5920 (ttm) REVERT: E 170 MET cc_start: 0.6847 (ttm) cc_final: 0.6643 (ttm) REVERT: E 182 GLU cc_start: 0.8133 (mp0) cc_final: 0.7812 (mp0) REVERT: E 302 MET cc_start: 0.8221 (mpp) cc_final: 0.7746 (mpt) REVERT: D 170 MET cc_start: 0.6758 (ttm) cc_final: 0.6502 (ttm) REVERT: D 182 GLU cc_start: 0.8336 (mp0) cc_final: 0.8060 (mp0) REVERT: C 178 TYR cc_start: 0.9038 (m-80) cc_final: 0.8514 (m-80) REVERT: C 182 GLU cc_start: 0.8276 (mp0) cc_final: 0.7959 (mp0) REVERT: C 302 MET cc_start: 0.7952 (mpp) cc_final: 0.7726 (mpt) REVERT: B 170 MET cc_start: 0.6627 (ttm) cc_final: 0.6325 (ttm) REVERT: B 182 GLU cc_start: 0.8352 (mp0) cc_final: 0.8080 (mp0) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 1.1928 time to fit residues: 144.8679 Evaluate side-chains 87 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 0.0040 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 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 = 0.3714 r_free = 0.3714 target = 0.101859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.072990 restraints weight = 18306.397| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.84 r_work: 0.3012 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8590 Z= 0.192 Angle : 0.623 6.993 11730 Z= 0.307 Chirality : 0.038 0.140 1490 Planarity : 0.005 0.033 1385 Dihedral : 4.424 20.747 1155 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.91 % Allowed : 14.51 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.25), residues: 1075 helix: 2.71 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -2.11 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 344 HIS 0.013 0.005 HIS A 190 PHE 0.007 0.001 PHE E 163 TYR 0.005 0.002 TYR B 178 ARG 0.005 0.000 ARG C 194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.868 Fit side-chains REVERT: A 170 MET cc_start: 0.6402 (ttm) cc_final: 0.6190 (ttm) REVERT: A 182 GLU cc_start: 0.8633 (mp0) cc_final: 0.8309 (mp0) REVERT: E 182 GLU cc_start: 0.8687 (mp0) cc_final: 0.8291 (mp0) REVERT: E 302 MET cc_start: 0.8195 (mpp) cc_final: 0.7806 (mpt) REVERT: D 170 MET cc_start: 0.6702 (ttm) cc_final: 0.6484 (ttm) REVERT: D 182 GLU cc_start: 0.8772 (mp0) cc_final: 0.8396 (mp0) REVERT: C 57 LYS cc_start: 0.9596 (ttmm) cc_final: 0.9248 (pttp) REVERT: C 178 TYR cc_start: 0.9195 (m-80) cc_final: 0.8749 (m-80) REVERT: C 182 GLU cc_start: 0.8789 (mp0) cc_final: 0.8314 (mp0) REVERT: B 57 LYS cc_start: 0.9721 (ttmm) cc_final: 0.9480 (pttm) REVERT: B 170 MET cc_start: 0.6596 (ttm) cc_final: 0.6342 (ttm) REVERT: B 182 GLU cc_start: 0.8834 (mp0) cc_final: 0.8436 (mp0) outliers start: 8 outliers final: 6 residues processed: 102 average time/residue: 1.2561 time to fit residues: 136.0351 Evaluate side-chains 95 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain B residue 64 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 87 optimal weight: 9.9990 chunk 74 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 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 = 0.3719 r_free = 0.3719 target = 0.102406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.073339 restraints weight = 18458.679| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.85 r_work: 0.3022 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8590 Z= 0.170 Angle : 0.565 7.583 11730 Z= 0.278 Chirality : 0.037 0.137 1490 Planarity : 0.004 0.031 1385 Dihedral : 4.251 20.076 1155 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.60 % Allowed : 19.77 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.26), residues: 1075 helix: 2.91 (0.17), residues: 870 sheet: None (None), residues: 0 loop : -1.94 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 344 HIS 0.010 0.005 HIS E 190 PHE 0.008 0.001 PHE A 163 TYR 0.006 0.002 TYR E 178 ARG 0.004 0.000 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.8754 (mtm) cc_final: 0.8553 (mtm) REVERT: A 182 GLU cc_start: 0.8631 (mp0) cc_final: 0.8264 (mp0) REVERT: E 182 GLU cc_start: 0.8659 (mp0) cc_final: 0.8234 (mp0) REVERT: D 182 GLU cc_start: 0.8746 (mp0) cc_final: 0.8305 (mp0) REVERT: D 294 VAL cc_start: 0.7140 (OUTLIER) cc_final: 0.6938 (t) REVERT: C 57 LYS cc_start: 0.9573 (ttmm) cc_final: 0.9225 (pttp) REVERT: C 178 TYR cc_start: 0.9167 (m-80) cc_final: 0.8641 (m-80) REVERT: C 182 GLU cc_start: 0.8774 (mp0) cc_final: 0.8284 (mp0) REVERT: B 182 GLU cc_start: 0.8823 (mp0) cc_final: 0.8421 (mp0) outliers start: 14 outliers final: 6 residues processed: 105 average time/residue: 1.1903 time to fit residues: 133.3142 Evaluate side-chains 96 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 chunk 65 optimal weight: 0.0020 chunk 94 optimal weight: 5.9990 chunk 92 optimal weight: 0.3980 chunk 58 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.6568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 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 = 0.3724 r_free = 0.3724 target = 0.102563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.073655 restraints weight = 18419.224| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.86 r_work: 0.3028 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8590 Z= 0.159 Angle : 0.553 7.865 11730 Z= 0.272 Chirality : 0.037 0.142 1490 Planarity : 0.004 0.031 1385 Dihedral : 4.193 19.866 1155 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.17 % Allowed : 22.51 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.26), residues: 1075 helix: 2.98 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -2.02 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 344 HIS 0.009 0.004 HIS E 190 PHE 0.007 0.001 PHE C 163 TYR 0.005 0.001 TYR A 178 ARG 0.003 0.000 ARG C 194 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8644 (mp0) cc_final: 0.8251 (mp0) REVERT: E 182 GLU cc_start: 0.8652 (mp0) cc_final: 0.8206 (mp0) REVERT: D 182 GLU cc_start: 0.8741 (mp0) cc_final: 0.8277 (mp0) REVERT: C 178 TYR cc_start: 0.9091 (m-80) cc_final: 0.8548 (m-80) REVERT: C 182 GLU cc_start: 0.8761 (mp0) cc_final: 0.8226 (mp0) REVERT: B 182 GLU cc_start: 0.8813 (mp0) cc_final: 0.8373 (mp0) outliers start: 19 outliers final: 9 residues processed: 110 average time/residue: 1.4846 time to fit residues: 174.3552 Evaluate side-chains 96 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 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 = 0.3711 r_free = 0.3711 target = 0.101884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072843 restraints weight = 18395.915| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.84 r_work: 0.3009 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8590 Z= 0.200 Angle : 0.548 8.788 11730 Z= 0.269 Chirality : 0.037 0.129 1490 Planarity : 0.004 0.031 1385 Dihedral : 4.147 19.779 1155 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.26 % Allowed : 26.40 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.26), residues: 1075 helix: 2.99 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -2.00 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 277 HIS 0.008 0.004 HIS E 190 PHE 0.006 0.001 PHE B 163 TYR 0.004 0.001 TYR C 178 ARG 0.003 0.000 ARG D 194 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8683 (mp0) cc_final: 0.8269 (mp0) REVERT: E 182 GLU cc_start: 0.8660 (mp0) cc_final: 0.8202 (mp0) REVERT: D 182 GLU cc_start: 0.8782 (mp0) cc_final: 0.8295 (mp0) REVERT: C 178 TYR cc_start: 0.9226 (m-80) cc_final: 0.8648 (m-80) REVERT: C 182 GLU cc_start: 0.8792 (mp0) cc_final: 0.8248 (mp0) REVERT: B 57 LYS cc_start: 0.9717 (ttmm) cc_final: 0.9460 (tmmt) REVERT: B 182 GLU cc_start: 0.8817 (mp0) cc_final: 0.8370 (mp0) outliers start: 11 outliers final: 9 residues processed: 98 average time/residue: 1.7741 time to fit residues: 184.8897 Evaluate side-chains 99 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 97 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 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 = 0.3710 r_free = 0.3710 target = 0.101662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.072545 restraints weight = 18494.115| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.87 r_work: 0.3003 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8590 Z= 0.199 Angle : 0.549 9.639 11730 Z= 0.270 Chirality : 0.036 0.131 1490 Planarity : 0.004 0.033 1385 Dihedral : 4.141 19.722 1155 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.83 % Allowed : 28.11 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.26), residues: 1075 helix: 3.01 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.99 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 344 HIS 0.007 0.004 HIS E 190 PHE 0.006 0.001 PHE B 163 TYR 0.004 0.001 TYR B 178 ARG 0.004 0.000 ARG E 301 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8717 (mp0) cc_final: 0.8291 (mp0) REVERT: E 182 GLU cc_start: 0.8666 (mp0) cc_final: 0.8198 (mp0) REVERT: E 284 TRP cc_start: 0.6394 (m100) cc_final: 0.6044 (m100) REVERT: D 182 GLU cc_start: 0.8773 (mp0) cc_final: 0.8276 (mp0) REVERT: C 182 GLU cc_start: 0.8780 (mp0) cc_final: 0.8226 (mp0) REVERT: C 284 TRP cc_start: 0.6182 (m100) cc_final: 0.5733 (m100) REVERT: B 57 LYS cc_start: 0.9711 (ttmm) cc_final: 0.9466 (tmmt) REVERT: B 182 GLU cc_start: 0.8820 (mp0) cc_final: 0.8363 (mp0) outliers start: 16 outliers final: 10 residues processed: 103 average time/residue: 1.1276 time to fit residues: 124.0162 Evaluate side-chains 100 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 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 = 0.3697 r_free = 0.3697 target = 0.101044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.071967 restraints weight = 18588.046| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.88 r_work: 0.2990 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8590 Z= 0.236 Angle : 0.571 10.693 11730 Z= 0.278 Chirality : 0.037 0.128 1490 Planarity : 0.004 0.032 1385 Dihedral : 4.127 19.699 1155 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.63 % Allowed : 28.00 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.26), residues: 1075 helix: 3.00 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.96 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 277 HIS 0.008 0.004 HIS E 190 PHE 0.007 0.001 PHE E 163 TYR 0.005 0.001 TYR B 178 ARG 0.002 0.000 ARG D 194 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.9691 (ttmm) cc_final: 0.9425 (tmmt) REVERT: A 182 GLU cc_start: 0.8729 (mp0) cc_final: 0.8254 (mp0) REVERT: A 284 TRP cc_start: 0.6373 (m100) cc_final: 0.6003 (m100) REVERT: E 182 GLU cc_start: 0.8685 (mp0) cc_final: 0.8213 (mp0) REVERT: D 59 MET cc_start: 0.9040 (ttp) cc_final: 0.8530 (ptp) REVERT: D 182 GLU cc_start: 0.8770 (mp0) cc_final: 0.8266 (mp0) REVERT: D 313 SER cc_start: 0.9118 (t) cc_final: 0.8655 (m) REVERT: C 182 GLU cc_start: 0.8777 (mp0) cc_final: 0.8223 (mp0) REVERT: C 284 TRP cc_start: 0.6146 (m100) cc_final: 0.5747 (m100) REVERT: B 57 LYS cc_start: 0.9718 (ttmm) cc_final: 0.9465 (tmmt) REVERT: B 182 GLU cc_start: 0.8816 (mp0) cc_final: 0.8358 (mp0) outliers start: 23 outliers final: 12 residues processed: 110 average time/residue: 1.1336 time to fit residues: 133.3295 Evaluate side-chains 102 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 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 = 0.3714 r_free = 0.3714 target = 0.101933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.072865 restraints weight = 18567.742| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.88 r_work: 0.3009 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8590 Z= 0.176 Angle : 0.572 11.556 11730 Z= 0.277 Chirality : 0.036 0.131 1490 Planarity : 0.004 0.032 1385 Dihedral : 4.081 19.494 1155 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.29 % Allowed : 28.91 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.33 (0.26), residues: 1075 helix: 3.04 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.97 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 344 HIS 0.007 0.004 HIS E 166 PHE 0.006 0.001 PHE B 163 TYR 0.005 0.001 TYR B 178 ARG 0.003 0.000 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8737 (mp0) cc_final: 0.8272 (mp0) REVERT: E 182 GLU cc_start: 0.8695 (mp0) cc_final: 0.8227 (mp0) REVERT: D 59 MET cc_start: 0.8905 (ttp) cc_final: 0.8650 (ttp) REVERT: D 182 GLU cc_start: 0.8771 (mp0) cc_final: 0.8274 (mp0) REVERT: D 313 SER cc_start: 0.9168 (t) cc_final: 0.8752 (m) REVERT: C 182 GLU cc_start: 0.8771 (mp0) cc_final: 0.8217 (mp0) REVERT: C 284 TRP cc_start: 0.6200 (m100) cc_final: 0.5834 (m100) REVERT: B 57 LYS cc_start: 0.9705 (ttmm) cc_final: 0.9463 (tmmt) REVERT: B 182 GLU cc_start: 0.8839 (mp0) cc_final: 0.8372 (mp0) outliers start: 20 outliers final: 8 residues processed: 112 average time/residue: 1.0756 time to fit residues: 129.0434 Evaluate side-chains 101 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 0.0070 chunk 60 optimal weight: 0.8980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.102100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.073349 restraints weight = 18512.136| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.82 r_work: 0.3019 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8590 Z= 0.173 Angle : 0.601 12.608 11730 Z= 0.289 Chirality : 0.036 0.178 1490 Planarity : 0.004 0.032 1385 Dihedral : 4.035 19.158 1155 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.94 % Allowed : 29.03 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.38 (0.26), residues: 1075 helix: 3.08 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.96 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 49 HIS 0.007 0.004 HIS D 166 PHE 0.006 0.001 PHE B 163 TYR 0.005 0.001 TYR B 178 ARG 0.005 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8735 (mp0) cc_final: 0.8270 (mp0) REVERT: E 182 GLU cc_start: 0.8694 (mp0) cc_final: 0.8224 (mp0) REVERT: D 59 MET cc_start: 0.8907 (ttp) cc_final: 0.8611 (ttp) REVERT: D 182 GLU cc_start: 0.8757 (mp0) cc_final: 0.8277 (mp0) REVERT: D 313 SER cc_start: 0.9226 (t) cc_final: 0.8770 (m) REVERT: C 182 GLU cc_start: 0.8775 (mp0) cc_final: 0.8224 (mp0) REVERT: C 284 TRP cc_start: 0.6260 (m100) cc_final: 0.5905 (m100) REVERT: B 182 GLU cc_start: 0.8841 (mp0) cc_final: 0.8373 (mp0) REVERT: B 284 TRP cc_start: 0.6370 (m100) cc_final: 0.6017 (m100) outliers start: 17 outliers final: 9 residues processed: 108 average time/residue: 1.1274 time to fit residues: 130.1327 Evaluate side-chains 101 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 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 = 0.3697 r_free = 0.3697 target = 0.100880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.071859 restraints weight = 18305.375| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.82 r_work: 0.2986 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8590 Z= 0.267 Angle : 0.648 13.388 11730 Z= 0.309 Chirality : 0.037 0.186 1490 Planarity : 0.004 0.032 1385 Dihedral : 4.107 19.762 1155 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.49 % Allowed : 29.49 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.26), residues: 1075 helix: 2.93 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -2.05 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 277 HIS 0.008 0.005 HIS B 190 PHE 0.007 0.001 PHE A 163 TYR 0.005 0.002 TYR B 178 ARG 0.003 0.000 ARG E 301 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8786 (mp0) cc_final: 0.8314 (mp0) REVERT: A 284 TRP cc_start: 0.6343 (m100) cc_final: 0.6013 (m100) REVERT: A 313 SER cc_start: 0.9130 (t) cc_final: 0.8766 (m) REVERT: E 71 THR cc_start: 0.8841 (m) cc_final: 0.8632 (m) REVERT: E 182 GLU cc_start: 0.8720 (mp0) cc_final: 0.8249 (mp0) REVERT: D 59 MET cc_start: 0.8923 (ttp) cc_final: 0.8626 (ttp) REVERT: D 182 GLU cc_start: 0.8811 (mp0) cc_final: 0.8298 (mp0) REVERT: D 313 SER cc_start: 0.9217 (t) cc_final: 0.8771 (m) REVERT: C 182 GLU cc_start: 0.8786 (mp0) cc_final: 0.8230 (mp0) REVERT: C 284 TRP cc_start: 0.6338 (m100) cc_final: 0.5975 (m100) REVERT: B 182 GLU cc_start: 0.8819 (mp0) cc_final: 0.8359 (mp0) REVERT: B 284 TRP cc_start: 0.6361 (m100) cc_final: 0.6076 (m100) outliers start: 13 outliers final: 9 residues processed: 104 average time/residue: 1.2173 time to fit residues: 134.7833 Evaluate side-chains 102 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 87 optimal weight: 0.0060 chunk 34 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 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 = 0.3705 r_free = 0.3705 target = 0.101503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.072569 restraints weight = 18667.372| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.83 r_work: 0.2995 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8590 Z= 0.211 Angle : 0.649 13.376 11730 Z= 0.308 Chirality : 0.036 0.183 1490 Planarity : 0.004 0.033 1385 Dihedral : 4.071 19.386 1155 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.14 % Allowed : 29.83 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.26), residues: 1075 helix: 2.92 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.99 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 49 HIS 0.007 0.004 HIS D 166 PHE 0.006 0.001 PHE B 163 TYR 0.006 0.001 TYR E 178 ARG 0.005 0.000 ARG A 301 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5028.89 seconds wall clock time: 88 minutes 21.88 seconds (5301.88 seconds total)