Starting phenix.real_space_refine on Wed Feb 12 14:48:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xht_33198/02_2025/7xht_33198.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xht_33198/02_2025/7xht_33198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xht_33198/02_2025/7xht_33198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xht_33198/02_2025/7xht_33198.map" model { file = "/net/cci-nas-00/data/ceres_data/7xht_33198/02_2025/7xht_33198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xht_33198/02_2025/7xht_33198.cif" } resolution = 2.55 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= -0.001 sd= 0.177 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: 6 Type Number sf(0) Gaussians P 220 5.49 5 Mg 2 5.21 5 S 19 5.16 5 C 4108 2.51 5 N 1449 2.21 5 O 2041 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7839 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 3822 Classifications: {'RNA': 179} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 12, 'rna3p_pur': 84, 'rna3p_pyr': 69} Link IDs: {'rna2p': 26, 'rna3p': 152} Chain breaks: 3 Chain: "C" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 595 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 249 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3155 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 376} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Unusual residues: {' MG': 1, 'LDA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.94, per 1000 atoms: 0.76 Number of scatterers: 7839 At special positions: 0 Unit cell: (85.49, 110.39, 130.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 19 16.00 P 220 15.00 Mg 2 11.99 O 2041 8.00 N 1449 7.00 C 4108 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: 2.35 Conformation dependent library (CDL) restraints added in 422.6 milliseconds 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 6 sheets defined 32.9% alpha, 21.0% beta 82 base pairs and 138 stacking pairs defined. Time for finding SS restraints: 3.72 Creating SS restraints... Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 89 through 109 removed outlier: 4.419A pdb=" N LYS A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 122 Processing helix chain 'A' and resid 164 through 185 removed outlier: 3.670A pdb=" N VAL A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 315 Proline residue: A 305 - end of helix Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 342 through 349 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 removed outlier: 6.254A pdb=" N TYR A 6 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU A 45 " --> pdb=" O TYR A 6 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE A 8 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR A 42 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 319 through 323 removed outlier: 3.532A pdb=" N PHE A 80 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR A 73 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER A 78 " --> pdb=" O THR A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 132 Processing sheet with id=AA4, first strand: chain 'A' and resid 379 through 381 removed outlier: 6.375A pdb=" N GLN A 433 " --> pdb=" O HIS A 380 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 393 through 396 removed outlier: 6.752A pdb=" N TYR A 388 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 477 through 479 removed outlier: 6.789A pdb=" N VAL A 467 " --> pdb=" O ARG A 462 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ARG A 462 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE A 445 " --> pdb=" O LEU A 486 " (cutoff:3.500A) 132 hydrogen bonds defined for protein. 375 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 208 hydrogen bonds 388 hydrogen bond angles 0 basepair planarities 82 basepair parallelities 138 stacking parallelities Total time for adding SS restraints: 3.31 Time building geometry restraints manager: 2.62 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: 1283 1.33 - 1.45: 3178 1.45 - 1.57: 3525 1.57 - 1.69: 434 1.69 - 1.81: 29 Bond restraints: 8449 Sorted by residual: bond pdb=" N1 LDA A 501 " pdb=" O1 LDA A 501 " ideal model delta sigma weight residual 1.354 1.249 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C1 LDA A 501 " pdb=" N1 LDA A 501 " ideal model delta sigma weight residual 1.503 1.454 0.049 2.00e-02 2.50e+03 6.03e+00 bond pdb=" O3' DC D 8 " pdb=" P DC D 9 " ideal model delta sigma weight residual 1.607 1.579 0.028 1.50e-02 4.44e+03 3.56e+00 bond pdb=" O3' A B 195 " pdb=" P A B 196 " ideal model delta sigma weight residual 1.607 1.579 0.028 1.50e-02 4.44e+03 3.42e+00 bond pdb=" O3' DG C 16 " pdb=" P DC C 17 " ideal model delta sigma weight residual 1.607 1.580 0.027 1.50e-02 4.44e+03 3.19e+00 ... (remaining 8444 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.36: 12431 5.36 - 10.72: 10 10.72 - 16.08: 2 16.08 - 21.44: 1 21.44 - 26.80: 1 Bond angle restraints: 12445 Sorted by residual: angle pdb=" O3' DT C 10 " pdb=" P DT C 11 " pdb=" OP1 DT C 11 " ideal model delta sigma weight residual 108.00 81.20 26.80 3.00e+00 1.11e-01 7.98e+01 angle pdb=" O3' DT C 10 " pdb=" P DT C 11 " pdb=" O5' DT C 11 " ideal model delta sigma weight residual 104.00 115.97 -11.97 1.50e+00 4.44e-01 6.36e+01 angle pdb=" O3' DT C 11 " pdb=" P DA C 12 " pdb=" OP1 DA C 12 " ideal model delta sigma weight residual 108.00 89.06 18.94 3.00e+00 1.11e-01 3.99e+01 angle pdb=" C3' DT C 11 " pdb=" O3' DT C 11 " pdb=" P DA C 12 " ideal model delta sigma weight residual 120.20 110.80 9.40 1.50e+00 4.44e-01 3.93e+01 angle pdb=" O3' DT C 11 " pdb=" P DA C 12 " pdb=" O5' DA C 12 " ideal model delta sigma weight residual 104.00 113.30 -9.30 1.50e+00 4.44e-01 3.84e+01 ... (remaining 12440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.65: 4621 33.65 - 67.30: 510 67.30 - 100.95: 53 100.95 - 134.60: 0 134.60 - 168.25: 2 Dihedral angle restraints: 5186 sinusoidal: 4037 harmonic: 1149 Sorted by residual: dihedral pdb=" O4' U B 92 " pdb=" C1' U B 92 " pdb=" N1 U B 92 " pdb=" C2 U B 92 " ideal model delta sinusoidal sigma weight residual 232.00 94.55 137.45 1 1.70e+01 3.46e-03 5.77e+01 dihedral pdb=" C4' G B 76 " pdb=" C3' G B 76 " pdb=" O3' G B 76 " pdb=" P A B 77 " ideal model delta sinusoidal sigma weight residual 220.00 51.75 168.25 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" CA ASN A 148 " pdb=" C ASN A 148 " pdb=" N LYS A 149 " pdb=" CA LYS A 149 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 5183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1390 0.056 - 0.112: 126 0.112 - 0.168: 12 0.168 - 0.224: 0 0.224 - 0.280: 1 Chirality restraints: 1529 Sorted by residual: chirality pdb=" CB ILE A 146 " pdb=" CA ILE A 146 " pdb=" CG1 ILE A 146 " pdb=" CG2 ILE A 146 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C1' A B 81 " pdb=" O4' A B 81 " pdb=" C2' A B 81 " pdb=" N9 A B 81 " both_signs ideal model delta sigma weight residual False 2.46 2.30 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" C3' G B 76 " pdb=" C4' G B 76 " pdb=" O3' G B 76 " pdb=" C2' G B 76 " both_signs ideal model delta sigma weight residual False -2.48 -2.34 -0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 1526 not shown) Planarity restraints: 776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 51 " 0.030 2.00e-02 2.50e+03 1.30e-02 4.66e+00 pdb=" N9 A B 51 " -0.027 2.00e-02 2.50e+03 pdb=" C8 A B 51 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A B 51 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A B 51 " -0.004 2.00e-02 2.50e+03 pdb=" C6 A B 51 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 51 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A B 51 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A B 51 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A B 51 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A B 51 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B -8 " -0.028 2.00e-02 2.50e+03 1.41e-02 4.45e+00 pdb=" N1 C B -8 " 0.029 2.00e-02 2.50e+03 pdb=" C2 C B -8 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C B -8 " 0.005 2.00e-02 2.50e+03 pdb=" N3 C B -8 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C B -8 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C B -8 " -0.007 2.00e-02 2.50e+03 pdb=" C5 C B -8 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C B -8 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 112 " -0.022 2.00e-02 2.50e+03 1.08e-02 3.19e+00 pdb=" N9 A B 112 " 0.027 2.00e-02 2.50e+03 pdb=" C8 A B 112 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A B 112 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A B 112 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 112 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B 112 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A B 112 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A B 112 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B 112 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A B 112 " 0.002 2.00e-02 2.50e+03 ... (remaining 773 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 66 2.59 - 3.17: 5661 3.17 - 3.75: 15108 3.75 - 4.32: 21418 4.32 - 4.90: 28200 Nonbonded interactions: 70453 Sorted by model distance: nonbonded pdb=" OD1 ASP A 61 " pdb="MG MG A 502 " model vdw 2.014 2.170 nonbonded pdb=" O2' A B 69 " pdb=" O4' A B 70 " model vdw 2.139 3.040 nonbonded pdb=" OP1 U B 190 " pdb=" OH TYR A 47 " model vdw 2.204 3.040 nonbonded pdb=" O2' C B 82 " pdb=" O ASN A 155 " model vdw 2.222 3.040 nonbonded pdb=" O2' G B 76 " pdb=" O5' A B 77 " model vdw 2.230 3.040 ... (remaining 70448 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.020 Find NCS groups from input model: 0.060 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:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 8449 Z= 0.200 Angle : 0.680 26.798 12445 Z= 0.350 Chirality : 0.033 0.280 1529 Planarity : 0.005 0.038 776 Dihedral : 21.149 168.253 4446 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.35 (0.42), residues: 391 helix: 1.08 (0.50), residues: 120 sheet: 0.76 (0.61), residues: 72 loop : -0.45 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 479 HIS 0.006 0.001 HIS A 105 PHE 0.009 0.001 PHE A 315 TYR 0.017 0.002 TYR A 6 ARG 0.004 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.518 Fit side-chains REVERT: A 77 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7117 (tp30) REVERT: A 100 GLN cc_start: 0.8038 (tt0) cc_final: 0.7788 (tt0) REVERT: A 119 LYS cc_start: 0.8401 (mttt) cc_final: 0.8182 (mtmt) REVERT: A 168 ASN cc_start: 0.8526 (m-40) cc_final: 0.8007 (t0) REVERT: A 341 TYR cc_start: 0.7728 (p90) cc_final: 0.7521 (p90) REVERT: A 466 GLN cc_start: 0.7799 (mt0) cc_final: 0.7595 (tp40) REVERT: A 481 ARG cc_start: 0.7737 (mtt90) cc_final: 0.7510 (mtt90) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 1.5548 time to fit residues: 120.5935 Evaluate side-chains 50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 0.0170 chunk 53 optimal weight: 2.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 169 HIS A 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.179851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.129021 restraints weight = 5450.048| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 0.61 r_work: 0.3149 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8449 Z= 0.148 Angle : 0.515 6.651 12445 Z= 0.284 Chirality : 0.032 0.199 1529 Planarity : 0.004 0.040 776 Dihedral : 22.181 170.793 3639 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.17 % Allowed : 9.06 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.65 (0.42), residues: 391 helix: 1.53 (0.50), residues: 120 sheet: 0.59 (0.60), residues: 72 loop : -0.27 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 479 HIS 0.005 0.001 HIS A 105 PHE 0.005 0.001 PHE A 371 TYR 0.013 0.002 TYR A 6 ARG 0.004 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.531 Fit side-chains REVERT: A 77 GLU cc_start: 0.7683 (mt-10) cc_final: 0.6918 (tp30) REVERT: A 100 GLN cc_start: 0.8106 (tt0) cc_final: 0.7333 (tm-30) REVERT: A 119 LYS cc_start: 0.8267 (mttt) cc_final: 0.7843 (mtmt) REVERT: A 168 ASN cc_start: 0.8519 (m-40) cc_final: 0.7834 (t0) REVERT: A 301 ASN cc_start: 0.7827 (OUTLIER) cc_final: 0.7608 (m-40) REVERT: A 341 TYR cc_start: 0.7620 (p90) cc_final: 0.7150 (p90) REVERT: A 411 GLU cc_start: 0.7194 (tt0) cc_final: 0.6918 (mt-10) REVERT: A 466 GLN cc_start: 0.7797 (mt0) cc_final: 0.7253 (mm-40) REVERT: A 484 GLN cc_start: 0.8418 (tp-100) cc_final: 0.8102 (tp40) outliers start: 4 outliers final: 2 residues processed: 47 average time/residue: 1.4460 time to fit residues: 71.7518 Evaluate side-chains 46 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 321 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 16 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.178189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125961 restraints weight = 5542.691| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 0.64 r_work: 0.3116 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8449 Z= 0.165 Angle : 0.509 6.607 12445 Z= 0.280 Chirality : 0.032 0.170 1529 Planarity : 0.004 0.043 776 Dihedral : 22.061 168.181 3639 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.05 % Allowed : 10.53 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.79 (0.42), residues: 391 helix: 1.81 (0.49), residues: 120 sheet: 0.52 (0.60), residues: 72 loop : -0.23 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 162 HIS 0.004 0.001 HIS A 105 PHE 0.005 0.001 PHE A 371 TYR 0.014 0.001 TYR A 6 ARG 0.006 0.001 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.564 Fit side-chains REVERT: A 77 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7050 (tp30) REVERT: A 100 GLN cc_start: 0.8173 (tt0) cc_final: 0.7884 (tt0) REVERT: A 119 LYS cc_start: 0.8339 (mttt) cc_final: 0.7918 (mtmt) REVERT: A 127 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: A 168 ASN cc_start: 0.8521 (m110) cc_final: 0.7880 (t0) REVERT: A 301 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7732 (m110) REVERT: A 341 TYR cc_start: 0.7696 (p90) cc_final: 0.7291 (p90) REVERT: A 466 GLN cc_start: 0.7851 (mt0) cc_final: 0.7325 (mm-40) outliers start: 7 outliers final: 4 residues processed: 47 average time/residue: 1.5736 time to fit residues: 77.7698 Evaluate side-chains 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 321 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 22 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.170323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.114191 restraints weight = 5480.856| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 0.95 r_work: 0.2991 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 8449 Z= 0.528 Angle : 0.785 7.986 12445 Z= 0.413 Chirality : 0.046 0.190 1529 Planarity : 0.007 0.050 776 Dihedral : 22.413 172.602 3639 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.05 % Allowed : 10.82 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.42 (0.41), residues: 391 helix: 1.31 (0.48), residues: 120 sheet: 0.42 (0.61), residues: 72 loop : -0.35 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 479 HIS 0.006 0.002 HIS A 429 PHE 0.010 0.002 PHE A 315 TYR 0.023 0.004 TYR A 6 ARG 0.006 0.001 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.506 Fit side-chains REVERT: A 77 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7324 (tt0) REVERT: A 96 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8209 (ttpt) REVERT: A 119 LYS cc_start: 0.8437 (mttt) cc_final: 0.7994 (mtmt) REVERT: A 341 TYR cc_start: 0.7852 (p90) cc_final: 0.7422 (p90) REVERT: A 466 GLN cc_start: 0.7775 (mt0) cc_final: 0.7314 (tp40) REVERT: A 484 GLN cc_start: 0.8589 (tp-100) cc_final: 0.8276 (tp40) outliers start: 7 outliers final: 4 residues processed: 47 average time/residue: 1.4735 time to fit residues: 73.0290 Evaluate side-chains 49 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 321 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.176576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.123933 restraints weight = 5440.952| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 0.75 r_work: 0.3098 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8449 Z= 0.175 Angle : 0.536 6.948 12445 Z= 0.294 Chirality : 0.033 0.180 1529 Planarity : 0.005 0.045 776 Dihedral : 22.140 170.911 3639 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.75 % Allowed : 11.99 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.77 (0.42), residues: 391 helix: 1.90 (0.48), residues: 120 sheet: 0.34 (0.60), residues: 72 loop : -0.23 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 479 HIS 0.003 0.001 HIS A 105 PHE 0.006 0.001 PHE A 315 TYR 0.015 0.002 TYR A 6 ARG 0.004 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.487 Fit side-chains REVERT: A 77 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7155 (tt0) REVERT: A 119 LYS cc_start: 0.8307 (mttt) cc_final: 0.7851 (mtmt) REVERT: A 126 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6811 (mp0) REVERT: A 301 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7731 (m110) REVERT: A 341 TYR cc_start: 0.7609 (p90) cc_final: 0.7212 (p90) REVERT: A 466 GLN cc_start: 0.7705 (mt0) cc_final: 0.7280 (tp40) outliers start: 6 outliers final: 3 residues processed: 44 average time/residue: 1.6007 time to fit residues: 74.0869 Evaluate side-chains 45 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 321 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 52 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 0.0030 chunk 50 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.0570 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.6912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.177207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.125538 restraints weight = 5498.826| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 0.71 r_work: 0.3093 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8449 Z= 0.156 Angle : 0.525 6.936 12445 Z= 0.289 Chirality : 0.032 0.168 1529 Planarity : 0.004 0.045 776 Dihedral : 22.133 170.232 3639 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.92 % Allowed : 11.11 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.92 (0.42), residues: 391 helix: 2.17 (0.48), residues: 120 sheet: 0.23 (0.60), residues: 72 loop : -0.16 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 162 HIS 0.003 0.001 HIS A 105 PHE 0.005 0.001 PHE A 41 TYR 0.014 0.001 TYR A 6 ARG 0.005 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.526 Fit side-chains REVERT: A 52 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6233 (mp0) REVERT: A 77 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7253 (tt0) REVERT: A 119 LYS cc_start: 0.8341 (mttt) cc_final: 0.7908 (mtmt) REVERT: A 126 GLU cc_start: 0.7504 (mm-30) cc_final: 0.6891 (mp0) REVERT: A 301 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7808 (m110) REVERT: A 341 TYR cc_start: 0.7664 (p90) cc_final: 0.7303 (p90) REVERT: A 466 GLN cc_start: 0.7776 (mt0) cc_final: 0.7381 (tp40) outliers start: 10 outliers final: 6 residues processed: 46 average time/residue: 1.5654 time to fit residues: 75.8007 Evaluate side-chains 48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 321 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 37 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 0.0670 chunk 33 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.178300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.126324 restraints weight = 5488.513| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 0.61 r_work: 0.3148 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8449 Z= 0.149 Angle : 0.505 6.500 12445 Z= 0.279 Chirality : 0.031 0.164 1529 Planarity : 0.004 0.044 776 Dihedral : 22.077 169.122 3639 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.63 % Allowed : 11.11 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.02 (0.42), residues: 391 helix: 2.23 (0.48), residues: 120 sheet: 0.37 (0.61), residues: 71 loop : -0.12 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 479 HIS 0.004 0.001 HIS A 23 PHE 0.005 0.001 PHE A 371 TYR 0.014 0.001 TYR A 6 ARG 0.003 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.804 Fit side-chains REVERT: A 77 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7196 (tt0) REVERT: A 119 LYS cc_start: 0.8303 (mttt) cc_final: 0.7880 (mtmt) REVERT: A 126 GLU cc_start: 0.7551 (mm-30) cc_final: 0.6883 (mp0) REVERT: A 301 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7767 (m110) REVERT: A 466 GLN cc_start: 0.7737 (mt0) cc_final: 0.7359 (tp40) outliers start: 9 outliers final: 5 residues processed: 49 average time/residue: 1.5357 time to fit residues: 79.1628 Evaluate side-chains 48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 321 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 15 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.170993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.115415 restraints weight = 5543.904| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 0.83 r_work: 0.3016 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 8449 Z= 0.420 Angle : 0.702 7.419 12445 Z= 0.373 Chirality : 0.041 0.170 1529 Planarity : 0.006 0.046 776 Dihedral : 22.287 171.860 3639 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.34 % Allowed : 11.40 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.68 (0.42), residues: 391 helix: 1.73 (0.48), residues: 120 sheet: 0.38 (0.61), residues: 71 loop : -0.25 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 479 HIS 0.005 0.001 HIS A 429 PHE 0.009 0.002 PHE A 319 TYR 0.020 0.003 TYR A 6 ARG 0.006 0.001 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.559 Fit side-chains REVERT: A 30 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7136 (mt-10) REVERT: A 52 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6312 (mp0) REVERT: A 77 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7243 (tt0) REVERT: A 119 LYS cc_start: 0.8411 (mttt) cc_final: 0.7962 (mtmt) REVERT: A 126 GLU cc_start: 0.7582 (mm-30) cc_final: 0.6893 (mp0) REVERT: A 301 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7864 (m110) REVERT: A 341 TYR cc_start: 0.7821 (p90) cc_final: 0.7550 (p90) REVERT: A 466 GLN cc_start: 0.7756 (mt0) cc_final: 0.7328 (tp40) outliers start: 8 outliers final: 5 residues processed: 45 average time/residue: 1.4886 time to fit residues: 70.6329 Evaluate side-chains 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 321 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.174826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.122486 restraints weight = 5581.162| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 0.65 r_work: 0.3103 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 8449 Z= 0.216 Angle : 0.557 7.074 12445 Z= 0.304 Chirality : 0.034 0.161 1529 Planarity : 0.005 0.045 776 Dihedral : 22.159 170.873 3639 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.05 % Allowed : 12.57 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.86 (0.42), residues: 391 helix: 1.97 (0.48), residues: 120 sheet: 0.37 (0.61), residues: 71 loop : -0.16 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 479 HIS 0.003 0.001 HIS A 429 PHE 0.007 0.001 PHE A 315 TYR 0.018 0.002 TYR A 341 ARG 0.003 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.589 Fit side-chains REVERT: A 77 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7221 (tt0) REVERT: A 119 LYS cc_start: 0.8353 (mttt) cc_final: 0.7927 (mtmt) REVERT: A 126 GLU cc_start: 0.7539 (mm-30) cc_final: 0.6963 (mp0) REVERT: A 301 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7797 (m110) REVERT: A 341 TYR cc_start: 0.7801 (p90) cc_final: 0.7571 (p90) REVERT: A 466 GLN cc_start: 0.7718 (mt0) cc_final: 0.7372 (tp40) outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 1.5609 time to fit residues: 73.9010 Evaluate side-chains 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 321 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 24 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 13 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 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.174370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.119031 restraints weight = 5535.871| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 0.68 r_work: 0.3074 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8449 Z= 0.235 Angle : 0.567 7.094 12445 Z= 0.309 Chirality : 0.034 0.156 1529 Planarity : 0.005 0.046 776 Dihedral : 22.164 170.555 3639 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.75 % Allowed : 12.87 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.85 (0.42), residues: 391 helix: 1.96 (0.48), residues: 120 sheet: 0.36 (0.61), residues: 71 loop : -0.16 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 162 HIS 0.003 0.001 HIS A 429 PHE 0.006 0.001 PHE A 315 TYR 0.017 0.002 TYR A 341 ARG 0.004 0.001 ARG A 414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.510 Fit side-chains REVERT: A 77 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7169 (tt0) REVERT: A 119 LYS cc_start: 0.8358 (mttt) cc_final: 0.7927 (mtmt) REVERT: A 126 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6949 (mp0) REVERT: A 301 ASN cc_start: 0.8147 (OUTLIER) cc_final: 0.7800 (m110) REVERT: A 341 TYR cc_start: 0.7782 (p90) cc_final: 0.7553 (p90) REVERT: A 466 GLN cc_start: 0.7735 (mt0) cc_final: 0.7377 (tp40) outliers start: 6 outliers final: 5 residues processed: 44 average time/residue: 1.5211 time to fit residues: 70.5093 Evaluate side-chains 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 321 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 42 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.174559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.119272 restraints weight = 5546.903| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 0.73 r_work: 0.3082 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8449 Z= 0.206 Angle : 0.561 7.060 12445 Z= 0.307 Chirality : 0.034 0.156 1529 Planarity : 0.005 0.046 776 Dihedral : 22.162 170.358 3639 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.34 % Allowed : 11.99 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.86 (0.42), residues: 391 helix: 1.97 (0.48), residues: 120 sheet: 0.36 (0.61), residues: 71 loop : -0.16 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 162 HIS 0.002 0.001 HIS A 429 PHE 0.006 0.001 PHE A 315 TYR 0.017 0.002 TYR A 341 ARG 0.003 0.001 ARG A 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6099.04 seconds wall clock time: 108 minutes 6.29 seconds (6486.29 seconds total)