Starting phenix.real_space_refine on Tue Feb 11 16:39:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qg0_18386/02_2025/8qg0_18386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qg0_18386/02_2025/8qg0_18386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qg0_18386/02_2025/8qg0_18386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qg0_18386/02_2025/8qg0_18386.map" model { file = "/net/cci-nas-00/data/ceres_data/8qg0_18386/02_2025/8qg0_18386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qg0_18386/02_2025/8qg0_18386.cif" } resolution = 3.43 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= 1.000 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 P 33 5.49 5 S 13 5.16 5 C 3811 2.51 5 N 1012 2.21 5 O 1211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6080 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3478 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 403} Chain: "B" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1894 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "P" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "Q" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 363 Classifications: {'RNA': 17} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna2p': 1, 'rna3p': 15} Time building chain proxies: 4.23, per 1000 atoms: 0.70 Number of scatterers: 6080 At special positions: 0 Unit cell: (67.1, 91.3, 104.5, 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 13 16.00 P 33 15.00 O 1211 8.00 N 1012 7.00 C 3811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 872.2 milliseconds 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1236 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 11 sheets defined 33.5% alpha, 13.7% beta 6 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 58 through 73 Processing helix chain 'A' and resid 92 through 107 removed outlier: 3.583A pdb=" N ASN A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 removed outlier: 3.972A pdb=" N TYR A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 147 removed outlier: 3.808A pdb=" N ASN A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 removed outlier: 3.948A pdb=" N ASN A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 241 removed outlier: 3.534A pdb=" N VAL A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 359 through 376 removed outlier: 3.516A pdb=" N HIS A 365 " --> pdb=" O TYR A 361 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 407 Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 417 through 421 removed outlier: 3.660A pdb=" N GLN A 421 " --> pdb=" O ARG A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 93 removed outlier: 4.078A pdb=" N GLY B 81 " --> pdb=" O ASN B 77 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LYS B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 175 through 187 removed outlier: 3.829A pdb=" N VAL B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 216 removed outlier: 3.531A pdb=" N PHE B 205 " --> pdb=" O MET B 201 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 87 Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 184 removed outlier: 6.841A pdb=" N ILE A 183 " --> pdb=" O HIS A 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 189 removed outlier: 3.557A pdb=" N CYS A 197 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 195 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 199 through 201 removed outlier: 3.874A pdb=" N GLU A 212 " --> pdb=" O MET A 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 291 through 293 Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 26 removed outlier: 6.608A pdb=" N ARG B 110 " --> pdb=" O LYS B 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB1, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.705A pdb=" N ASN B 30 " --> pdb=" O LYS B 233 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE B 234 " --> pdb=" O LYS B 223 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS B 223 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 41 removed outlier: 3.716A pdb=" N SER B 38 " --> pdb=" O LEU B 61 " (cutoff:3.500A) 188 hydrogen bonds defined for protein. 522 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1447 1.33 - 1.45: 1410 1.45 - 1.57: 3348 1.57 - 1.69: 65 1.69 - 1.80: 25 Bond restraints: 6295 Sorted by residual: bond pdb=" N LEU A 249 " pdb=" CA LEU A 249 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.52e-02 4.33e+03 9.71e+00 bond pdb=" N ARG A 383 " pdb=" CA ARG A 383 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.21e-02 6.83e+03 9.59e+00 bond pdb=" N SER B 163 " pdb=" CA SER B 163 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.43e+00 bond pdb=" N ILE B 167 " pdb=" CA ILE B 167 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.19e-02 7.06e+03 8.26e+00 bond pdb=" N SER A 384 " pdb=" CA SER A 384 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.31e-02 5.83e+03 7.84e+00 ... (remaining 6290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 8424 1.91 - 3.82: 223 3.82 - 5.72: 30 5.72 - 7.63: 5 7.63 - 9.54: 2 Bond angle restraints: 8684 Sorted by residual: angle pdb=" C LYS B 168 " pdb=" CA LYS B 168 " pdb=" CB LYS B 168 " ideal model delta sigma weight residual 116.54 110.28 6.26 1.15e+00 7.56e-01 2.97e+01 angle pdb=" N LEU A 249 " pdb=" CA LEU A 249 " pdb=" CB LEU A 249 " ideal model delta sigma weight residual 111.65 104.47 7.18 1.40e+00 5.10e-01 2.63e+01 angle pdb=" N LEU A 249 " pdb=" CA LEU A 249 " pdb=" C LEU A 249 " ideal model delta sigma weight residual 110.61 105.67 4.94 1.25e+00 6.40e-01 1.56e+01 angle pdb=" CA ILE B 167 " pdb=" C ILE B 167 " pdb=" O ILE B 167 " ideal model delta sigma weight residual 121.05 116.93 4.12 1.11e+00 8.12e-01 1.38e+01 angle pdb=" N TYR B 171 " pdb=" CA TYR B 171 " pdb=" C TYR B 171 " ideal model delta sigma weight residual 113.38 109.05 4.33 1.17e+00 7.31e-01 1.37e+01 ... (remaining 8679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 3219 17.93 - 35.85: 360 35.85 - 53.78: 108 53.78 - 71.70: 38 71.70 - 89.63: 12 Dihedral angle restraints: 3737 sinusoidal: 1807 harmonic: 1930 Sorted by residual: dihedral pdb=" N LEU A 249 " pdb=" C LEU A 249 " pdb=" CA LEU A 249 " pdb=" CB LEU A 249 " ideal model delta harmonic sigma weight residual 122.80 111.66 11.14 0 2.50e+00 1.60e-01 1.99e+01 dihedral pdb=" CA VAL A 300 " pdb=" C VAL A 300 " pdb=" N MET A 301 " pdb=" CA MET A 301 " ideal model delta harmonic sigma weight residual 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA TYR B 22 " pdb=" C TYR B 22 " pdb=" N ILE B 23 " pdb=" CA ILE B 23 " ideal model delta harmonic sigma weight residual -180.00 -158.59 -21.41 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 3734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 930 0.103 - 0.205: 40 0.205 - 0.308: 1 0.308 - 0.411: 0 0.411 - 0.514: 1 Chirality restraints: 972 Sorted by residual: chirality pdb=" CA LEU A 249 " pdb=" N LEU A 249 " pdb=" C LEU A 249 " pdb=" CB LEU A 249 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.59e+00 chirality pdb=" CB ILE B 167 " pdb=" CA ILE B 167 " pdb=" CG1 ILE B 167 " pdb=" CG2 ILE B 167 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA TYR B 164 " pdb=" N TYR B 164 " pdb=" C TYR B 164 " pdb=" CB TYR B 164 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.16e-01 ... (remaining 969 not shown) Planarity restraints: 974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 40 " 0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO B 41 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 41 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 41 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 355 " 0.011 2.00e-02 2.50e+03 9.58e-03 2.29e+00 pdb=" CG TRP A 355 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 355 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 355 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 355 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 355 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 355 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 355 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 355 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 355 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 341 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO A 342 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 342 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 342 " 0.021 5.00e-02 4.00e+02 ... (remaining 971 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 543 2.74 - 3.28: 6374 3.28 - 3.82: 10696 3.82 - 4.36: 13200 4.36 - 4.90: 21656 Nonbonded interactions: 52469 Sorted by model distance: nonbonded pdb=" O6 DG P 11 " pdb=" N6 A Q 6 " model vdw 2.198 3.120 nonbonded pdb=" NE ARG A 257 " pdb=" O2' A Q 15 " model vdw 2.208 3.120 nonbonded pdb=" O2 DC P 8 " pdb=" N2 G Q 11 " model vdw 2.220 3.120 nonbonded pdb=" OG1 THR A 250 " pdb=" O ALA A 288 " model vdw 2.239 3.040 nonbonded pdb=" O ILE A 87 " pdb=" NE2 GLN A 99 " model vdw 2.246 3.120 ... (remaining 52464 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.470 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 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 : 0.004 0.052 6295 Z= 0.270 Angle : 0.728 9.538 8684 Z= 0.439 Chirality : 0.049 0.514 972 Planarity : 0.005 0.079 974 Dihedral : 17.660 89.630 2501 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.50 % Allowed : 0.50 % Favored : 99.00 % Cbeta Deviations : 0.32 % 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 (0.33), residues: 652 helix: 0.39 (0.39), residues: 179 sheet: -2.31 (0.46), residues: 132 loop : -1.62 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 355 HIS 0.004 0.001 HIS A 291 PHE 0.018 0.002 PHE A 382 TYR 0.014 0.002 TYR A 323 ARG 0.007 0.001 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.516 Fit side-chains REVERT: B 21 LEU cc_start: 0.7830 (mp) cc_final: 0.7626 (mp) outliers start: 3 outliers final: 1 residues processed: 116 average time/residue: 0.1755 time to fit residues: 26.9967 Evaluate side-chains 99 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN B 158 ASN B 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.210239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.190389 restraints weight = 7621.075| |-----------------------------------------------------------------------------| r_work (start): 0.4556 rms_B_bonded: 2.13 r_work: 0.4371 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6295 Z= 0.297 Angle : 0.686 9.347 8684 Z= 0.361 Chirality : 0.049 0.209 972 Planarity : 0.005 0.058 974 Dihedral : 18.166 93.461 1155 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.65 % Allowed : 10.95 % Favored : 86.40 % 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: -1.97 (0.33), residues: 652 helix: 0.31 (0.38), residues: 194 sheet: -2.25 (0.45), residues: 138 loop : -1.87 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 355 HIS 0.004 0.001 HIS A 365 PHE 0.011 0.002 PHE B 205 TYR 0.014 0.002 TYR A 287 ARG 0.005 0.001 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.927 Fit side-chains REVERT: A 307 ARG cc_start: 0.7096 (tpp-160) cc_final: 0.6893 (tpp-160) REVERT: A 355 TRP cc_start: 0.7155 (m-10) cc_final: 0.6562 (m-90) REVERT: B 110 ARG cc_start: 0.5990 (mmm160) cc_final: 0.5361 (mmm160) outliers start: 16 outliers final: 12 residues processed: 108 average time/residue: 0.1716 time to fit residues: 25.0932 Evaluate side-chains 106 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 165 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 28 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 37 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: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 GLN A 211 ASN A 354 ASN A 378 ASN A 417 ASN B 187 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.212274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.192419 restraints weight = 7655.118| |-----------------------------------------------------------------------------| r_work (start): 0.4576 rms_B_bonded: 2.15 r_work: 0.4390 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6295 Z= 0.258 Angle : 0.641 9.026 8684 Z= 0.336 Chirality : 0.047 0.198 972 Planarity : 0.005 0.054 974 Dihedral : 18.201 94.522 1155 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.32 % Allowed : 13.76 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.89 (0.33), residues: 652 helix: 0.28 (0.37), residues: 196 sheet: -2.18 (0.47), residues: 129 loop : -1.80 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 76 HIS 0.004 0.001 HIS A 252 PHE 0.012 0.001 PHE B 205 TYR 0.015 0.001 TYR B 164 ARG 0.003 0.001 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.608 Fit side-chains REVERT: A 307 ARG cc_start: 0.7117 (tpp-160) cc_final: 0.6852 (tpp-160) REVERT: A 355 TRP cc_start: 0.7171 (m-10) cc_final: 0.6777 (m-10) REVERT: B 187 HIS cc_start: 0.7418 (OUTLIER) cc_final: 0.6151 (t-170) outliers start: 20 outliers final: 16 residues processed: 104 average time/residue: 0.1613 time to fit residues: 22.8306 Evaluate side-chains 108 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 38 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.215253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.195089 restraints weight = 7757.647| |-----------------------------------------------------------------------------| r_work (start): 0.4613 rms_B_bonded: 2.19 r_work: 0.4427 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6295 Z= 0.206 Angle : 0.602 7.896 8684 Z= 0.318 Chirality : 0.045 0.187 972 Planarity : 0.005 0.080 974 Dihedral : 18.195 94.666 1155 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.15 % Allowed : 15.92 % Favored : 80.93 % 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 (0.33), residues: 652 helix: 0.27 (0.37), residues: 200 sheet: -2.00 (0.48), residues: 131 loop : -1.65 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 76 HIS 0.009 0.001 HIS B 187 PHE 0.009 0.001 PHE B 205 TYR 0.015 0.001 TYR A 323 ARG 0.005 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.599 Fit side-chains REVERT: A 355 TRP cc_start: 0.7142 (m-10) cc_final: 0.6775 (m-10) REVERT: A 364 VAL cc_start: 0.8486 (t) cc_final: 0.8273 (t) REVERT: B 170 LYS cc_start: 0.6717 (OUTLIER) cc_final: 0.6230 (pttt) outliers start: 19 outliers final: 16 residues processed: 109 average time/residue: 0.1772 time to fit residues: 26.0059 Evaluate side-chains 114 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 170 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 24 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.215005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.194587 restraints weight = 7817.348| |-----------------------------------------------------------------------------| r_work (start): 0.4592 rms_B_bonded: 2.22 r_work: 0.4414 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6295 Z= 0.197 Angle : 0.602 9.655 8684 Z= 0.313 Chirality : 0.044 0.172 972 Planarity : 0.005 0.065 974 Dihedral : 18.210 94.647 1155 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.48 % Allowed : 17.58 % Favored : 78.94 % 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 (0.33), residues: 652 helix: 0.45 (0.37), residues: 198 sheet: -1.77 (0.49), residues: 129 loop : -1.58 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 76 HIS 0.003 0.001 HIS A 252 PHE 0.008 0.001 PHE A 202 TYR 0.010 0.001 TYR B 64 ARG 0.005 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.518 Fit side-chains REVERT: A 147 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6773 (ptp-170) REVERT: A 355 TRP cc_start: 0.7113 (m-10) cc_final: 0.6830 (m-10) REVERT: B 151 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7337 (mt) REVERT: B 170 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.6326 (pttt) REVERT: B 187 HIS cc_start: 0.7324 (OUTLIER) cc_final: 0.6018 (t70) outliers start: 21 outliers final: 14 residues processed: 111 average time/residue: 0.1720 time to fit residues: 26.0644 Evaluate side-chains 114 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 187 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 51 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 62 optimal weight: 0.0570 chunk 12 optimal weight: 4.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 ASN ** 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 = 0.4740 r_free = 0.4740 target = 0.212780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.192350 restraints weight = 7755.943| |-----------------------------------------------------------------------------| r_work (start): 0.4551 rms_B_bonded: 2.21 r_work: 0.4378 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6295 Z= 0.226 Angle : 0.623 9.837 8684 Z= 0.320 Chirality : 0.045 0.205 972 Planarity : 0.005 0.061 974 Dihedral : 18.287 95.925 1154 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.65 % Allowed : 17.58 % Favored : 78.77 % 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 (0.33), residues: 652 helix: 0.47 (0.37), residues: 198 sheet: -1.72 (0.49), residues: 129 loop : -1.56 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 76 HIS 0.004 0.001 HIS A 252 PHE 0.010 0.001 PHE B 205 TYR 0.010 0.001 TYR B 197 ARG 0.004 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.605 Fit side-chains REVERT: B 170 LYS cc_start: 0.6725 (OUTLIER) cc_final: 0.6309 (pttt) REVERT: B 187 HIS cc_start: 0.7430 (OUTLIER) cc_final: 0.6178 (t70) outliers start: 22 outliers final: 18 residues processed: 107 average time/residue: 0.2116 time to fit residues: 30.2408 Evaluate side-chains 114 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 187 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 62 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.212648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.192273 restraints weight = 7789.480| |-----------------------------------------------------------------------------| r_work (start): 0.4553 rms_B_bonded: 2.21 r_work: 0.4379 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6295 Z= 0.225 Angle : 0.624 10.993 8684 Z= 0.321 Chirality : 0.045 0.172 972 Planarity : 0.005 0.061 974 Dihedral : 18.357 96.838 1154 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.65 % Allowed : 19.40 % Favored : 76.95 % 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: -1.40 (0.33), residues: 652 helix: 0.51 (0.37), residues: 198 sheet: -1.65 (0.50), residues: 129 loop : -1.51 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 76 HIS 0.003 0.001 HIS A 252 PHE 0.011 0.001 PHE A 426 TYR 0.013 0.001 TYR B 64 ARG 0.005 0.001 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.634 Fit side-chains REVERT: A 355 TRP cc_start: 0.7086 (m-10) cc_final: 0.6507 (m-10) REVERT: B 170 LYS cc_start: 0.6753 (OUTLIER) cc_final: 0.6365 (pttt) REVERT: B 187 HIS cc_start: 0.7384 (OUTLIER) cc_final: 0.6741 (m-70) outliers start: 22 outliers final: 18 residues processed: 106 average time/residue: 0.1654 time to fit residues: 23.5419 Evaluate side-chains 114 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 187 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 2 optimal weight: 0.1980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.211017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.190739 restraints weight = 7749.716| |-----------------------------------------------------------------------------| r_work (start): 0.4539 rms_B_bonded: 2.20 r_work: 0.4367 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6295 Z= 0.244 Angle : 0.643 12.316 8684 Z= 0.328 Chirality : 0.045 0.223 972 Planarity : 0.005 0.060 974 Dihedral : 18.428 97.827 1154 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.15 % Allowed : 19.07 % Favored : 76.78 % 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: -1.40 (0.33), residues: 652 helix: 0.56 (0.37), residues: 195 sheet: -1.63 (0.50), residues: 129 loop : -1.54 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 76 HIS 0.004 0.001 HIS A 252 PHE 0.008 0.001 PHE A 426 TYR 0.012 0.001 TYR B 64 ARG 0.006 0.001 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.663 Fit side-chains REVERT: A 355 TRP cc_start: 0.7098 (m-10) cc_final: 0.6474 (m-10) REVERT: B 170 LYS cc_start: 0.6700 (OUTLIER) cc_final: 0.6253 (pttt) REVERT: B 187 HIS cc_start: 0.7304 (OUTLIER) cc_final: 0.6194 (t70) outliers start: 25 outliers final: 20 residues processed: 109 average time/residue: 0.1710 time to fit residues: 25.0215 Evaluate side-chains 114 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 187 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 0.3980 chunk 62 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.4701 r_free = 0.4701 target = 0.209155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.188756 restraints weight = 7849.393| |-----------------------------------------------------------------------------| r_work (start): 0.4534 rms_B_bonded: 2.22 r_work: 0.4350 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6295 Z= 0.286 Angle : 0.703 14.742 8684 Z= 0.355 Chirality : 0.047 0.174 972 Planarity : 0.005 0.061 974 Dihedral : 18.539 99.616 1154 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.98 % Allowed : 19.40 % Favored : 76.62 % 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: -1.52 (0.33), residues: 652 helix: 0.42 (0.37), residues: 197 sheet: -1.67 (0.50), residues: 129 loop : -1.61 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 76 HIS 0.004 0.001 HIS B 187 PHE 0.009 0.001 PHE A 298 TYR 0.013 0.002 TYR B 197 ARG 0.006 0.001 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.665 Fit side-chains REVERT: A 48 GLN cc_start: 0.5476 (tp40) cc_final: 0.5191 (tp40) REVERT: A 355 TRP cc_start: 0.7026 (m-10) cc_final: 0.6512 (m-10) REVERT: B 170 LYS cc_start: 0.6567 (OUTLIER) cc_final: 0.6075 (pttt) outliers start: 24 outliers final: 20 residues processed: 105 average time/residue: 0.1849 time to fit residues: 25.8862 Evaluate side-chains 111 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 187 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 28 optimal weight: 0.0170 chunk 22 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.213783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.193641 restraints weight = 7790.739| |-----------------------------------------------------------------------------| r_work (start): 0.4588 rms_B_bonded: 2.20 r_work: 0.4413 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6295 Z= 0.209 Angle : 0.660 14.854 8684 Z= 0.334 Chirality : 0.045 0.158 972 Planarity : 0.005 0.060 974 Dihedral : 18.594 99.368 1154 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.32 % Allowed : 20.23 % Favored : 76.45 % 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: -1.41 (0.34), residues: 652 helix: 0.58 (0.37), residues: 197 sheet: -1.61 (0.50), residues: 129 loop : -1.58 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 76 HIS 0.003 0.001 HIS A 252 PHE 0.007 0.001 PHE A 426 TYR 0.012 0.001 TYR B 64 ARG 0.007 0.001 ARG B 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.631 Fit side-chains REVERT: A 355 TRP cc_start: 0.7094 (m-10) cc_final: 0.6597 (m-10) REVERT: B 170 LYS cc_start: 0.6541 (OUTLIER) cc_final: 0.6046 (pttt) REVERT: B 187 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.6273 (t70) outliers start: 20 outliers final: 17 residues processed: 106 average time/residue: 0.1890 time to fit residues: 27.0044 Evaluate side-chains 110 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 187 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 chunk 29 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.222062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.202397 restraints weight = 8149.480| |-----------------------------------------------------------------------------| r_work (start): 0.4624 rms_B_bonded: 2.23 r_work: 0.4448 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6295 Z= 0.188 Angle : 0.651 13.961 8684 Z= 0.330 Chirality : 0.045 0.214 972 Planarity : 0.005 0.058 974 Dihedral : 18.637 98.917 1154 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.82 % Allowed : 21.06 % Favored : 76.12 % 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: -1.35 (0.34), residues: 652 helix: 0.71 (0.38), residues: 196 sheet: -1.68 (0.49), residues: 129 loop : -1.56 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 76 HIS 0.003 0.001 HIS B 187 PHE 0.009 0.001 PHE A 202 TYR 0.013 0.001 TYR A 152 ARG 0.005 0.001 ARG B 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2713.70 seconds wall clock time: 49 minutes 19.02 seconds (2959.02 seconds total)