Starting phenix.real_space_refine on Thu Jun 5 13:24:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qg0_18386/06_2025/8qg0_18386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qg0_18386/06_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_18386/06_2025/8qg0_18386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qg0_18386/06_2025/8qg0_18386.map" model { file = "/net/cci-nas-00/data/ceres_data/8qg0_18386/06_2025/8qg0_18386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qg0_18386/06_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-5710/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: 4.61, per 1000 atoms: 0.76 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: 1.92 Conformation dependent library (CDL) restraints added in 879.6 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: 2.03 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: 1.89 Time building geometry restraints manager: 2.00 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: 0.530 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: 0.040 Set scattering table: 0.060 Process input model: 20.930 Find NCS groups from input model: 0.050 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.490 ------------------------------------------------------------------------------- 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= 0.231 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 Details of bonding type rmsd hydrogen bonds : bond 0.22439 ( 195) hydrogen bonds : angle 8.76424 ( 548) covalent geometry : bond 0.00433 ( 6295) covalent geometry : angle 0.72768 ( 8684) *********************** 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 : 0.590 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: 0.1811 time to fit residues: 28.1294 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 : 0.600 ------------------------------------------------------------------------------- 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 = 55)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.190363 restraints weight = 7621.075| |-----------------------------------------------------------------------------| r_work (start): 0.4555 rms_B_bonded: 2.14 r_work: 0.4370 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4370 ------------------------------------------------------------------------------- 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= 0.202 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 Details of bonding type rmsd hydrogen bonds : bond 0.05206 ( 195) hydrogen bonds : angle 5.87997 ( 548) covalent geometry : bond 0.00472 ( 6295) covalent geometry : angle 0.68584 ( 8684) *********************** 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 : 0.782 Fit side-chains REVERT: A 307 ARG cc_start: 0.7099 (tpp-160) cc_final: 0.6894 (tpp-160) REVERT: A 355 TRP cc_start: 0.7156 (m-10) cc_final: 0.6563 (m-90) REVERT: B 110 ARG cc_start: 0.5992 (mmm160) cc_final: 0.5363 (mmm160) outliers start: 16 outliers final: 12 residues processed: 108 average time/residue: 0.1838 time to fit residues: 27.6558 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 : 0.609 ------------------------------------------------------------------------------- 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: 0.0980 chunk 50 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4742 r_free = 0.4742 target = 0.212057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.192216 restraints weight = 7654.742| |-----------------------------------------------------------------------------| r_work (start): 0.4574 rms_B_bonded: 2.14 r_work: 0.4388 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6295 Z= 0.174 Angle : 0.642 9.370 8684 Z= 0.336 Chirality : 0.047 0.200 972 Planarity : 0.005 0.059 974 Dihedral : 18.207 94.516 1155 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % 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: -1.88 (0.33), residues: 652 helix: 0.29 (0.37), residues: 196 sheet: -2.17 (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 0.003 0.001 HIS A 252 PHE 0.012 0.001 PHE B 205 TYR 0.014 0.001 TYR B 164 ARG 0.004 0.001 ARG A 383 Details of bonding type rmsd hydrogen bonds : bond 0.04760 ( 195) hydrogen bonds : angle 5.49732 ( 548) covalent geometry : bond 0.00403 ( 6295) covalent geometry : angle 0.64221 ( 8684) *********************** 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 116 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.634 Fit side-chains REVERT: A 139 MET cc_start: 0.6322 (ptt) cc_final: 0.6109 (ptt) REVERT: A 307 ARG cc_start: 0.7118 (tpp-160) cc_final: 0.6839 (tpp-160) REVERT: A 355 TRP cc_start: 0.7178 (m-10) cc_final: 0.6841 (m-10) REVERT: B 151 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7216 (mt) REVERT: B 187 HIS cc_start: 0.7414 (OUTLIER) cc_final: 0.6216 (t70) outliers start: 20 outliers final: 15 residues processed: 106 average time/residue: 0.1730 time to fit residues: 25.1219 Evaluate side-chains 109 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 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 151 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: 0.6980 chunk 41 optimal weight: 0.0040 chunk 54 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 38 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 = 0.4744 r_free = 0.4744 target = 0.213471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.192880 restraints weight = 7908.546| |-----------------------------------------------------------------------------| r_work (start): 0.4560 rms_B_bonded: 2.24 r_work: 0.4392 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6295 Z= 0.131 Angle : 0.593 7.772 8684 Z= 0.313 Chirality : 0.045 0.185 972 Planarity : 0.005 0.078 974 Dihedral : 18.163 93.980 1155 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.82 % Allowed : 15.92 % Favored : 81.26 % 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: -1.66 (0.33), residues: 652 helix: 0.32 (0.37), residues: 200 sheet: -1.90 (0.48), residues: 129 loop : -1.65 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 76 HIS 0.007 0.001 HIS B 187 PHE 0.008 0.001 PHE B 205 TYR 0.014 0.001 TYR A 323 ARG 0.005 0.000 ARG B 110 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 195) hydrogen bonds : angle 5.12664 ( 548) covalent geometry : bond 0.00295 ( 6295) covalent geometry : angle 0.59256 ( 8684) *********************** 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 122 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 355 TRP cc_start: 0.7116 (m-10) cc_final: 0.6722 (m-10) REVERT: A 364 VAL cc_start: 0.8465 (t) cc_final: 0.8256 (t) REVERT: B 170 LYS cc_start: 0.6709 (OUTLIER) cc_final: 0.6224 (pttt) outliers start: 17 outliers final: 13 residues processed: 114 average time/residue: 0.2014 time to fit residues: 30.5731 Evaluate side-chains 112 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 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 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 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: 5.9990 chunk 31 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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** A 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.217469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.196928 restraints weight = 8136.262| |-----------------------------------------------------------------------------| r_work (start): 0.4510 rms_B_bonded: 2.35 r_work: 0.4328 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6295 Z= 0.224 Angle : 0.694 10.203 8684 Z= 0.357 Chirality : 0.047 0.189 972 Planarity : 0.005 0.069 974 Dihedral : 18.411 98.384 1155 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.48 % Allowed : 16.25 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.33), residues: 652 helix: 0.17 (0.37), residues: 200 sheet: -1.90 (0.50), residues: 127 loop : -1.78 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 76 HIS 0.005 0.001 HIS A 252 PHE 0.012 0.002 PHE A 202 TYR 0.016 0.002 TYR B 197 ARG 0.005 0.001 ARG B 110 Details of bonding type rmsd hydrogen bonds : bond 0.04789 ( 195) hydrogen bonds : angle 5.30112 ( 548) covalent geometry : bond 0.00528 ( 6295) covalent geometry : angle 0.69385 ( 8684) *********************** 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 121 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 1.174 Fit side-chains REVERT: B 145 ILE cc_start: 0.7198 (OUTLIER) cc_final: 0.6771 (tt) REVERT: B 170 LYS cc_start: 0.6742 (OUTLIER) cc_final: 0.6307 (pttt) REVERT: B 187 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.6339 (t-170) outliers start: 27 outliers final: 21 residues processed: 108 average time/residue: 0.2301 time to fit residues: 33.2973 Evaluate side-chains 113 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 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 234 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 A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL 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 145 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: 4.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4777 r_free = 0.4777 target = 0.220183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.199512 restraints weight = 7999.358| |-----------------------------------------------------------------------------| r_work (start): 0.4592 rms_B_bonded: 2.33 r_work: 0.4415 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6295 Z= 0.154 Angle : 0.632 9.658 8684 Z= 0.326 Chirality : 0.045 0.172 972 Planarity : 0.005 0.063 974 Dihedral : 18.376 98.277 1154 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.15 % Allowed : 18.91 % 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: -1.65 (0.33), residues: 652 helix: 0.35 (0.37), residues: 198 sheet: -1.82 (0.50), residues: 129 loop : -1.68 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 76 HIS 0.003 0.001 HIS A 252 PHE 0.009 0.001 PHE B 205 TYR 0.010 0.001 TYR B 64 ARG 0.005 0.001 ARG B 110 Details of bonding type rmsd hydrogen bonds : bond 0.04344 ( 195) hydrogen bonds : angle 5.04849 ( 548) covalent geometry : bond 0.00359 ( 6295) covalent geometry : angle 0.63171 ( 8684) *********************** 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 113 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.691 Fit side-chains REVERT: B 145 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6672 (tt) REVERT: B 170 LYS cc_start: 0.6689 (OUTLIER) cc_final: 0.6186 (pttt) REVERT: B 187 HIS cc_start: 0.7507 (OUTLIER) cc_final: 0.6820 (m-70) outliers start: 25 outliers final: 16 residues processed: 102 average time/residue: 0.2454 time to fit residues: 34.5838 Evaluate side-chains 107 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 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 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 145 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: 0.7980 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 13 optimal weight: 0.0370 chunk 1 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 62 optimal weight: 0.0870 overall best weight: 0.3636 ------------------------------------------------------------------------------- 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 = 0.4793 r_free = 0.4793 target = 0.219202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.199026 restraints weight = 7722.927| |-----------------------------------------------------------------------------| r_work (start): 0.4649 rms_B_bonded: 2.25 r_work: 0.4490 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6295 Z= 0.121 Angle : 0.589 9.645 8684 Z= 0.306 Chirality : 0.044 0.160 972 Planarity : 0.005 0.061 974 Dihedral : 18.405 96.449 1154 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.99 % Allowed : 19.57 % Favored : 77.45 % 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: -1.36 (0.34), residues: 652 helix: 0.61 (0.38), residues: 197 sheet: -1.74 (0.49), residues: 129 loop : -1.47 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 76 HIS 0.002 0.001 HIS A 365 PHE 0.009 0.001 PHE A 138 TYR 0.014 0.001 TYR A 152 ARG 0.006 0.001 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 195) hydrogen bonds : angle 4.73798 ( 548) covalent geometry : bond 0.00269 ( 6295) covalent geometry : angle 0.58899 ( 8684) *********************** 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 114 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.848 Fit side-chains REVERT: A 307 ARG cc_start: 0.7061 (tpp-160) cc_final: 0.6778 (tpp-160) REVERT: A 355 TRP cc_start: 0.7084 (m-10) cc_final: 0.6705 (m-10) REVERT: B 145 ILE cc_start: 0.6895 (OUTLIER) cc_final: 0.6529 (tt) REVERT: B 170 LYS cc_start: 0.6677 (OUTLIER) cc_final: 0.6218 (pttt) outliers start: 18 outliers final: 13 residues processed: 105 average time/residue: 0.1922 time to fit residues: 27.9942 Evaluate side-chains 104 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 158 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU 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 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 145 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: 3.9990 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.215175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.194307 restraints weight = 8076.945| |-----------------------------------------------------------------------------| r_work (start): 0.4538 rms_B_bonded: 2.33 r_work: 0.4359 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6295 Z= 0.192 Angle : 0.674 12.085 8684 Z= 0.347 Chirality : 0.046 0.173 972 Planarity : 0.005 0.062 974 Dihedral : 18.546 99.788 1154 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.65 % Allowed : 20.40 % Favored : 75.95 % 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: -1.52 (0.33), residues: 652 helix: 0.49 (0.37), residues: 195 sheet: -1.71 (0.50), residues: 129 loop : -1.62 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 76 HIS 0.005 0.001 HIS A 252 PHE 0.011 0.002 PHE A 202 TYR 0.013 0.002 TYR B 31 ARG 0.010 0.001 ARG B 110 Details of bonding type rmsd hydrogen bonds : bond 0.04515 ( 195) hydrogen bonds : angle 5.05184 ( 548) covalent geometry : bond 0.00452 ( 6295) covalent geometry : angle 0.67364 ( 8684) *********************** 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 116 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 1.423 Fit side-chains REVERT: A 355 TRP cc_start: 0.7165 (m-10) cc_final: 0.6677 (m-10) REVERT: A 377 MET cc_start: 0.6697 (tpp) cc_final: 0.6343 (tpp) REVERT: B 110 ARG cc_start: 0.6003 (mmm160) cc_final: 0.5734 (mmm160) REVERT: B 145 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6733 (tt) REVERT: B 170 LYS cc_start: 0.6535 (OUTLIER) cc_final: 0.6067 (pttt) outliers start: 22 outliers final: 18 residues processed: 105 average time/residue: 0.2527 time to fit residues: 35.6503 Evaluate side-chains 110 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 158 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 391 VAL 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 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 145 ILE Chi-restraints excluded: chain B residue 170 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN 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 = 0.213921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.193417 restraints weight = 7783.361| |-----------------------------------------------------------------------------| r_work (start): 0.4581 rms_B_bonded: 2.25 r_work: 0.4407 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6295 Z= 0.148 Angle : 0.664 12.884 8684 Z= 0.332 Chirality : 0.046 0.228 972 Planarity : 0.005 0.059 974 Dihedral : 18.563 99.908 1154 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.15 % Allowed : 21.89 % Favored : 74.96 % 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: -1.46 (0.33), residues: 652 helix: 0.51 (0.37), residues: 200 sheet: -1.72 (0.50), residues: 129 loop : -1.57 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 76 HIS 0.003 0.001 HIS A 252 PHE 0.007 0.001 PHE A 202 TYR 0.011 0.001 TYR A 152 ARG 0.010 0.001 ARG B 110 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 195) hydrogen bonds : angle 4.88978 ( 548) covalent geometry : bond 0.00344 ( 6295) covalent geometry : angle 0.66448 ( 8684) *********************** 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 111 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.690 Fit side-chains REVERT: A 112 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7269 (mtp) REVERT: A 307 ARG cc_start: 0.7080 (tpp-160) cc_final: 0.6816 (tpp-160) REVERT: A 355 TRP cc_start: 0.7133 (m-10) cc_final: 0.6794 (m-10) REVERT: B 145 ILE cc_start: 0.7137 (OUTLIER) cc_final: 0.6712 (tt) REVERT: B 170 LYS cc_start: 0.6572 (OUTLIER) cc_final: 0.6051 (pttt) outliers start: 19 outliers final: 15 residues processed: 100 average time/residue: 0.1956 time to fit residues: 26.8661 Evaluate side-chains 108 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 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 145 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: 6.9990 chunk 22 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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** B 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.212281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.191699 restraints weight = 7832.887| |-----------------------------------------------------------------------------| r_work (start): 0.4556 rms_B_bonded: 2.25 r_work: 0.4383 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.2984 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= 0.161 Angle : 0.679 13.980 8684 Z= 0.340 Chirality : 0.046 0.203 972 Planarity : 0.005 0.059 974 Dihedral : 18.645 100.332 1154 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.15 % Allowed : 22.22 % Favored : 74.63 % 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: -1.51 (0.33), residues: 652 helix: 0.57 (0.37), residues: 197 sheet: -1.74 (0.50), residues: 129 loop : -1.67 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 76 HIS 0.004 0.001 HIS A 252 PHE 0.009 0.001 PHE A 202 TYR 0.013 0.001 TYR B 31 ARG 0.009 0.001 ARG B 110 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 195) hydrogen bonds : angle 4.91759 ( 548) covalent geometry : bond 0.00375 ( 6295) covalent geometry : angle 0.67877 ( 8684) ********************** 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 108 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.611 Fit side-chains REVERT: A 307 ARG cc_start: 0.7101 (tpp-160) cc_final: 0.6810 (tpp-160) REVERT: B 145 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6756 (tt) REVERT: B 170 LYS cc_start: 0.6533 (OUTLIER) cc_final: 0.6021 (pttt) outliers start: 19 outliers final: 15 residues processed: 98 average time/residue: 0.1493 time to fit residues: 20.2615 Evaluate side-chains 105 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 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 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 145 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: 2.9990 chunk 21 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 10 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** B 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.215461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.194882 restraints weight = 7901.478| |-----------------------------------------------------------------------------| r_work (start): 0.4598 rms_B_bonded: 2.27 r_work: 0.4433 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.3065 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= 0.144 Angle : 0.669 14.410 8684 Z= 0.337 Chirality : 0.045 0.200 972 Planarity : 0.005 0.058 974 Dihedral : 18.656 100.244 1154 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.15 % Allowed : 22.39 % Favored : 74.46 % 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: -1.46 (0.33), residues: 652 helix: 0.56 (0.37), residues: 200 sheet: -1.73 (0.49), residues: 129 loop : -1.61 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 355 HIS 0.007 0.001 HIS B 189 PHE 0.008 0.001 PHE A 202 TYR 0.012 0.001 TYR B 31 ARG 0.008 0.001 ARG B 110 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 195) hydrogen bonds : angle 4.82585 ( 548) covalent geometry : bond 0.00330 ( 6295) covalent geometry : angle 0.66929 ( 8684) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3500.27 seconds wall clock time: 64 minutes 9.47 seconds (3849.47 seconds total)