Starting phenix.real_space_refine on Tue Sep 24 12:13:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xht_33198/09_2024/7xht_33198.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xht_33198/09_2024/7xht_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xht_33198/09_2024/7xht_33198.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xht_33198/09_2024/7xht_33198.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xht_33198/09_2024/7xht_33198.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xht_33198/09_2024/7xht_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-5461/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: 5.65, per 1000 atoms: 0.72 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: 2.28 Conformation dependent library (CDL) restraints added in 412.1 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: 3.84 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: 3.44 Time building geometry restraints manager: 2.55 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: 1.810 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.240 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.170 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.410 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: 1.4673 time to fit residues: 113.8016 Evaluate side-chains 50 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.472 Fit side-chains REVERT: A 77 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7155 (tp30) REVERT: A 100 GLN cc_start: 0.8088 (tt0) cc_final: 0.7553 (tm-30) REVERT: A 119 LYS cc_start: 0.8313 (mttt) cc_final: 0.8063 (mtmt) REVERT: A 168 ASN cc_start: 0.8596 (m-40) cc_final: 0.7998 (t0) REVERT: A 341 TYR cc_start: 0.7700 (p90) cc_final: 0.7368 (p90) REVERT: A 411 GLU cc_start: 0.7391 (tt0) cc_final: 0.7127 (mt-10) REVERT: A 466 GLN cc_start: 0.7799 (mt0) cc_final: 0.7498 (mm-40) REVERT: A 484 GLN cc_start: 0.8529 (tp-100) cc_final: 0.8279 (tp40) outliers start: 4 outliers final: 2 residues processed: 47 average time/residue: 1.4481 time to fit residues: 71.8489 Evaluate side-chains 45 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 MET 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 29 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 57 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 0.0070 overall best weight: 0.9802 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8449 Z= 0.184 Angle : 0.525 6.775 12445 Z= 0.288 Chirality : 0.032 0.169 1529 Planarity : 0.005 0.043 776 Dihedral : 22.072 168.000 3639 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.75 % Allowed : 10.53 % 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: 0.78 (0.42), residues: 391 helix: 1.81 (0.49), residues: 120 sheet: 0.51 (0.60), residues: 72 loop : -0.24 (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 0.002 TYR A 6 ARG 0.007 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 50 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.544 Fit side-chains REVERT: A 77 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7194 (tp30) REVERT: A 100 GLN cc_start: 0.8101 (tt0) cc_final: 0.7814 (tt0) REVERT: A 119 LYS cc_start: 0.8370 (mttt) cc_final: 0.8114 (mtmt) REVERT: A 127 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: A 168 ASN cc_start: 0.8526 (m110) cc_final: 0.7984 (t0) REVERT: A 341 TYR cc_start: 0.7781 (p90) cc_final: 0.7456 (p90) outliers start: 6 outliers final: 4 residues processed: 47 average time/residue: 1.4978 time to fit residues: 74.0635 Evaluate side-chains 44 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 321 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.003 0.022 8449 Z= 0.157 Angle : 0.511 6.780 12445 Z= 0.282 Chirality : 0.032 0.162 1529 Planarity : 0.004 0.044 776 Dihedral : 22.053 167.996 3639 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.44 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: 0.87 (0.42), residues: 391 helix: 2.01 (0.48), residues: 120 sheet: 0.44 (0.60), residues: 72 loop : -0.22 (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 371 TYR 0.013 0.001 TYR A 6 ARG 0.004 0.000 ARG A 481 *********************** 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 46 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.522 Fit side-chains REVERT: A 77 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7182 (tt0) REVERT: A 100 GLN cc_start: 0.8065 (tt0) cc_final: 0.7541 (tm-30) REVERT: A 119 LYS cc_start: 0.8359 (mttt) cc_final: 0.8095 (mtmt) REVERT: A 168 ASN cc_start: 0.8494 (m110) cc_final: 0.7989 (t0) REVERT: A 301 ASN cc_start: 0.7950 (OUTLIER) cc_final: 0.7745 (m110) REVERT: A 411 GLU cc_start: 0.7463 (tt0) cc_final: 0.7239 (mt-10) outliers start: 6 outliers final: 4 residues processed: 41 average time/residue: 1.4524 time to fit residues: 62.8731 Evaluate side-chains 45 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 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 0 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8449 Z= 0.302 Angle : 0.616 7.270 12445 Z= 0.332 Chirality : 0.037 0.150 1529 Planarity : 0.006 0.046 776 Dihedral : 22.150 169.689 3639 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.07 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: 0.73 (0.42), residues: 391 helix: 1.82 (0.48), residues: 120 sheet: 0.32 (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 429 PHE 0.008 0.002 PHE A 315 TYR 0.018 0.003 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 49 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.528 Fit side-chains REVERT: A 77 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7260 (tt0) REVERT: A 96 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8230 (ttpt) REVERT: A 119 LYS cc_start: 0.8440 (mttt) cc_final: 0.8154 (mtmt) REVERT: A 126 GLU cc_start: 0.7476 (mm-30) cc_final: 0.6973 (mp0) REVERT: A 168 ASN cc_start: 0.8585 (m110) cc_final: 0.8037 (t0) REVERT: A 301 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.7921 (m110) REVERT: A 341 TYR cc_start: 0.7909 (p90) cc_final: 0.7646 (p90) outliers start: 8 outliers final: 4 residues processed: 45 average time/residue: 1.4072 time to fit residues: 66.8407 Evaluate side-chains 47 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8449 Z= 0.195 Angle : 0.555 7.425 12445 Z= 0.304 Chirality : 0.034 0.165 1529 Planarity : 0.005 0.046 776 Dihedral : 22.121 169.174 3639 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: 0.82 (0.42), residues: 391 helix: 2.05 (0.49), residues: 120 sheet: 0.19 (0.59), residues: 72 loop : -0.21 (0.42), residues: 199 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 0.000 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 49 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.485 Fit side-chains REVERT: A 77 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7238 (tt0) REVERT: A 119 LYS cc_start: 0.8394 (mttt) cc_final: 0.8111 (mtmt) REVERT: A 126 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7013 (mp0) REVERT: A 168 ASN cc_start: 0.8573 (m110) cc_final: 0.8039 (t0) REVERT: A 301 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7860 (m110) REVERT: A 341 TYR cc_start: 0.7891 (p90) cc_final: 0.7680 (p90) outliers start: 7 outliers final: 4 residues processed: 46 average time/residue: 1.4159 time to fit residues: 68.6823 Evaluate side-chains 47 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 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 32 optimal weight: 0.0470 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.0370 chunk 26 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 0.1980 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8449 Z= 0.132 Angle : 0.511 7.168 12445 Z= 0.282 Chirality : 0.032 0.177 1529 Planarity : 0.004 0.044 776 Dihedral : 22.068 168.338 3639 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.34 % Allowed : 12.28 % 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: 1.01 (0.42), residues: 391 helix: 2.36 (0.49), residues: 120 sheet: 0.15 (0.59), residues: 72 loop : -0.13 (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 429 PHE 0.005 0.001 PHE A 371 TYR 0.017 0.001 TYR A 341 ARG 0.004 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 50 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.528 Fit side-chains REVERT: A 77 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7195 (tt0) REVERT: A 100 GLN cc_start: 0.7927 (tt0) cc_final: 0.7518 (tm-30) REVERT: A 119 LYS cc_start: 0.8350 (mttt) cc_final: 0.8061 (mtmt) REVERT: A 126 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7014 (mp0) REVERT: A 168 ASN cc_start: 0.8546 (m110) cc_final: 0.8000 (t0) REVERT: A 301 ASN cc_start: 0.8116 (OUTLIER) cc_final: 0.7850 (m110) outliers start: 8 outliers final: 6 residues processed: 45 average time/residue: 1.4327 time to fit residues: 68.2834 Evaluate side-chains 48 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 321 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1275 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 : 0.511 6.812 12445 Z= 0.281 Chirality : 0.032 0.162 1529 Planarity : 0.004 0.044 776 Dihedral : 22.033 168.599 3639 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.75 % Allowed : 13.45 % Favored : 84.80 % 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: 1.06 (0.42), residues: 391 helix: 2.34 (0.48), residues: 120 sheet: 0.24 (0.59), residues: 71 loop : -0.10 (0.43), residues: 200 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 0.004 0.001 PHE A 41 TYR 0.022 0.002 TYR A 341 ARG 0.003 0.000 ARG A 481 *********************** 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 47 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.553 Fit side-chains REVERT: A 77 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7208 (tt0) REVERT: A 100 GLN cc_start: 0.8037 (tt0) cc_final: 0.7576 (tm-30) REVERT: A 119 LYS cc_start: 0.8372 (mttt) cc_final: 0.8077 (mtmt) REVERT: A 126 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7035 (mp0) REVERT: A 168 ASN cc_start: 0.8560 (m110) cc_final: 0.8016 (t0) REVERT: A 301 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7856 (m110) outliers start: 6 outliers final: 4 residues processed: 44 average time/residue: 1.4454 time to fit residues: 67.0997 Evaluate side-chains 45 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 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 86 THR 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 23 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 20.0000 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1298 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= 0.169 Angle : 0.513 6.707 12445 Z= 0.282 Chirality : 0.032 0.159 1529 Planarity : 0.004 0.044 776 Dihedral : 22.026 168.374 3639 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.05 % Allowed : 12.87 % Favored : 85.09 % 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: 1.04 (0.42), residues: 391 helix: 2.29 (0.48), residues: 120 sheet: 0.22 (0.60), residues: 71 loop : -0.08 (0.43), residues: 200 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 0.005 0.001 PHE A 41 TYR 0.025 0.002 TYR A 341 ARG 0.002 0.000 ARG A 481 *********************** 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 46 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.551 Fit side-chains REVERT: A 77 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7219 (tt0) REVERT: A 119 LYS cc_start: 0.8378 (mttt) cc_final: 0.8083 (mtmt) REVERT: A 126 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7036 (mp0) REVERT: A 168 ASN cc_start: 0.8565 (m110) cc_final: 0.8018 (t0) REVERT: A 301 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7858 (m110) outliers start: 7 outliers final: 5 residues processed: 43 average time/residue: 1.3695 time to fit residues: 62.2427 Evaluate side-chains 45 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 54 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8449 Z= 0.334 Angle : 0.636 7.353 12445 Z= 0.342 Chirality : 0.038 0.151 1529 Planarity : 0.006 0.042 776 Dihedral : 22.173 170.168 3639 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: 0.82 (0.42), residues: 391 helix: 1.94 (0.48), residues: 120 sheet: 0.22 (0.60), residues: 72 loop : -0.14 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 479 HIS 0.004 0.001 HIS A 429 PHE 0.009 0.002 PHE A 315 TYR 0.024 0.003 TYR A 341 ARG 0.005 0.001 ARG A 373 ********************** 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 fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.534 Fit side-chains REVERT: A 77 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7223 (tt0) REVERT: A 119 LYS cc_start: 0.8439 (mttt) cc_final: 0.8143 (mtmt) REVERT: A 126 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7006 (mp0) REVERT: A 301 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7930 (m110) outliers start: 7 outliers final: 6 residues processed: 45 average time/residue: 1.3776 time to fit residues: 65.5101 Evaluate side-chains 46 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.174867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.121696 restraints weight = 5439.136| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 0.66 r_work: 0.3085 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8449 Z= 0.209 Angle : 0.563 7.504 12445 Z= 0.309 Chirality : 0.034 0.165 1529 Planarity : 0.005 0.044 776 Dihedral : 22.135 169.538 3639 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.34 % Allowed : 12.57 % Favored : 85.09 % 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: 0.90 (0.42), residues: 391 helix: 2.07 (0.48), residues: 120 sheet: 0.27 (0.60), residues: 71 loop : -0.14 (0.43), 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 0.026 0.002 TYR A 341 ARG 0.003 0.001 ARG A 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2371.73 seconds wall clock time: 42 minutes 33.22 seconds (2553.22 seconds total)