Starting phenix.real_space_refine on Mon Apr 28 06:43:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s7e_19768/04_2025/8s7e_19768.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s7e_19768/04_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_19768/04_2025/8s7e_19768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s7e_19768/04_2025/8s7e_19768.map" model { file = "/net/cci-nas-00/data/ceres_data/8s7e_19768/04_2025/8s7e_19768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s7e_19768/04_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-5669/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: 4.10, per 1000 atoms: 0.56 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: 1.97 Conformation dependent library (CDL) restraints added in 752.0 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: 2.57 Time building geometry restraints manager: 2.42 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: 1.060 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: 0.120 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.580 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.920 ------------------------------------------------------------------------------- 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= 0.130 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 Details of bonding type rmsd hydrogen bonds : bond 0.24113 ( 161) hydrogen bonds : angle 9.29810 ( 468) covalent geometry : bond 0.00284 ( 3729) covalent geometry : angle 0.55002 ( 5045) *********************** 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 : 0.567 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: 0.4802 time to fit residues: 34.8211 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 : 0.539 ------------------------------------------------------------------------------- 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: 2.9990 chunk 41 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.5069 r_free = 0.5069 target = 0.223402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.192430 restraints weight = 16046.427| |-----------------------------------------------------------------------------| r_work (start): 0.4748 rms_B_bonded: 4.63 r_work: 0.4585 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.4585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3729 Z= 0.206 Angle : 0.649 5.090 5045 Z= 0.356 Chirality : 0.046 0.354 585 Planarity : 0.005 0.040 649 Dihedral : 5.077 26.654 490 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 4.94 % Allowed : 28.15 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.92 (0.40), residues: 448 helix: -0.42 (0.36), residues: 178 sheet: -2.25 (0.58), residues: 79 loop : -1.52 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 52 HIS 0.006 0.001 HIS B 63 PHE 0.008 0.002 PHE B 349 TYR 0.009 0.001 TYR B 104 ARG 0.005 0.001 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.05517 ( 161) hydrogen bonds : angle 7.86240 ( 468) covalent geometry : bond 0.00447 ( 3729) covalent geometry : angle 0.64932 ( 5045) *********************** 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 85 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.599 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: 0.5670 (OUTLIER) cc_final: 0.4995 (mt) REVERT: B 392 THR cc_start: 0.3418 (OUTLIER) cc_final: 0.3173 (m) REVERT: B 394 MET cc_start: 0.8299 (mmm) cc_final: 0.8014 (mmm) outliers start: 20 outliers final: 11 residues processed: 81 average time/residue: 0.4308 time to fit residues: 41.2152 Evaluate side-chains 75 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5107 r_free = 0.5107 target = 0.227627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.196670 restraints weight = 15785.420| |-----------------------------------------------------------------------------| r_work (start): 0.4789 rms_B_bonded: 4.63 r_work: 0.4634 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.4634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 0.1271 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= 0.130 Angle : 0.583 4.423 5045 Z= 0.315 Chirality : 0.046 0.351 585 Planarity : 0.004 0.026 649 Dihedral : 4.871 31.444 490 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.70 % Allowed : 28.15 % 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: -1.68 (0.40), residues: 448 helix: -0.16 (0.37), residues: 178 sheet: -2.48 (0.54), residues: 79 loop : -1.28 (0.49), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 68 HIS 0.004 0.001 HIS B 63 PHE 0.010 0.001 PHE B 345 TYR 0.008 0.001 TYR B 235 ARG 0.005 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.04690 ( 161) hydrogen bonds : angle 7.11795 ( 468) covalent geometry : bond 0.00280 ( 3729) covalent geometry : angle 0.58322 ( 5045) *********************** 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 76 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.586 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: 0.5713 (OUTLIER) cc_final: 0.5076 (mt) REVERT: B 392 THR cc_start: 0.3185 (OUTLIER) cc_final: 0.2379 (m) REVERT: B 394 MET cc_start: 0.8160 (mmm) cc_final: 0.7788 (mmm) outliers start: 15 outliers final: 11 residues processed: 71 average time/residue: 0.4695 time to fit residues: 39.4687 Evaluate side-chains 72 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 129 MET Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 323 MET 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: 4.9990 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.5129 r_free = 0.5129 target = 0.230383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.199314 restraints weight = 15494.958| |-----------------------------------------------------------------------------| r_work (start): 0.4815 rms_B_bonded: 4.70 r_work: 0.4657 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.4657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5890 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3729 Z= 0.111 Angle : 0.553 4.044 5045 Z= 0.296 Chirality : 0.045 0.352 585 Planarity : 0.003 0.030 649 Dihedral : 4.592 29.175 489 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.96 % Allowed : 26.67 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.40), residues: 448 helix: 0.13 (0.38), residues: 178 sheet: -2.83 (0.48), residues: 85 loop : -0.98 (0.50), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 68 HIS 0.003 0.001 HIS B 63 PHE 0.012 0.001 PHE B 345 TYR 0.004 0.001 TYR B 235 ARG 0.005 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 161) hydrogen bonds : angle 6.49939 ( 468) covalent geometry : bond 0.00246 ( 3729) covalent geometry : angle 0.55317 ( 5045) *********************** 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 75 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.549 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: 0.7725 (OUTLIER) cc_final: 0.7499 (mm-30) REVERT: B 238 GLN cc_start: 0.8699 (mp10) cc_final: 0.8490 (mp10) REVERT: B 320 ILE cc_start: 0.5841 (OUTLIER) cc_final: 0.5251 (mt) REVERT: B 392 THR cc_start: 0.3077 (OUTLIER) cc_final: 0.2273 (m) REVERT: B 394 MET cc_start: 0.8123 (mmm) cc_final: 0.7797 (mmm) outliers start: 12 outliers final: 9 residues processed: 71 average time/residue: 0.4706 time to fit residues: 39.4149 Evaluate side-chains 74 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 287 SER Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 370 THR 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: 8.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.5112 r_free = 0.5112 target = 0.230524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.201315 restraints weight = 15429.631| |-----------------------------------------------------------------------------| r_work (start): 0.4798 rms_B_bonded: 4.34 r_work: 0.4637 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.4637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.1718 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= 0.138 Angle : 0.568 4.286 5045 Z= 0.305 Chirality : 0.045 0.353 585 Planarity : 0.004 0.031 649 Dihedral : 4.657 28.275 489 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 4.44 % Allowed : 26.42 % Favored : 69.14 % 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: -1.53 (0.40), residues: 448 helix: 0.07 (0.38), residues: 178 sheet: -2.81 (0.50), residues: 85 loop : -1.01 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 52 HIS 0.005 0.001 HIS B 63 PHE 0.009 0.001 PHE B 345 TYR 0.005 0.001 TYR B 104 ARG 0.006 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 161) hydrogen bonds : angle 6.55434 ( 468) covalent geometry : bond 0.00304 ( 3729) covalent geometry : angle 0.56834 ( 5045) *********************** 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 81 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.531 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 172 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7561 (mm-30) REVERT: B 238 GLN cc_start: 0.8687 (mp10) cc_final: 0.8452 (mp10) REVERT: B 320 ILE cc_start: 0.5779 (OUTLIER) cc_final: 0.5172 (mt) REVERT: B 394 MET cc_start: 0.8066 (mmm) cc_final: 0.7785 (mmm) outliers start: 18 outliers final: 14 residues processed: 75 average time/residue: 0.4558 time to fit residues: 40.1016 Evaluate side-chains 77 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 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 403 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 13 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.5118 r_free = 0.5118 target = 0.229269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.198948 restraints weight = 15423.013| |-----------------------------------------------------------------------------| r_work (start): 0.4811 rms_B_bonded: 4.46 r_work: 0.4657 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.4657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5939 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3729 Z= 0.118 Angle : 0.551 4.050 5045 Z= 0.295 Chirality : 0.045 0.353 585 Planarity : 0.003 0.033 649 Dihedral : 4.602 28.897 489 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.44 % Allowed : 25.93 % 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: -1.48 (0.40), residues: 448 helix: 0.16 (0.38), residues: 178 sheet: -2.91 (0.49), residues: 85 loop : -0.96 (0.50), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 52 HIS 0.016 0.002 HIS B 398 PHE 0.011 0.001 PHE B 345 TYR 0.004 0.001 TYR B 104 ARG 0.006 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 161) hydrogen bonds : angle 6.33480 ( 468) covalent geometry : bond 0.00257 ( 3729) covalent geometry : angle 0.55095 ( 5045) *********************** 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 80 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.602 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 238 GLN cc_start: 0.8682 (mp10) cc_final: 0.8426 (mp10) REVERT: B 320 ILE cc_start: 0.5708 (OUTLIER) cc_final: 0.5095 (mt) outliers start: 18 outliers final: 13 residues processed: 74 average time/residue: 0.4660 time to fit residues: 41.1227 Evaluate side-chains 75 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 129 MET 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 281 SER Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 370 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: 10.0000 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.5083 r_free = 0.5083 target = 0.225626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.194866 restraints weight = 15309.079| |-----------------------------------------------------------------------------| r_work (start): 0.4756 rms_B_bonded: 4.49 r_work: 0.4594 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.4594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6022 moved from start: 0.1955 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= 0.168 Angle : 0.595 4.948 5045 Z= 0.321 Chirality : 0.046 0.354 585 Planarity : 0.004 0.036 649 Dihedral : 4.817 29.274 489 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 4.20 % Allowed : 26.42 % Favored : 69.38 % 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: -1.72 (0.40), residues: 448 helix: 0.01 (0.37), residues: 178 sheet: -3.04 (0.48), residues: 88 loop : -1.10 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 52 HIS 0.010 0.001 HIS B 398 PHE 0.011 0.001 PHE B 179 TYR 0.008 0.001 TYR B 104 ARG 0.007 0.001 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 161) hydrogen bonds : angle 6.58589 ( 468) covalent geometry : bond 0.00369 ( 3729) covalent geometry : angle 0.59488 ( 5045) *********************** 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 77 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.540 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 238 GLN cc_start: 0.8685 (mp10) cc_final: 0.8420 (mp10) REVERT: B 320 ILE cc_start: 0.5629 (OUTLIER) cc_final: 0.4988 (mt) outliers start: 17 outliers final: 14 residues processed: 71 average time/residue: 0.5702 time to fit residues: 48.6830 Evaluate side-chains 74 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 129 MET 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 281 SER Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 387 PHE 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: 0.0670 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- 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 = 0.5119 r_free = 0.5119 target = 0.231377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.202406 restraints weight = 15536.286| |-----------------------------------------------------------------------------| r_work (start): 0.4812 rms_B_bonded: 4.35 r_work: 0.4654 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.4654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3729 Z= 0.111 Angle : 0.552 4.034 5045 Z= 0.295 Chirality : 0.045 0.353 585 Planarity : 0.003 0.035 649 Dihedral : 4.647 29.551 489 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.46 % Allowed : 27.65 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.40), residues: 448 helix: 0.17 (0.38), residues: 178 sheet: -2.99 (0.47), residues: 85 loop : -1.03 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 61 HIS 0.009 0.001 HIS B 398 PHE 0.012 0.001 PHE B 345 TYR 0.003 0.001 TYR B 225 ARG 0.007 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 161) hydrogen bonds : angle 6.25402 ( 468) covalent geometry : bond 0.00245 ( 3729) covalent geometry : angle 0.55229 ( 5045) *********************** 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 76 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.606 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 238 GLN cc_start: 0.8676 (mp10) cc_final: 0.8408 (mp10) REVERT: B 320 ILE cc_start: 0.5609 (OUTLIER) cc_final: 0.4985 (mt) outliers start: 14 outliers final: 13 residues processed: 71 average time/residue: 0.4891 time to fit residues: 42.0384 Evaluate side-chains 74 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 129 MET 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 281 SER Chi-restraints excluded: chain B residue 320 ILE 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: 3.9990 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 0.0670 chunk 34 optimal weight: 6.9990 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 = 0.5148 r_free = 0.5148 target = 0.234523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.205730 restraints weight = 15639.244| |-----------------------------------------------------------------------------| r_work (start): 0.4845 rms_B_bonded: 4.34 r_work: 0.4694 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.4694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5864 moved from start: 0.2228 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= 0.101 Angle : 0.543 4.250 5045 Z= 0.288 Chirality : 0.045 0.351 585 Planarity : 0.003 0.043 649 Dihedral : 4.451 26.517 489 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.96 % Allowed : 27.41 % 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: -1.29 (0.40), residues: 448 helix: 0.40 (0.38), residues: 179 sheet: -2.83 (0.47), residues: 85 loop : -0.96 (0.50), residues: 184 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 0.007 0.001 PHE B 345 TYR 0.003 0.001 TYR B 235 ARG 0.007 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03326 ( 161) hydrogen bonds : angle 5.97523 ( 468) covalent geometry : bond 0.00227 ( 3729) covalent geometry : angle 0.54347 ( 5045) *********************** 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 : 0.579 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: 0.8076 (OUTLIER) cc_final: 0.7852 (tt) REVERT: B 238 GLN cc_start: 0.8650 (mp10) cc_final: 0.8377 (mp10) outliers start: 12 outliers final: 10 residues processed: 70 average time/residue: 0.4705 time to fit residues: 39.0279 Evaluate side-chains 72 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 225 TYR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 399 LEU 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: 0.5980 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.5138 r_free = 0.5138 target = 0.233029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.204309 restraints weight = 15561.493| |-----------------------------------------------------------------------------| r_work (start): 0.4834 rms_B_bonded: 4.35 r_work: 0.4680 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.4680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3729 Z= 0.111 Angle : 0.564 9.601 5045 Z= 0.294 Chirality : 0.045 0.352 585 Planarity : 0.003 0.042 649 Dihedral : 4.439 26.037 489 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % 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: -1.26 (0.40), residues: 448 helix: 0.47 (0.38), residues: 178 sheet: -2.82 (0.47), residues: 85 loop : -0.98 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 68 HIS 0.003 0.001 HIS B 63 PHE 0.013 0.001 PHE A 145 TYR 0.003 0.001 TYR B 333 ARG 0.008 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 161) hydrogen bonds : angle 6.00652 ( 468) covalent geometry : bond 0.00249 ( 3729) covalent geometry : angle 0.56448 ( 5045) ********************** 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 71 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.563 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: B 51 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7873 (tt) REVERT: B 238 GLN cc_start: 0.8660 (mp10) cc_final: 0.8385 (mp10) outliers start: 11 outliers final: 10 residues processed: 66 average time/residue: 0.4598 time to fit residues: 35.6287 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 : 0.563 ------------------------------------------------------------------------------- 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 102 VAL Chi-restraints excluded: chain B residue 129 MET 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 281 SER 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: 5.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 = 0.5161 r_free = 0.5161 target = 0.232976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.202046 restraints weight = 15483.077| |-----------------------------------------------------------------------------| r_work (start): 0.4885 rms_B_bonded: 4.71 r_work: 0.4760 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.4760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5898 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3729 Z= 0.109 Angle : 0.554 6.837 5045 Z= 0.291 Chirality : 0.045 0.353 585 Planarity : 0.003 0.046 649 Dihedral : 4.406 26.710 489 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % 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: -1.23 (0.40), residues: 448 helix: 0.48 (0.38), residues: 179 sheet: -2.85 (0.47), residues: 85 loop : -0.92 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 68 HIS 0.003 0.001 HIS B 63 PHE 0.009 0.001 PHE A 145 TYR 0.003 0.001 TYR B 225 ARG 0.007 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 161) hydrogen bonds : angle 5.95129 ( 468) covalent geometry : bond 0.00246 ( 3729) covalent geometry : angle 0.55445 ( 5045) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4809.37 seconds wall clock time: 83 minutes 53.78 seconds (5033.78 seconds total)