Starting phenix.real_space_refine on Thu Mar 6 03:31:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8efp_28087/03_2025/8efp_28087.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efp_28087/03_2025/8efp_28087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8efp_28087/03_2025/8efp_28087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efp_28087/03_2025/8efp_28087.map" model { file = "/net/cci-nas-00/data/ceres_data/8efp_28087/03_2025/8efp_28087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efp_28087/03_2025/8efp_28087.cif" } resolution = 3.8 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= 0.009 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 13 5.16 5 C 2977 2.51 5 N 808 2.21 5 O 907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4705 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1976 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 18, 'TRANS': 224} Chain: "C" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2729 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 Time building chain proxies: 3.36, per 1000 atoms: 0.71 Number of scatterers: 4705 At special positions: 0 Unit cell: (76.176, 74.52, 113.436, 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) S 13 16.00 O 907 8.00 N 808 7.00 C 2977 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: 1.06 Conformation dependent library (CDL) restraints added in 551.0 milliseconds 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1150 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 3 sheets defined 40.2% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 217 through 222 removed outlier: 3.524A pdb=" N PHE B 220 " --> pdb=" O PRO B 217 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER B 221 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 249 Processing helix chain 'C' and resid 4 through 18 removed outlier: 3.527A pdb=" N ALA C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 68 through 77 removed outlier: 4.179A pdb=" N ASP C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 136 Processing helix chain 'C' and resid 143 through 150 removed outlier: 3.660A pdb=" N ARG C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 186 removed outlier: 4.258A pdb=" N HIS C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 262 Processing helix chain 'C' and resid 264 through 279 Processing helix chain 'C' and resid 281 through 299 Processing helix chain 'C' and resid 307 through 315 Processing helix chain 'C' and resid 322 through 339 Processing helix chain 'C' and resid 342 through 353 Processing helix chain 'C' and resid 354 through 369 Processing helix chain 'C' and resid 371 through 376 Processing helix chain 'C' and resid 383 through 404 Processing sheet with id=AA1, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.594A pdb=" N LEU B 82 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 102 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 161 through 163 removed outlier: 3.521A pdb=" N CYS B 183 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LYS B 204 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN B 230 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N TYR B 206 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 22 through 24 removed outlier: 3.853A pdb=" N SER C 206 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU C 160 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS C 210 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL C 158 " --> pdb=" O LYS C 210 " (cutoff:3.500A) 177 hydrogen bonds defined for protein. 522 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: 1.32 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 959 1.33 - 1.45: 1038 1.45 - 1.57: 2773 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 4790 Sorted by residual: bond pdb=" N LEU C 263 " pdb=" CA LEU C 263 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.14e-02 7.69e+03 1.42e+01 bond pdb=" N ASP C 173 " pdb=" CA ASP C 173 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.70e-03 1.06e+04 9.06e+00 bond pdb=" N LYS C 177 " pdb=" CA LYS C 177 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.26e-02 6.30e+03 8.83e+00 bond pdb=" CA LYS C 177 " pdb=" C LYS C 177 " ideal model delta sigma weight residual 1.519 1.534 -0.016 5.30e-03 3.56e+04 8.82e+00 bond pdb=" N THR C 264 " pdb=" CA THR C 264 " ideal model delta sigma weight residual 1.454 1.494 -0.039 1.33e-02 5.65e+03 8.68e+00 ... (remaining 4785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 6360 4.02 - 8.05: 109 8.05 - 12.07: 15 12.07 - 16.09: 5 16.09 - 20.12: 6 Bond angle restraints: 6495 Sorted by residual: angle pdb=" C PHE B 98 " pdb=" CA PHE B 98 " pdb=" CB PHE B 98 " ideal model delta sigma weight residual 113.37 93.25 20.12 1.61e+00 3.86e-01 1.56e+02 angle pdb=" N SER C 180 " pdb=" CA SER C 180 " pdb=" C SER C 180 " ideal model delta sigma weight residual 112.94 95.36 17.58 1.41e+00 5.03e-01 1.56e+02 angle pdb=" N PRO C 215 " pdb=" CA PRO C 215 " pdb=" C PRO C 215 " ideal model delta sigma weight residual 111.19 94.15 17.04 1.57e+00 4.06e-01 1.18e+02 angle pdb=" N GLN C 194 " pdb=" CA GLN C 194 " pdb=" C GLN C 194 " ideal model delta sigma weight residual 108.23 89.70 18.53 1.72e+00 3.38e-01 1.16e+02 angle pdb=" N ARG C 195 " pdb=" CA ARG C 195 " pdb=" C ARG C 195 " ideal model delta sigma weight residual 108.76 93.60 15.16 1.69e+00 3.50e-01 8.05e+01 ... (remaining 6490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.18: 2474 18.18 - 36.37: 360 36.37 - 54.55: 101 54.55 - 72.73: 11 72.73 - 90.91: 8 Dihedral angle restraints: 2954 sinusoidal: 1197 harmonic: 1757 Sorted by residual: dihedral pdb=" C PHE B 98 " pdb=" N PHE B 98 " pdb=" CA PHE B 98 " pdb=" CB PHE B 98 " ideal model delta harmonic sigma weight residual -122.60 -97.68 -24.92 0 2.50e+00 1.60e-01 9.94e+01 dihedral pdb=" C VAL C 213 " pdb=" N VAL C 213 " pdb=" CA VAL C 213 " pdb=" CB VAL C 213 " ideal model delta harmonic sigma weight residual -122.00 -103.01 -18.99 0 2.50e+00 1.60e-01 5.77e+01 dihedral pdb=" C GLN C 194 " pdb=" N GLN C 194 " pdb=" CA GLN C 194 " pdb=" CB GLN C 194 " ideal model delta harmonic sigma weight residual -122.60 -104.35 -18.25 0 2.50e+00 1.60e-01 5.33e+01 ... (remaining 2951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 709 0.147 - 0.293: 30 0.293 - 0.440: 3 0.440 - 0.586: 0 0.586 - 0.733: 5 Chirality restraints: 747 Sorted by residual: chirality pdb=" CA VAL C 213 " pdb=" N VAL C 213 " pdb=" C VAL C 213 " pdb=" CB VAL C 213 " both_signs ideal model delta sigma weight residual False 2.44 3.17 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CA TYR C 176 " pdb=" N TYR C 176 " pdb=" C TYR C 176 " pdb=" CB TYR C 176 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CA TRP C 179 " pdb=" N TRP C 179 " pdb=" C TRP C 179 " pdb=" CB TRP C 179 " both_signs ideal model delta sigma weight residual False 2.51 3.13 -0.62 2.00e-01 2.50e+01 9.68e+00 ... (remaining 744 not shown) Planarity restraints: 848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 95 " -0.024 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" C LEU B 95 " 0.080 2.00e-02 2.50e+03 pdb=" O LEU B 95 " -0.029 2.00e-02 2.50e+03 pdb=" N PRO B 96 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 37 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C ASN B 37 " 0.046 2.00e-02 2.50e+03 pdb=" O ASN B 37 " -0.018 2.00e-02 2.50e+03 pdb=" N SER B 38 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 398 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C ILE C 398 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE C 398 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU C 399 " -0.013 2.00e-02 2.50e+03 ... (remaining 845 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 64 2.51 - 3.10: 3894 3.10 - 3.70: 7797 3.70 - 4.30: 10845 4.30 - 4.90: 16554 Nonbonded interactions: 39154 Sorted by model distance: nonbonded pdb=" O TRP C 179 " pdb=" CG TRP C 179 " model vdw 1.908 3.260 nonbonded pdb=" O TRP C 179 " pdb=" CD2 TRP C 179 " model vdw 2.113 3.260 nonbonded pdb=" N VAL C 213 " pdb=" O VAL C 213 " model vdw 2.191 2.496 nonbonded pdb=" OG1 THR C 151 " pdb=" NH1 ARG C 152 " model vdw 2.219 3.120 nonbonded pdb=" O LYS C 359 " pdb=" N VAL C 362 " model vdw 2.258 3.120 ... (remaining 39149 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.260 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 4790 Z= 0.385 Angle : 1.460 20.115 6495 Z= 0.886 Chirality : 0.085 0.733 747 Planarity : 0.007 0.067 848 Dihedral : 18.607 90.911 1804 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 33.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.31 % Favored : 86.69 % Rotamer: Outliers : 3.07 % Allowed : 31.03 % Favored : 65.90 % Cbeta Deviations : 1.22 % 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: -4.26 (0.29), residues: 586 helix: -2.31 (0.31), residues: 203 sheet: -3.30 (0.61), residues: 49 loop : -3.21 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 34 HIS 0.006 0.001 HIS B 26 PHE 0.021 0.003 PHE B 98 TYR 0.027 0.002 TYR C 129 ARG 0.008 0.001 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 TYR cc_start: 0.7911 (m-10) cc_final: 0.7477 (m-10) REVERT: C 275 LEU cc_start: 0.8243 (pp) cc_final: 0.7875 (pp) outliers start: 16 outliers final: 4 residues processed: 77 average time/residue: 0.1749 time to fit residues: 17.0945 Evaluate side-chains 50 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain C residue 86 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 23 optimal weight: 0.0270 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 HIS B 87 ASN ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN C 186 HIS ** C 343 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 = 0.4307 r_free = 0.4307 target = 0.083083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.065262 restraints weight = 28668.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.066511 restraints weight = 20148.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.067640 restraints weight = 15738.091| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4790 Z= 0.263 Angle : 0.888 11.621 6495 Z= 0.446 Chirality : 0.047 0.161 747 Planarity : 0.006 0.067 848 Dihedral : 7.616 59.333 647 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 22.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 3.26 % Allowed : 29.69 % Favored : 67.05 % 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: -3.89 (0.30), residues: 586 helix: -1.86 (0.31), residues: 212 sheet: -3.48 (0.56), residues: 54 loop : -3.00 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP C 179 HIS 0.005 0.001 HIS C 51 PHE 0.017 0.002 PHE C 34 TYR 0.018 0.001 TYR B 27 ARG 0.011 0.001 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 LEU cc_start: 0.8615 (pp) cc_final: 0.8097 (mt) REVERT: B 108 ARG cc_start: 0.6514 (OUTLIER) cc_final: 0.5380 (pmt-80) REVERT: C 122 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8273 (pp20) REVERT: C 275 LEU cc_start: 0.8563 (pp) cc_final: 0.8315 (pp) outliers start: 17 outliers final: 10 residues processed: 67 average time/residue: 0.1690 time to fit residues: 14.6721 Evaluate side-chains 57 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 394 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 51 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 0.0020 chunk 46 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 25 optimal weight: 0.0970 chunk 52 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.083009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.064948 restraints weight = 29012.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.066361 restraints weight = 19925.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.067516 restraints weight = 15280.406| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4790 Z= 0.231 Angle : 0.805 12.319 6495 Z= 0.399 Chirality : 0.043 0.150 747 Planarity : 0.005 0.065 848 Dihedral : 6.879 56.056 645 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 3.83 % Allowed : 28.35 % Favored : 67.82 % 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: -3.54 (0.31), residues: 586 helix: -1.47 (0.31), residues: 224 sheet: -3.37 (0.55), residues: 56 loop : -2.89 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 34 HIS 0.007 0.001 HIS C 186 PHE 0.011 0.002 PHE B 192 TYR 0.012 0.001 TYR B 27 ARG 0.007 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 LEU cc_start: 0.8802 (pp) cc_final: 0.8239 (mt) REVERT: B 108 ARG cc_start: 0.6546 (OUTLIER) cc_final: 0.5314 (pmt-80) REVERT: C 15 GLU cc_start: 0.9030 (tp30) cc_final: 0.8004 (mp0) REVERT: C 62 LEU cc_start: 0.9453 (tt) cc_final: 0.9231 (mm) REVERT: C 216 ASN cc_start: 0.8754 (m-40) cc_final: 0.8074 (t0) outliers start: 20 outliers final: 6 residues processed: 66 average time/residue: 0.1614 time to fit residues: 13.9569 Evaluate side-chains 49 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 44 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 38 optimal weight: 0.0470 chunk 27 optimal weight: 0.1980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** 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 = 0.4322 r_free = 0.4322 target = 0.083801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.065736 restraints weight = 28896.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.067239 restraints weight = 19939.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.068294 restraints weight = 15215.054| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4790 Z= 0.212 Angle : 0.801 15.327 6495 Z= 0.387 Chirality : 0.042 0.127 747 Planarity : 0.005 0.061 848 Dihedral : 6.214 28.801 643 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 1.92 % Allowed : 27.39 % Favored : 70.69 % 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: -3.31 (0.31), residues: 586 helix: -1.29 (0.32), residues: 225 sheet: -3.30 (0.55), residues: 56 loop : -2.74 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 34 HIS 0.005 0.001 HIS C 186 PHE 0.011 0.001 PHE C 315 TYR 0.009 0.001 TYR C 393 ARG 0.011 0.001 ARG C 285 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ILE cc_start: 0.9477 (tp) cc_final: 0.9176 (pt) REVERT: B 53 GLN cc_start: 0.8962 (pt0) cc_final: 0.8710 (pt0) REVERT: B 75 LEU cc_start: 0.8833 (pp) cc_final: 0.8414 (mt) REVERT: B 108 ARG cc_start: 0.6464 (OUTLIER) cc_final: 0.5165 (pmt-80) REVERT: C 15 GLU cc_start: 0.9035 (tp30) cc_final: 0.7985 (mp0) REVERT: C 62 LEU cc_start: 0.9444 (tt) cc_final: 0.9206 (mm) outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.1545 time to fit residues: 13.1029 Evaluate side-chains 55 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 379 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 40 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 HIS ** 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 = 0.4186 r_free = 0.4186 target = 0.076927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.059588 restraints weight = 28126.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.060883 restraints weight = 19745.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.061866 restraints weight = 15209.435| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 4790 Z= 0.334 Angle : 0.853 15.532 6495 Z= 0.418 Chirality : 0.044 0.141 747 Planarity : 0.006 0.065 848 Dihedral : 6.358 29.071 643 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 27.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.29 % Favored : 87.71 % Rotamer: Outliers : 3.07 % Allowed : 28.35 % Favored : 68.58 % 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 (0.32), residues: 586 helix: -1.08 (0.32), residues: 219 sheet: -3.36 (0.53), residues: 66 loop : -2.62 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 34 HIS 0.008 0.002 HIS C 302 PHE 0.016 0.002 PHE B 192 TYR 0.014 0.002 TYR C 156 ARG 0.005 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ILE cc_start: 0.9481 (tp) cc_final: 0.9195 (pt) REVERT: B 75 LEU cc_start: 0.8887 (pp) cc_final: 0.8340 (mt) REVERT: B 108 ARG cc_start: 0.6463 (OUTLIER) cc_final: 0.5466 (pmt-80) REVERT: C 15 GLU cc_start: 0.9090 (tp30) cc_final: 0.8502 (mp0) REVERT: C 62 LEU cc_start: 0.9389 (tt) cc_final: 0.9139 (mm) outliers start: 16 outliers final: 12 residues processed: 55 average time/residue: 0.1528 time to fit residues: 11.4251 Evaluate side-chains 56 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 379 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 56 optimal weight: 0.0010 chunk 30 optimal weight: 6.9990 chunk 35 optimal weight: 0.0270 chunk 47 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 22 optimal weight: 0.0470 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 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 = 0.4245 r_free = 0.4245 target = 0.080766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.063011 restraints weight = 29092.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.064347 restraints weight = 20281.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.065312 restraints weight = 15618.101| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4790 Z= 0.207 Angle : 0.803 16.183 6495 Z= 0.381 Chirality : 0.043 0.145 747 Planarity : 0.004 0.055 848 Dihedral : 5.973 30.367 643 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 2.87 % Allowed : 28.54 % Favored : 68.58 % 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: -2.82 (0.33), residues: 586 helix: -0.80 (0.33), residues: 219 sheet: -3.18 (0.54), residues: 66 loop : -2.40 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 34 HIS 0.013 0.002 HIS B 163 PHE 0.014 0.002 PHE C 315 TYR 0.016 0.001 TYR C 393 ARG 0.004 0.000 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ILE cc_start: 0.9423 (tp) cc_final: 0.9143 (pt) REVERT: B 75 LEU cc_start: 0.8871 (pp) cc_final: 0.8474 (mt) REVERT: B 108 ARG cc_start: 0.6534 (OUTLIER) cc_final: 0.5160 (pmt-80) REVERT: B 163 HIS cc_start: 0.7590 (OUTLIER) cc_final: 0.7159 (t-90) REVERT: C 15 GLU cc_start: 0.9066 (tp30) cc_final: 0.8052 (mp0) REVERT: C 62 LEU cc_start: 0.9409 (tt) cc_final: 0.9188 (mm) outliers start: 15 outliers final: 8 residues processed: 61 average time/residue: 0.1449 time to fit residues: 11.8822 Evaluate side-chains 57 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 0.3980 chunk 1 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 44 optimal weight: 30.0000 chunk 49 optimal weight: 20.0000 chunk 52 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 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 = 0.4226 r_free = 0.4226 target = 0.078827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.060853 restraints weight = 27026.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.062206 restraints weight = 18654.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.063235 restraints weight = 14211.235| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4790 Z= 0.222 Angle : 0.808 15.153 6495 Z= 0.386 Chirality : 0.041 0.128 747 Planarity : 0.004 0.053 848 Dihedral : 5.898 29.331 643 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 1.72 % Allowed : 29.69 % Favored : 68.58 % 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: -2.80 (0.34), residues: 586 helix: -0.81 (0.33), residues: 219 sheet: -3.18 (0.56), residues: 68 loop : -2.35 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 179 HIS 0.008 0.001 HIS B 163 PHE 0.012 0.001 PHE C 315 TYR 0.009 0.001 TYR C 393 ARG 0.003 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ILE cc_start: 0.9406 (tp) cc_final: 0.9172 (pt) REVERT: B 75 LEU cc_start: 0.8899 (pp) cc_final: 0.8462 (mt) REVERT: B 108 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.5119 (pmt-80) REVERT: C 15 GLU cc_start: 0.9043 (tp30) cc_final: 0.8113 (mp0) REVERT: C 51 HIS cc_start: 0.6395 (m-70) cc_final: 0.5873 (t-90) REVERT: C 62 LEU cc_start: 0.9372 (tt) cc_final: 0.9149 (mm) outliers start: 9 outliers final: 5 residues processed: 58 average time/residue: 0.1811 time to fit residues: 13.5979 Evaluate side-chains 54 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 332 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 19 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 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 = 0.4229 r_free = 0.4229 target = 0.078960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.061085 restraints weight = 26827.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.062453 restraints weight = 18385.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.063494 restraints weight = 13975.498| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4790 Z= 0.213 Angle : 0.812 15.377 6495 Z= 0.390 Chirality : 0.042 0.137 747 Planarity : 0.004 0.050 848 Dihedral : 5.838 29.791 643 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 1.92 % Allowed : 30.08 % Favored : 68.01 % 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: -2.73 (0.34), residues: 586 helix: -0.74 (0.33), residues: 217 sheet: -3.14 (0.57), residues: 68 loop : -2.32 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 34 HIS 0.004 0.001 HIS C 186 PHE 0.011 0.001 PHE C 315 TYR 0.007 0.001 TYR C 393 ARG 0.009 0.001 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ILE cc_start: 0.9385 (tp) cc_final: 0.9166 (pt) REVERT: B 75 LEU cc_start: 0.8871 (pp) cc_final: 0.8434 (mt) REVERT: B 108 ARG cc_start: 0.6617 (OUTLIER) cc_final: 0.5216 (pmt-80) REVERT: B 205 GLU cc_start: 0.8285 (mp0) cc_final: 0.7938 (mm-30) REVERT: B 258 ILE cc_start: 0.9287 (pt) cc_final: 0.8864 (mt) REVERT: C 15 GLU cc_start: 0.9014 (tp30) cc_final: 0.8119 (mp0) REVERT: C 51 HIS cc_start: 0.6512 (m-70) cc_final: 0.5872 (t-90) outliers start: 10 outliers final: 8 residues processed: 57 average time/residue: 0.1724 time to fit residues: 12.9316 Evaluate side-chains 56 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 332 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 HIS ** 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 = 0.4211 r_free = 0.4211 target = 0.078022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.060562 restraints weight = 27384.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.061922 restraints weight = 18471.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.062926 restraints weight = 13979.944| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4790 Z= 0.237 Angle : 0.875 17.558 6495 Z= 0.414 Chirality : 0.042 0.155 747 Planarity : 0.004 0.051 848 Dihedral : 5.853 29.726 643 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 1.72 % Allowed : 30.08 % Favored : 68.20 % 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: -2.74 (0.34), residues: 586 helix: -0.72 (0.33), residues: 217 sheet: -3.39 (0.56), residues: 66 loop : -2.30 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 34 HIS 0.004 0.001 HIS B 26 PHE 0.008 0.001 PHE C 47 TYR 0.008 0.001 TYR C 393 ARG 0.006 0.001 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ILE cc_start: 0.9361 (tp) cc_final: 0.9147 (pt) REVERT: B 75 LEU cc_start: 0.8888 (pp) cc_final: 0.8433 (mt) REVERT: B 108 ARG cc_start: 0.6561 (OUTLIER) cc_final: 0.5182 (pmt-80) REVERT: B 258 ILE cc_start: 0.9354 (pt) cc_final: 0.8991 (mt) REVERT: C 15 GLU cc_start: 0.9031 (tp30) cc_final: 0.8434 (mp0) REVERT: C 51 HIS cc_start: 0.6706 (m-70) cc_final: 0.6101 (t-90) outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 0.1738 time to fit residues: 12.4221 Evaluate side-chains 54 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 332 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 16 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: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN ** C 302 HIS ** 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 = 0.4187 r_free = 0.4187 target = 0.076913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.059876 restraints weight = 27601.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.061213 restraints weight = 18765.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.062186 restraints weight = 14220.093| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4790 Z= 0.254 Angle : 0.888 15.264 6495 Z= 0.420 Chirality : 0.042 0.177 747 Planarity : 0.004 0.049 848 Dihedral : 5.979 30.943 643 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 1.53 % Allowed : 30.46 % Favored : 68.01 % 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: -2.73 (0.34), residues: 586 helix: -0.72 (0.33), residues: 219 sheet: -3.47 (0.54), residues: 66 loop : -2.27 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 34 HIS 0.006 0.001 HIS B 209 PHE 0.010 0.002 PHE B 195 TYR 0.011 0.001 TYR C 393 ARG 0.006 0.001 ARG B 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 LEU cc_start: 0.8857 (pp) cc_final: 0.8386 (mt) REVERT: B 108 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.5131 (pmt-80) REVERT: B 174 ASP cc_start: 0.7934 (p0) cc_final: 0.7507 (t70) REVERT: B 205 GLU cc_start: 0.8312 (mp0) cc_final: 0.7770 (mm-30) REVERT: B 258 ILE cc_start: 0.9417 (pt) cc_final: 0.9140 (mt) REVERT: C 15 GLU cc_start: 0.9005 (tp30) cc_final: 0.8481 (mp0) REVERT: C 51 HIS cc_start: 0.6890 (m-70) cc_final: 0.6242 (t-90) REVERT: C 62 LEU cc_start: 0.9275 (tt) cc_final: 0.9018 (mm) REVERT: C 85 GLN cc_start: 0.7612 (tp-100) cc_final: 0.7349 (tp-100) outliers start: 8 outliers final: 7 residues processed: 54 average time/residue: 0.1782 time to fit residues: 12.4346 Evaluate side-chains 55 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 332 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 58 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 52 optimal weight: 0.0980 chunk 40 optimal weight: 30.0000 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 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 = 0.4220 r_free = 0.4220 target = 0.078552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.060470 restraints weight = 30057.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.061849 restraints weight = 20464.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.062848 restraints weight = 15607.275| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4790 Z= 0.251 Angle : 0.867 16.399 6495 Z= 0.411 Chirality : 0.042 0.134 747 Planarity : 0.004 0.048 848 Dihedral : 5.945 31.017 643 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 21.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 1.92 % Allowed : 30.27 % Favored : 67.82 % 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: -2.70 (0.34), residues: 586 helix: -0.63 (0.33), residues: 219 sheet: -3.51 (0.53), residues: 66 loop : -2.28 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 179 HIS 0.006 0.001 HIS B 26 PHE 0.010 0.002 PHE C 47 TYR 0.019 0.002 TYR C 382 ARG 0.006 0.001 ARG B 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2297.87 seconds wall clock time: 40 minutes 31.55 seconds (2431.55 seconds total)