Starting phenix.real_space_refine on Wed Mar 12 15:17:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xht_33198/03_2025/7xht_33198.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xht_33198/03_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_33198/03_2025/7xht_33198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xht_33198/03_2025/7xht_33198.map" model { file = "/net/cci-nas-00/data/ceres_data/7xht_33198/03_2025/7xht_33198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xht_33198/03_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-5624/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: 5.46, per 1000 atoms: 0.70 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: 2.15 Conformation dependent library (CDL) restraints added in 398.4 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: 3.41 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: 3.06 Time building geometry restraints manager: 2.46 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.570 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:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.290 ------------------------------------------------------------------------------- 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 : 0.483 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: 1.4786 time to fit residues: 114.7347 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 : 0.575 ------------------------------------------------------------------------------- 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: 3.9990 chunk 17 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.0170 chunk 53 optimal weight: 2.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.178926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.128111 restraints weight = 5428.878| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 0.62 r_work: 0.3127 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0969 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= 0.166 Angle : 0.525 6.707 12445 Z= 0.289 Chirality : 0.032 0.205 1529 Planarity : 0.005 0.041 776 Dihedral : 22.173 170.593 3639 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.46 % Allowed : 9.06 % Favored : 89.47 % 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: 0.63 (0.42), residues: 391 helix: 1.52 (0.50), residues: 120 sheet: 0.62 (0.61), residues: 72 loop : -0.29 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 479 HIS 0.005 0.001 HIS A 105 PHE 0.006 0.001 PHE A 315 TYR 0.015 0.002 TYR A 6 ARG 0.005 0.001 ARG A 38 *********************** 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: 5 poor density : 45 time to evaluate : 0.528 Fit side-chains REVERT: A 77 GLU cc_start: 0.7673 (mt-10) cc_final: 0.6928 (tp30) REVERT: A 100 GLN cc_start: 0.8127 (tt0) cc_final: 0.7378 (tm-30) REVERT: A 119 LYS cc_start: 0.8285 (mttt) cc_final: 0.7862 (mtmt) REVERT: A 127 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: A 168 ASN cc_start: 0.8527 (m-40) cc_final: 0.7829 (t0) REVERT: A 301 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7629 (m110) REVERT: A 341 TYR cc_start: 0.7665 (p90) cc_final: 0.7236 (p90) REVERT: A 411 GLU cc_start: 0.7269 (tt0) cc_final: 0.6970 (mt-10) REVERT: A 466 GLN cc_start: 0.7805 (mt0) cc_final: 0.7259 (mm-40) REVERT: A 484 GLN cc_start: 0.8431 (tp-100) cc_final: 0.8109 (tp40) outliers start: 5 outliers final: 2 residues processed: 47 average time/residue: 1.4421 time to fit residues: 71.4537 Evaluate side-chains 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 MET 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 16 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.174749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.118807 restraints weight = 5535.054| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 0.73 r_work: 0.3080 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8449 Z= 0.255 Angle : 0.582 7.100 12445 Z= 0.316 Chirality : 0.035 0.167 1529 Planarity : 0.005 0.045 776 Dihedral : 22.160 169.670 3639 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.05 % Allowed : 10.23 % Favored : 87.72 % 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: 0.62 (0.42), residues: 391 helix: 1.60 (0.48), residues: 120 sheet: 0.47 (0.60), residues: 72 loop : -0.30 (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 374 PHE 0.006 0.001 PHE A 41 TYR 0.017 0.002 TYR A 6 ARG 0.005 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 49 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.529 Fit side-chains REVERT: A 77 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7012 (tp30) REVERT: A 119 LYS cc_start: 0.8349 (mttt) cc_final: 0.7932 (mtmt) REVERT: A 127 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: A 168 ASN cc_start: 0.8543 (m110) cc_final: 0.7823 (t0) REVERT: A 301 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7761 (m110) REVERT: A 341 TYR cc_start: 0.7716 (p90) cc_final: 0.7271 (p90) REVERT: A 466 GLN cc_start: 0.7811 (mt0) cc_final: 0.7410 (tp40) outliers start: 7 outliers final: 4 residues processed: 45 average time/residue: 1.4887 time to fit residues: 70.6656 Evaluate side-chains 46 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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: 3.9990 chunk 51 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3888 r_free = 0.3888 target = 0.175031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.119253 restraints weight = 5459.630| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 0.70 r_work: 0.3078 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8449 Z= 0.231 Angle : 0.562 7.096 12445 Z= 0.307 Chirality : 0.034 0.157 1529 Planarity : 0.005 0.045 776 Dihedral : 22.114 169.683 3639 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: 0.71 (0.42), residues: 391 helix: 1.82 (0.48), residues: 120 sheet: 0.34 (0.59), residues: 72 loop : -0.27 (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 0.007 0.001 PHE A 315 TYR 0.016 0.002 TYR A 6 ARG 0.003 0.001 ARG A 414 *********************** 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 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.522 Fit side-chains REVERT: A 77 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7217 (tt0) REVERT: A 119 LYS cc_start: 0.8349 (mttt) cc_final: 0.7929 (mtmt) REVERT: A 126 GLU cc_start: 0.7578 (mm-30) cc_final: 0.6911 (mp0) REVERT: A 127 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: A 168 ASN cc_start: 0.8528 (m110) cc_final: 0.7846 (t0) REVERT: A 301 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7783 (m110) REVERT: A 341 TYR cc_start: 0.7650 (p90) cc_final: 0.7255 (p90) REVERT: A 466 GLN cc_start: 0.7765 (mt0) cc_final: 0.7366 (tp40) REVERT: A 484 GLN cc_start: 0.8559 (tp-100) cc_final: 0.8252 (tp40) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 1.4364 time to fit residues: 65.1588 Evaluate side-chains 46 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 58 optimal weight: 4.9990 chunk 20 optimal weight: 0.0050 chunk 15 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.172717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.118496 restraints weight = 5446.023| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 0.70 r_work: 0.3051 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8449 Z= 0.318 Angle : 0.630 7.434 12445 Z= 0.340 Chirality : 0.037 0.154 1529 Planarity : 0.006 0.046 776 Dihedral : 22.220 170.779 3639 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.63 % Allowed : 10.82 % Favored : 86.55 % 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: 1.73 (0.48), residues: 120 sheet: 0.32 (0.60), residues: 72 loop : -0.28 (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 429 PHE 0.009 0.002 PHE A 315 TYR 0.018 0.002 TYR A 6 ARG 0.004 0.001 ARG A 414 *********************** 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 50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.542 Fit side-chains REVERT: A 77 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7281 (tt0) REVERT: A 96 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8253 (ttpt) REVERT: A 119 LYS cc_start: 0.8387 (mttt) cc_final: 0.7963 (mtmt) REVERT: A 126 GLU cc_start: 0.7621 (mm-30) cc_final: 0.6906 (mp0) REVERT: A 301 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7885 (m110) REVERT: A 341 TYR cc_start: 0.7744 (p90) cc_final: 0.7361 (p90) REVERT: A 466 GLN cc_start: 0.7755 (mt0) cc_final: 0.7376 (tp40) outliers start: 9 outliers final: 5 residues processed: 46 average time/residue: 1.4149 time to fit residues: 68.7415 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 : 0.412 ------------------------------------------------------------------------------- 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 189 LYS Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 360 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 52 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 50 optimal weight: 0.0980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.177834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.124362 restraints weight = 5476.205| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 0.80 r_work: 0.3119 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1335 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= 0.154 Angle : 0.513 6.736 12445 Z= 0.282 Chirality : 0.032 0.179 1529 Planarity : 0.004 0.046 776 Dihedral : 22.075 169.534 3639 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.63 % Allowed : 11.40 % 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: 0.89 (0.42), residues: 391 helix: 2.08 (0.48), residues: 120 sheet: 0.30 (0.60), residues: 71 loop : -0.18 (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 105 PHE 0.006 0.001 PHE A 315 TYR 0.014 0.001 TYR A 6 ARG 0.002 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 48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.458 Fit side-chains REVERT: A 77 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7130 (tt0) REVERT: A 119 LYS cc_start: 0.8284 (mttt) cc_final: 0.7821 (mtmt) REVERT: A 126 GLU cc_start: 0.7573 (mm-30) cc_final: 0.6830 (mp0) REVERT: A 301 ASN cc_start: 0.8006 (OUTLIER) cc_final: 0.7703 (m110) REVERT: A 341 TYR cc_start: 0.7606 (p90) cc_final: 0.7209 (p90) REVERT: A 466 GLN cc_start: 0.7707 (mt0) cc_final: 0.7268 (tp40) outliers start: 9 outliers final: 6 residues processed: 45 average time/residue: 1.3522 time to fit residues: 64.3569 Evaluate side-chains 46 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 360 SER 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: 4.9990 chunk 41 optimal weight: 0.6980 chunk 36 optimal weight: 0.2980 chunk 42 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 0.0170 chunk 33 optimal weight: 0.6980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.178704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.126614 restraints weight = 5529.505| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 0.64 r_work: 0.3149 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8449 Z= 0.129 Angle : 0.503 6.659 12445 Z= 0.278 Chirality : 0.031 0.169 1529 Planarity : 0.004 0.045 776 Dihedral : 22.059 169.002 3639 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.63 % Allowed : 11.70 % 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: 0.98 (0.42), residues: 391 helix: 2.24 (0.49), residues: 120 sheet: 0.24 (0.60), residues: 71 loop : -0.12 (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 105 PHE 0.005 0.001 PHE A 454 TYR 0.012 0.001 TYR A 6 ARG 0.002 0.000 ARG A 414 *********************** 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 48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.561 Fit side-chains REVERT: A 77 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7198 (tt0) REVERT: A 119 LYS cc_start: 0.8297 (mttt) cc_final: 0.7871 (mtmt) REVERT: A 126 GLU cc_start: 0.7590 (mm-30) cc_final: 0.6897 (mp0) REVERT: A 301 ASN cc_start: 0.8063 (OUTLIER) cc_final: 0.7769 (m110) REVERT: A 466 GLN cc_start: 0.7743 (mt0) cc_final: 0.7353 (tp40) outliers start: 9 outliers final: 6 residues processed: 45 average time/residue: 1.5331 time to fit residues: 72.9672 Evaluate side-chains 46 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 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 360 SER 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: 0.8980 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.173773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.117961 restraints weight = 5531.103| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 0.79 r_work: 0.3051 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8449 Z= 0.284 Angle : 0.598 7.135 12445 Z= 0.324 Chirality : 0.036 0.151 1529 Planarity : 0.005 0.045 776 Dihedral : 22.145 169.991 3639 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: 0.85 (0.42), residues: 391 helix: 1.98 (0.48), residues: 120 sheet: 0.31 (0.60), residues: 71 loop : -0.16 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 162 HIS 0.003 0.001 HIS A 429 PHE 0.007 0.002 PHE A 315 TYR 0.019 0.002 TYR A 341 ARG 0.003 0.001 ARG A 414 *********************** 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: 9 poor density : 40 time to evaluate : 0.487 Fit side-chains REVERT: A 77 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7211 (tt0) REVERT: A 119 LYS cc_start: 0.8359 (mttt) cc_final: 0.7916 (mtmt) REVERT: A 126 GLU cc_start: 0.7583 (mm-30) cc_final: 0.6870 (mp0) REVERT: A 301 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7814 (m110) REVERT: A 341 TYR cc_start: 0.7774 (p90) cc_final: 0.7538 (p90) REVERT: A 466 GLN cc_start: 0.7748 (mt0) cc_final: 0.7350 (tp40) outliers start: 9 outliers final: 6 residues processed: 45 average time/residue: 1.5118 time to fit residues: 71.8528 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 : 0.493 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 360 SER 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: 0.6980 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.174151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.118603 restraints weight = 5580.166| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 0.76 r_work: 0.3045 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 8449 Z= 0.227 Angle : 0.574 7.152 12445 Z= 0.314 Chirality : 0.034 0.155 1529 Planarity : 0.005 0.046 776 Dihedral : 22.134 169.537 3639 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: 0.85 (0.42), residues: 391 helix: 1.99 (0.48), residues: 120 sheet: 0.29 (0.60), residues: 71 loop : -0.16 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 162 HIS 0.003 0.001 HIS A 429 PHE 0.007 0.001 PHE A 315 TYR 0.017 0.002 TYR A 341 ARG 0.003 0.001 ARG A 152 *********************** 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: 8 poor density : 40 time to evaluate : 0.492 Fit side-chains REVERT: A 77 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7214 (tt0) REVERT: A 119 LYS cc_start: 0.8372 (mttt) cc_final: 0.7926 (mtmt) REVERT: A 126 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6846 (mp0) REVERT: A 301 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7824 (m110) REVERT: A 341 TYR cc_start: 0.7771 (p90) cc_final: 0.7536 (p90) REVERT: A 466 GLN cc_start: 0.7774 (mt0) cc_final: 0.7366 (tp40) outliers start: 8 outliers final: 7 residues processed: 44 average time/residue: 1.4486 time to fit residues: 67.2427 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 : 0.525 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 421 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.174342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.118948 restraints weight = 5529.578| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 0.68 r_work: 0.3068 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1351 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= 0.231 Angle : 0.574 7.153 12445 Z= 0.313 Chirality : 0.034 0.156 1529 Planarity : 0.005 0.046 776 Dihedral : 22.136 169.680 3639 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: 0.86 (0.42), residues: 391 helix: 2.00 (0.48), residues: 120 sheet: 0.29 (0.60), residues: 71 loop : -0.16 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 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 0.003 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 48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.540 Fit side-chains REVERT: A 77 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7203 (tt0) REVERT: A 119 LYS cc_start: 0.8359 (mttt) cc_final: 0.7924 (mtmt) REVERT: A 126 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6883 (mp0) REVERT: A 301 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7823 (m110) REVERT: A 341 TYR cc_start: 0.7774 (p90) cc_final: 0.7538 (p90) REVERT: A 466 GLN cc_start: 0.7751 (mt0) cc_final: 0.7364 (tp40) outliers start: 8 outliers final: 7 residues processed: 44 average time/residue: 1.4463 time to fit residues: 67.2488 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 : 0.472 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 421 ASP 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: 0.6980 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.174332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.118540 restraints weight = 5547.500| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 0.73 r_work: 0.3058 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 8449 Z= 0.230 Angle : 0.571 7.184 12445 Z= 0.312 Chirality : 0.034 0.156 1529 Planarity : 0.005 0.046 776 Dihedral : 22.134 169.666 3639 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: 0.85 (0.42), residues: 391 helix: 2.00 (0.48), residues: 120 sheet: 0.28 (0.60), residues: 71 loop : -0.16 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 162 HIS 0.003 0.001 HIS A 429 PHE 0.007 0.001 PHE A 315 TYR 0.017 0.002 TYR A 341 ARG 0.003 0.001 ARG A 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6400.13 seconds wall clock time: 111 minutes 6.05 seconds (6666.05 seconds total)