Starting phenix.real_space_refine on Tue Jan 14 18:29:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s7e_19768/01_2025/8s7e_19768.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s7e_19768/01_2025/8s7e_19768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s7e_19768/01_2025/8s7e_19768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s7e_19768/01_2025/8s7e_19768.map" model { file = "/net/cci-nas-00/data/ceres_data/8s7e_19768/01_2025/8s7e_19768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s7e_19768/01_2025/8s7e_19768.cif" } resolution = 3.4 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= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 19 5.16 5 C 2335 2.51 5 N 627 2.21 5 O 683 1.98 5 H 3648 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7312 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2123 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain breaks: 2 Chain: "B" Number of atoms: 5189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 5189 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain breaks: 5 Time building chain proxies: 4.18, per 1000 atoms: 0.57 Number of scatterers: 7312 At special positions: 0 Unit cell: (71.94, 87.78, 75.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 O 683 8.00 N 627 7.00 C 2335 6.00 H 3648 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 807.2 milliseconds 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 872 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 4 sheets defined 43.3% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.960A pdb=" N SER A 24 " --> pdb=" O ILE A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 33 removed outlier: 3.784A pdb=" N MET A 30 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 66 Processing helix chain 'A' and resid 86 through 94 Processing helix chain 'A' and resid 96 through 111 Processing helix chain 'A' and resid 112 through 128 Processing helix chain 'A' and resid 131 through 139 removed outlier: 4.651A pdb=" N LYS A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 157 Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'B' and resid 26 through 36 removed outlier: 3.541A pdb=" N VAL B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 removed outlier: 3.966A pdb=" N CYS B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 62 Processing helix chain 'B' and resid 82 through 92 removed outlier: 4.429A pdb=" N VAL B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 202 through 209 removed outlier: 3.765A pdb=" N LEU B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 245 removed outlier: 3.730A pdb=" N PHE B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASP B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 312 removed outlier: 3.838A pdb=" N ALA B 312 " --> pdb=" O ARG B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 349 Processing sheet with id=AA1, first strand: chain 'B' and resid 144 through 145 removed outlier: 3.972A pdb=" N GLN B 144 " --> pdb=" O HIS B 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 144 through 145 removed outlier: 3.972A pdb=" N GLN B 144 " --> pdb=" O HIS B 100 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE B 148 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR B 104 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N THR B 150 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ALA B 106 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN B 257 " --> pdb=" O VAL B 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 166 through 168 removed outlier: 4.116A pdb=" N GLN B 166 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL B 155 " --> pdb=" O GLN B 166 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLY B 152 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE B 358 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL B 154 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY B 356 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 287 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 188 through 192 removed outlier: 3.737A pdb=" N GLN B 188 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL B 276 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL B 222 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU B 278 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL B 220 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE B 280 " --> pdb=" O ARG B 218 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS B 388 " --> pdb=" O GLU B 362 " (cutoff:3.500A) 162 hydrogen bonds defined for protein. 468 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: 2.39 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3639 1.03 - 1.23: 11 1.23 - 1.42: 1508 1.42 - 1.62: 2191 1.62 - 1.81: 28 Bond restraints: 7377 Sorted by residual: bond pdb=" C PHE B 36 " pdb=" N LEU B 37 " ideal model delta sigma weight residual 1.326 1.338 -0.012 1.12e-02 7.97e+03 1.14e+00 bond pdb=" N LEU B 37 " pdb=" CA LEU B 37 " ideal model delta sigma weight residual 1.453 1.462 -0.008 9.20e-03 1.18e+04 8.18e-01 bond pdb=" CA VAL B 222 " pdb=" CB VAL B 222 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.36e-02 5.41e+03 7.60e-01 bond pdb=" CB ASN A 143 " pdb=" CG ASN A 143 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 6.82e-01 bond pdb=" CB GLU B 208 " pdb=" CG GLU B 208 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.40e-01 ... (remaining 7372 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.01: 13347 7.01 - 14.02: 0 14.02 - 21.04: 0 21.04 - 28.05: 0 28.05 - 35.06: 3 Bond angle restraints: 13350 Sorted by residual: angle pdb=" CB THR B 20 " pdb=" CA THR B 20 " pdb=" HA THR B 20 " ideal model delta sigma weight residual 109.00 73.94 35.06 3.00e+00 1.11e-01 1.37e+02 angle pdb=" N THR B 20 " pdb=" CA THR B 20 " pdb=" HA THR B 20 " ideal model delta sigma weight residual 110.00 75.63 34.37 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C THR B 20 " pdb=" CA THR B 20 " pdb=" HA THR B 20 " ideal model delta sigma weight residual 109.00 74.70 34.30 3.00e+00 1.11e-01 1.31e+02 angle pdb=" N SER B 260 " pdb=" CA SER B 260 " pdb=" C SER B 260 " ideal model delta sigma weight residual 108.32 114.40 -6.08 1.64e+00 3.72e-01 1.37e+01 angle pdb=" CA MET B 306 " pdb=" CB MET B 306 " pdb=" CG MET B 306 " ideal model delta sigma weight residual 114.10 109.07 5.03 2.00e+00 2.50e-01 6.32e+00 ... (remaining 13345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 2926 16.91 - 33.82: 341 33.82 - 50.72: 134 50.72 - 67.63: 39 67.63 - 84.54: 13 Dihedral angle restraints: 3453 sinusoidal: 1903 harmonic: 1550 Sorted by residual: dihedral pdb=" C THR B 20 " pdb=" N THR B 20 " pdb=" CA THR B 20 " pdb=" CB THR B 20 " ideal model delta harmonic sigma weight residual -122.00 -131.33 9.33 0 2.50e+00 1.60e-01 1.39e+01 dihedral pdb=" CA SER B 260 " pdb=" C SER B 260 " pdb=" N LEU B 261 " pdb=" CA LEU B 261 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CG ARG B 346 " pdb=" CD ARG B 346 " pdb=" NE ARG B 346 " pdb=" CZ ARG B 346 " ideal model delta sinusoidal sigma weight residual -90.00 -134.01 44.01 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 3450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 529 0.071 - 0.141: 54 0.141 - 0.211: 1 0.211 - 0.282: 0 0.282 - 0.352: 1 Chirality restraints: 585 Sorted by residual: chirality pdb=" CA THR B 20 " pdb=" N THR B 20 " pdb=" C THR B 20 " pdb=" CB THR B 20 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA ILE B 320 " pdb=" N ILE B 320 " pdb=" C ILE B 320 " pdb=" CB ILE B 320 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE B 249 " pdb=" N ILE B 249 " pdb=" C ILE B 249 " pdb=" CB ILE B 249 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 582 not shown) Planarity restraints: 1082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 45 " -0.026 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 46 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 46 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 46 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 208 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" CD GLU B 208 " -0.020 2.00e-02 2.50e+03 pdb=" OE1 GLU B 208 " 0.007 2.00e-02 2.50e+03 pdb=" OE2 GLU B 208 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 154 " 0.095 9.50e-02 1.11e+02 3.21e-02 1.33e+00 pdb=" NE ARG A 154 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 154 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 154 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 154 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 154 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 154 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 154 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 154 " 0.000 2.00e-02 2.50e+03 ... (remaining 1079 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 647 2.19 - 2.79: 15645 2.79 - 3.40: 21183 3.40 - 4.00: 27183 4.00 - 4.60: 41290 Nonbonded interactions: 105948 Sorted by model distance: nonbonded pdb=" HE1 TRP B 68 " pdb=" O THR B 156 " model vdw 1.591 2.450 nonbonded pdb=" OE1 GLU B 362 " pdb=" H THR B 391 " model vdw 1.607 2.450 nonbonded pdb=" O ASP A 144 " pdb="HH12 ARG B 50 " model vdw 1.608 2.450 nonbonded pdb=" OE1 GLU A 19 " pdb=" H GLU A 19 " model vdw 1.626 2.450 nonbonded pdb=" OG1 THR B 156 " pdb=" H LEU B 354 " model vdw 1.631 2.450 ... (remaining 105943 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.140 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.880 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5833 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 : 0.003 0.024 3729 Z= 0.183 Angle : 0.550 6.076 5045 Z= 0.295 Chirality : 0.044 0.352 585 Planarity : 0.004 0.042 649 Dihedral : 18.594 84.537 1377 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.25 % Allowed : 28.89 % Favored : 70.86 % 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: -1.51 (0.40), residues: 448 helix: 0.05 (0.39), residues: 166 sheet: -2.06 (0.62), residues: 77 loop : -1.37 (0.46), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 88 HIS 0.002 0.001 HIS B 63 PHE 0.019 0.001 PHE B 36 TYR 0.008 0.001 TYR B 104 ARG 0.007 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 391 THR cc_start: 0.5762 (p) cc_final: 0.5470 (t) outliers start: 1 outliers final: 1 residues processed: 62 average time/residue: 0.5543 time to fit residues: 40.7506 Evaluate side-chains 60 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 351 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 41 optimal weight: 7.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5085 r_free = 0.5085 target = 0.224949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.194221 restraints weight = 15981.928| |-----------------------------------------------------------------------------| r_work (start): 0.4771 rms_B_bonded: 4.63 r_work: 0.4612 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.4612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3729 Z= 0.251 Angle : 0.619 4.797 5045 Z= 0.339 Chirality : 0.046 0.353 585 Planarity : 0.005 0.037 649 Dihedral : 4.877 24.526 490 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 4.44 % Allowed : 28.15 % Favored : 67.41 % 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: -1.74 (0.40), residues: 448 helix: -0.27 (0.37), residues: 178 sheet: -2.17 (0.58), residues: 79 loop : -1.42 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 52 HIS 0.005 0.001 HIS B 63 PHE 0.008 0.001 PHE B 345 TYR 0.007 0.001 TYR B 104 ARG 0.004 0.001 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 320 ILE cc_start: 0.5684 (OUTLIER) cc_final: 0.5017 (mt) REVERT: B 392 THR cc_start: 0.3327 (OUTLIER) cc_final: 0.3075 (m) REVERT: B 394 MET cc_start: 0.8277 (mmm) cc_final: 0.7981 (mmm) outliers start: 18 outliers final: 10 residues processed: 79 average time/residue: 0.4753 time to fit residues: 44.3599 Evaluate side-chains 75 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 403 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 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 = 0.5086 r_free = 0.5086 target = 0.225956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.195045 restraints weight = 15725.053| |-----------------------------------------------------------------------------| r_work (start): 0.4755 rms_B_bonded: 4.61 r_work: 0.4595 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.4595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3729 Z= 0.245 Angle : 0.610 4.682 5045 Z= 0.333 Chirality : 0.046 0.353 585 Planarity : 0.004 0.028 649 Dihedral : 4.928 31.558 489 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 4.94 % Allowed : 27.41 % Favored : 67.65 % 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: -1.84 (0.40), residues: 448 helix: -0.29 (0.37), residues: 178 sheet: -2.43 (0.56), residues: 79 loop : -1.43 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 68 HIS 0.006 0.001 HIS B 63 PHE 0.009 0.001 PHE B 179 TYR 0.007 0.001 TYR B 104 ARG 0.005 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ILE cc_start: 0.6046 (OUTLIER) cc_final: 0.5575 (tt) REVERT: B 320 ILE cc_start: 0.5633 (OUTLIER) cc_final: 0.4982 (mt) REVERT: B 392 THR cc_start: 0.3420 (OUTLIER) cc_final: 0.2571 (m) REVERT: B 394 MET cc_start: 0.8146 (mmm) cc_final: 0.7785 (mmm) outliers start: 20 outliers final: 13 residues processed: 75 average time/residue: 0.4495 time to fit residues: 40.2203 Evaluate side-chains 78 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 403 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 42 optimal weight: 0.0670 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5128 r_free = 0.5128 target = 0.229958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.199127 restraints weight = 15510.715| |-----------------------------------------------------------------------------| r_work (start): 0.4808 rms_B_bonded: 4.69 r_work: 0.4645 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.4645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3729 Z= 0.156 Angle : 0.552 4.060 5045 Z= 0.297 Chirality : 0.045 0.351 585 Planarity : 0.003 0.028 649 Dihedral : 4.675 30.989 489 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.72 % Allowed : 27.65 % Favored : 69.63 % 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: -1.56 (0.40), residues: 448 helix: 0.01 (0.38), residues: 178 sheet: -2.86 (0.48), residues: 85 loop : -0.96 (0.50), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 68 HIS 0.003 0.001 HIS B 63 PHE 0.010 0.001 PHE B 345 TYR 0.004 0.001 TYR B 235 ARG 0.005 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7439 (mm-30) REVERT: B 238 GLN cc_start: 0.8698 (mp10) cc_final: 0.8492 (mp10) REVERT: B 320 ILE cc_start: 0.5850 (OUTLIER) cc_final: 0.5254 (mt) REVERT: B 392 THR cc_start: 0.3188 (OUTLIER) cc_final: 0.2380 (m) REVERT: B 394 MET cc_start: 0.8116 (mmm) cc_final: 0.7811 (mmm) outliers start: 11 outliers final: 7 residues processed: 71 average time/residue: 0.4978 time to fit residues: 41.6647 Evaluate side-chains 72 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 403 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 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 = 0.5073 r_free = 0.5073 target = 0.226120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.196176 restraints weight = 15539.473| |-----------------------------------------------------------------------------| r_work (start): 0.4745 rms_B_bonded: 4.46 r_work: 0.4577 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.4577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3729 Z= 0.258 Angle : 0.609 5.007 5045 Z= 0.331 Chirality : 0.046 0.354 585 Planarity : 0.004 0.034 649 Dihedral : 4.965 29.840 489 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 4.69 % Allowed : 27.41 % Favored : 67.90 % 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: -1.86 (0.39), residues: 448 helix: -0.26 (0.37), residues: 178 sheet: -2.80 (0.54), residues: 78 loop : -1.33 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 52 HIS 0.006 0.001 HIS B 63 PHE 0.012 0.001 PHE B 179 TYR 0.006 0.001 TYR B 104 ARG 0.006 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7635 (mm-30) REVERT: B 238 GLN cc_start: 0.8707 (mp10) cc_final: 0.8484 (mp10) REVERT: B 320 ILE cc_start: 0.5617 (OUTLIER) cc_final: 0.4974 (mt) REVERT: B 392 THR cc_start: 0.3578 (OUTLIER) cc_final: 0.2713 (m) REVERT: B 394 MET cc_start: 0.8031 (mmm) cc_final: 0.7671 (mmm) outliers start: 19 outliers final: 14 residues processed: 76 average time/residue: 0.5016 time to fit residues: 45.1014 Evaluate side-chains 78 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 403 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 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 = 0.5134 r_free = 0.5134 target = 0.231122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.200238 restraints weight = 15296.748| |-----------------------------------------------------------------------------| r_work (start): 0.4803 rms_B_bonded: 4.63 r_work: 0.4642 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.4642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3729 Z= 0.158 Angle : 0.554 4.042 5045 Z= 0.297 Chirality : 0.045 0.352 585 Planarity : 0.003 0.030 649 Dihedral : 4.735 30.770 489 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.95 % Allowed : 27.65 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.64 (0.40), residues: 448 helix: -0.02 (0.38), residues: 178 sheet: -3.02 (0.48), residues: 85 loop : -1.00 (0.50), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 61 HIS 0.004 0.001 HIS B 63 PHE 0.006 0.001 PHE B 345 TYR 0.003 0.001 TYR B 225 ARG 0.005 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7585 (mm-30) REVERT: B 238 GLN cc_start: 0.8704 (mp10) cc_final: 0.8454 (mp10) REVERT: B 320 ILE cc_start: 0.5623 (OUTLIER) cc_final: 0.5013 (mt) REVERT: B 392 THR cc_start: 0.3163 (OUTLIER) cc_final: 0.2349 (m) outliers start: 16 outliers final: 12 residues processed: 74 average time/residue: 0.4559 time to fit residues: 40.5039 Evaluate side-chains 76 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 403 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 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 = 0.5065 r_free = 0.5065 target = 0.223749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.192852 restraints weight = 15405.969| |-----------------------------------------------------------------------------| r_work (start): 0.4723 rms_B_bonded: 4.51 r_work: 0.4556 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.4556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3729 Z= 0.291 Angle : 0.638 5.544 5045 Z= 0.347 Chirality : 0.046 0.355 585 Planarity : 0.004 0.039 649 Dihedral : 5.111 30.208 489 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 4.69 % Allowed : 27.16 % Favored : 68.15 % 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: -1.98 (0.40), residues: 448 helix: -0.23 (0.37), residues: 175 sheet: -3.14 (0.49), residues: 87 loop : -1.25 (0.48), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 52 HIS 0.007 0.001 HIS B 63 PHE 0.015 0.002 PHE B 345 TYR 0.008 0.001 TYR B 104 ARG 0.008 0.001 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ILE cc_start: 0.6099 (OUTLIER) cc_final: 0.5625 (tt) REVERT: B 92 LEU cc_start: 0.4767 (OUTLIER) cc_final: 0.4522 (mt) REVERT: B 172 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7634 (mm-30) REVERT: B 238 GLN cc_start: 0.8707 (mp10) cc_final: 0.8451 (mp10) REVERT: B 320 ILE cc_start: 0.5459 (OUTLIER) cc_final: 0.4806 (mt) REVERT: B 392 THR cc_start: 0.3106 (OUTLIER) cc_final: 0.2583 (m) outliers start: 19 outliers final: 14 residues processed: 76 average time/residue: 0.4327 time to fit residues: 39.4809 Evaluate side-chains 79 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 403 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 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 = 0.5105 r_free = 0.5105 target = 0.228454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.197876 restraints weight = 15419.588| |-----------------------------------------------------------------------------| r_work (start): 0.4771 rms_B_bonded: 4.53 r_work: 0.4609 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.4609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3729 Z= 0.181 Angle : 0.573 4.347 5045 Z= 0.307 Chirality : 0.046 0.354 585 Planarity : 0.004 0.036 649 Dihedral : 4.909 30.979 489 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.44 % Allowed : 27.65 % Favored : 67.90 % 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: -1.82 (0.40), residues: 448 helix: -0.10 (0.37), residues: 178 sheet: -2.84 (0.53), residues: 76 loop : -1.43 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 61 HIS 0.004 0.001 HIS B 63 PHE 0.006 0.001 PHE B 345 TYR 0.004 0.001 TYR B 225 ARG 0.006 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7913 (tt) REVERT: B 172 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7697 (mm-30) REVERT: B 238 GLN cc_start: 0.8711 (mp10) cc_final: 0.8447 (mp10) REVERT: B 320 ILE cc_start: 0.5452 (OUTLIER) cc_final: 0.4794 (mt) REVERT: B 392 THR cc_start: 0.2919 (OUTLIER) cc_final: 0.2451 (m) outliers start: 18 outliers final: 14 residues processed: 74 average time/residue: 0.4558 time to fit residues: 39.9470 Evaluate side-chains 79 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 403 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5124 r_free = 0.5124 target = 0.231120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.201637 restraints weight = 15777.250| |-----------------------------------------------------------------------------| r_work (start): 0.4809 rms_B_bonded: 4.49 r_work: 0.4643 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.4643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5924 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3729 Z= 0.158 Angle : 0.550 4.107 5045 Z= 0.294 Chirality : 0.045 0.353 585 Planarity : 0.004 0.042 649 Dihedral : 4.670 27.419 489 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.96 % Allowed : 29.14 % Favored : 67.90 % 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: -1.58 (0.40), residues: 448 helix: 0.20 (0.38), residues: 178 sheet: -3.05 (0.47), residues: 85 loop : -1.12 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 61 HIS 0.004 0.001 HIS B 63 PHE 0.022 0.001 PHE A 145 TYR 0.003 0.001 TYR B 235 ARG 0.008 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7816 (tt) REVERT: B 238 GLN cc_start: 0.8684 (mp10) cc_final: 0.8419 (mp10) REVERT: B 392 THR cc_start: 0.2927 (OUTLIER) cc_final: 0.2450 (m) outliers start: 12 outliers final: 9 residues processed: 72 average time/residue: 0.4419 time to fit residues: 37.9762 Evaluate side-chains 71 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 403 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 30 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 14 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5127 r_free = 0.5127 target = 0.230184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.199638 restraints weight = 15670.619| |-----------------------------------------------------------------------------| r_work (start): 0.4818 rms_B_bonded: 4.59 r_work: 0.4661 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.4661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5903 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3729 Z= 0.154 Angle : 0.550 4.002 5045 Z= 0.292 Chirality : 0.045 0.353 585 Planarity : 0.003 0.045 649 Dihedral : 4.553 26.164 489 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.72 % Allowed : 29.63 % Favored : 67.65 % 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: -1.37 (0.40), residues: 448 helix: 0.35 (0.38), residues: 178 sheet: -2.82 (0.47), residues: 85 loop : -1.03 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 61 HIS 0.003 0.001 HIS B 63 PHE 0.015 0.001 PHE A 145 TYR 0.003 0.001 TYR B 235 ARG 0.007 0.000 ARG A 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7833 (tt) REVERT: B 238 GLN cc_start: 0.8669 (mp10) cc_final: 0.8403 (mp10) REVERT: B 392 THR cc_start: 0.2889 (OUTLIER) cc_final: 0.2399 (m) outliers start: 11 outliers final: 9 residues processed: 67 average time/residue: 0.5093 time to fit residues: 40.8647 Evaluate side-chains 70 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 403 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 5 optimal weight: 0.0270 chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 4 optimal weight: 0.0870 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5142 r_free = 0.5142 target = 0.232820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.204421 restraints weight = 15418.211| |-----------------------------------------------------------------------------| r_work (start): 0.4844 rms_B_bonded: 4.36 r_work: 0.4680 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.4680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5893 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3729 Z= 0.157 Angle : 0.563 10.604 5045 Z= 0.292 Chirality : 0.045 0.351 585 Planarity : 0.003 0.043 649 Dihedral : 4.450 25.309 489 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.21 % Allowed : 28.89 % Favored : 67.90 % 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: -1.24 (0.40), residues: 448 helix: 0.49 (0.38), residues: 178 sheet: -2.73 (0.48), residues: 85 loop : -1.02 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 61 HIS 0.003 0.001 HIS B 63 PHE 0.018 0.001 PHE A 145 TYR 0.003 0.001 TYR B 235 ARG 0.008 0.000 ARG A 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4396.40 seconds wall clock time: 80 minutes 35.10 seconds (4835.10 seconds total)