Starting phenix.real_space_refine on Mon Mar 11 08:58:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xht_33198/03_2024/7xht_33198_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xht_33198/03_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_33198/03_2024/7xht_33198.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xht_33198/03_2024/7xht_33198.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xht_33198/03_2024/7xht_33198_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xht_33198/03_2024/7xht_33198_updated.pdb" } 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 Residue "A TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.19, per 1000 atoms: 0.66 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 - 3.50 Amino acid : False - 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: 4.53 Conformation dependent library (CDL) restraints added in 676.8 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... running ksdssp... Secondary structure from input PDB file: 10 helices and 6 sheets defined 29.4% alpha, 18.5% beta 82 base pairs and 138 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'A' and resid 21 through 29 Processing helix chain 'A' and resid 88 through 108 Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 111 through 121 Processing helix chain 'A' and resid 165 through 184 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 314 Proline residue: A 305 - end of helix Processing helix chain 'A' and resid 324 through 334 Processing helix chain 'A' and resid 340 through 351 removed outlier: 4.365A pdb=" N ALA A 344 " --> pdb=" O TYR A 341 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 348 " --> pdb=" O TYR A 345 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N CYS A 349 " --> pdb=" O CYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing sheet with id= A, first strand: chain 'A' and resid 6 through 8 removed outlier: 6.604A pdb=" N GLN A 44 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL A 35 " --> pdb=" O GLN A 44 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.407A pdb=" N VAL A 190 " --> pdb=" O CYS A 320 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N THR A 322 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU A 192 " --> pdb=" O THR A 322 " (cutoff:3.500A) 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) removed outlier: 6.148A pdb=" N TYR A 366 " --> pdb=" O GLN A 83 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLU A 85 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 368 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 129 through 132 Processing sheet with id= D, first strand: chain 'A' and resid 426 through 428 removed outlier: 3.521A pdb=" N ALA A 396 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N MET A 390 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU A 394 " --> pdb=" O MET A 390 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 453 through 455 removed outlier: 6.356A pdb=" N VAL A 447 " --> pdb=" O TYR A 485 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N TYR A 485 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 477 through 479 109 hydrogen bonds defined for protein. 288 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: 4.56 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: 81.20 - 91.76: 2 91.76 - 102.32: 267 102.32 - 112.87: 5676 112.87 - 123.43: 5418 123.43 - 133.99: 1082 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: 67 2.59 - 3.17: 5677 3.17 - 3.75: 15129 3.75 - 4.32: 21465 4.32 - 4.90: 28207 Nonbonded interactions: 70545 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 2.440 nonbonded pdb=" OP1 U B 190 " pdb=" OH TYR A 47 " model vdw 2.204 2.440 nonbonded pdb=" O2' C B 82 " pdb=" O ASN A 155 " model vdw 2.222 2.440 nonbonded pdb=" O2' G B 76 " pdb=" O5' A B 77 " model vdw 2.230 2.440 ... (remaining 70540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.760 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: 7.560 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 29.300 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.270 ------------------------------------------------------------------------------- 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= 0.191 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 : 0.534 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: 1.4312 time to fit residues: 111.1827 Evaluate side-chains 50 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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: 3.9990 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 28 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 131 GLN A 154 ASN A 169 HIS A 195 ASN A 405 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.0786 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= 0.159 Angle : 0.510 7.346 12445 Z= 0.279 Chirality : 0.032 0.204 1529 Planarity : 0.004 0.039 776 Dihedral : 22.140 167.828 3639 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.75 % Allowed : 8.77 % 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: 0.52 (0.42), residues: 391 helix: 1.31 (0.50), residues: 120 sheet: 0.64 (0.60), residues: 72 loop : -0.31 (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 125 TYR 0.015 0.001 TYR A 6 ARG 0.005 0.000 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 55 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.580 Fit side-chains REVERT: A 77 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7153 (tp30) REVERT: A 81 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.7977 (m110) REVERT: A 100 GLN cc_start: 0.8141 (tt0) cc_final: 0.7855 (tt0) REVERT: A 119 LYS cc_start: 0.8348 (mttt) cc_final: 0.8097 (mtmt) REVERT: A 127 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: A 168 ASN cc_start: 0.8543 (m-40) cc_final: 0.8007 (t0) REVERT: A 301 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7760 (m110) REVERT: A 481 ARG cc_start: 0.7776 (mtt90) cc_final: 0.7520 (mtt90) outliers start: 6 outliers final: 2 residues processed: 51 average time/residue: 1.2973 time to fit residues: 70.0128 Evaluate side-chains 54 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 81 ASN 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 29 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0953 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= 0.212 Angle : 0.541 7.606 12445 Z= 0.295 Chirality : 0.033 0.167 1529 Planarity : 0.005 0.041 776 Dihedral : 22.088 168.621 3639 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.34 % Allowed : 10.53 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.42), residues: 391 helix: 1.30 (0.50), residues: 120 sheet: 0.56 (0.60), residues: 72 loop : -0.25 (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 41 TYR 0.017 0.002 TYR A 341 ARG 0.004 0.001 ARG A 87 *********************** 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 53 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.530 Fit side-chains REVERT: A 77 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7235 (tt0) REVERT: A 100 GLN cc_start: 0.8103 (tt0) cc_final: 0.7830 (tt0) REVERT: A 119 LYS cc_start: 0.8386 (mttt) cc_final: 0.8124 (mtmt) REVERT: A 127 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: A 168 ASN cc_start: 0.8480 (m110) cc_final: 0.8025 (t0) REVERT: A 301 ASN cc_start: 0.8149 (OUTLIER) cc_final: 0.7844 (m110) REVERT: A 484 GLN cc_start: 0.8610 (tp-100) cc_final: 0.8352 (tp40) outliers start: 8 outliers final: 5 residues processed: 49 average time/residue: 1.4746 time to fit residues: 76.0002 Evaluate side-chains 51 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 189 LYS 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 27 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 32 optimal weight: 0.0670 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8449 Z= 0.229 Angle : 0.553 7.743 12445 Z= 0.300 Chirality : 0.034 0.148 1529 Planarity : 0.005 0.043 776 Dihedral : 22.066 169.167 3639 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.05 % Allowed : 11.99 % 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: 0.55 (0.42), residues: 391 helix: 1.32 (0.49), residues: 120 sheet: 0.52 (0.61), 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 169 PHE 0.006 0.001 PHE A 315 TYR 0.018 0.002 TYR A 341 ARG 0.004 0.001 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.553 Fit side-chains REVERT: A 77 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7211 (tt0) REVERT: A 119 LYS cc_start: 0.8404 (mttt) cc_final: 0.8126 (mtmt) REVERT: A 126 GLU cc_start: 0.7463 (mm-30) cc_final: 0.6980 (mp0) REVERT: A 168 ASN cc_start: 0.8537 (m110) cc_final: 0.8051 (t0) REVERT: A 301 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7894 (m110) REVERT: A 484 GLN cc_start: 0.8621 (tp-100) cc_final: 0.8367 (tp40) outliers start: 7 outliers final: 5 residues processed: 47 average time/residue: 1.3330 time to fit residues: 66.3550 Evaluate side-chains 47 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 189 LYS Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 321 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 405 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8449 Z= 0.178 Angle : 0.531 7.618 12445 Z= 0.291 Chirality : 0.033 0.150 1529 Planarity : 0.005 0.043 776 Dihedral : 22.061 168.715 3639 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.62 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: 0.59 (0.42), residues: 391 helix: 1.42 (0.49), residues: 120 sheet: 0.48 (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 0.002 0.001 HIS A 169 PHE 0.005 0.001 PHE A 315 TYR 0.017 0.002 TYR A 341 ARG 0.008 0.001 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.558 Fit side-chains REVERT: A 77 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7205 (tt0) REVERT: A 100 GLN cc_start: 0.7949 (tt0) cc_final: 0.7556 (tm-30) REVERT: A 119 LYS cc_start: 0.8389 (mttt) cc_final: 0.8107 (mtmt) REVERT: A 126 GLU cc_start: 0.7460 (mm-30) cc_final: 0.6978 (mp0) REVERT: A 168 ASN cc_start: 0.8535 (m110) cc_final: 0.8064 (t0) REVERT: A 301 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7830 (m110) REVERT: A 484 GLN cc_start: 0.8620 (tp-100) cc_final: 0.8365 (tp40) outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 1.4649 time to fit residues: 68.0046 Evaluate side-chains 47 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8449 Z= 0.238 Angle : 0.557 7.680 12445 Z= 0.302 Chirality : 0.034 0.149 1529 Planarity : 0.005 0.044 776 Dihedral : 22.069 169.414 3639 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % 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: 0.59 (0.42), residues: 391 helix: 1.43 (0.49), residues: 120 sheet: 0.43 (0.61), residues: 72 loop : -0.21 (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 0.006 0.001 PHE A 315 TYR 0.021 0.002 TYR A 341 ARG 0.004 0.001 ARG A 87 *********************** 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: 8 poor density : 41 time to evaluate : 0.551 Fit side-chains REVERT: A 77 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7220 (tt0) REVERT: A 119 LYS cc_start: 0.8404 (mttt) cc_final: 0.8119 (mtmt) REVERT: A 126 GLU cc_start: 0.7464 (mm-30) cc_final: 0.6991 (mp0) REVERT: A 168 ASN cc_start: 0.8571 (m110) cc_final: 0.8066 (t0) REVERT: A 301 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7900 (m110) REVERT: A 484 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8382 (tp40) outliers start: 8 outliers final: 6 residues processed: 45 average time/residue: 1.4340 time to fit residues: 68.2183 Evaluate side-chains 48 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 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 32 optimal weight: 0.0170 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- 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: 0.8332 moved from start: 0.1102 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= 0.170 Angle : 0.530 7.586 12445 Z= 0.291 Chirality : 0.032 0.150 1529 Planarity : 0.005 0.043 776 Dihedral : 22.056 168.595 3639 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: 0.61 (0.42), residues: 391 helix: 1.47 (0.50), residues: 120 sheet: 0.42 (0.61), residues: 72 loop : -0.20 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 162 HIS 0.002 0.001 HIS A 105 PHE 0.005 0.001 PHE A 41 TYR 0.021 0.002 TYR A 341 ARG 0.004 0.001 ARG A 147 *********************** 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 fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.496 Fit side-chains REVERT: A 77 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7186 (tt0) REVERT: A 119 LYS cc_start: 0.8386 (mttt) cc_final: 0.8099 (mtmt) REVERT: A 126 GLU cc_start: 0.7466 (mm-30) cc_final: 0.6990 (mp0) REVERT: A 168 ASN cc_start: 0.8568 (m110) cc_final: 0.8084 (t0) REVERT: A 301 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7858 (m110) REVERT: A 484 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8377 (tp40) outliers start: 7 outliers final: 6 residues processed: 44 average time/residue: 1.3465 time to fit residues: 62.6717 Evaluate side-chains 48 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8327 moved from start: 0.1098 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= 0.167 Angle : 0.526 7.674 12445 Z= 0.288 Chirality : 0.032 0.151 1529 Planarity : 0.004 0.043 776 Dihedral : 22.056 168.827 3639 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.05 % Allowed : 13.45 % Favored : 84.50 % 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: 0.64 (0.42), residues: 391 helix: 1.52 (0.50), residues: 120 sheet: 0.49 (0.61), residues: 71 loop : -0.22 (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 105 PHE 0.005 0.001 PHE A 41 TYR 0.023 0.002 TYR A 341 ARG 0.010 0.001 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 48 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.528 Fit side-chains REVERT: A 77 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7187 (tt0) REVERT: A 119 LYS cc_start: 0.8386 (mttt) cc_final: 0.8096 (mtmt) REVERT: A 126 GLU cc_start: 0.7465 (mm-30) cc_final: 0.6990 (mp0) REVERT: A 168 ASN cc_start: 0.8569 (m110) cc_final: 0.8074 (t0) REVERT: A 301 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7856 (m110) REVERT: A 484 GLN cc_start: 0.8630 (tp-100) cc_final: 0.8376 (tp40) outliers start: 7 outliers final: 6 residues processed: 44 average time/residue: 1.3802 time to fit residues: 64.1519 Evaluate side-chains 48 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 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 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 16 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8309 moved from start: 0.1098 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= 0.138 Angle : 0.510 7.591 12445 Z= 0.281 Chirality : 0.032 0.161 1529 Planarity : 0.004 0.042 776 Dihedral : 22.038 168.049 3639 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.05 % Allowed : 13.16 % 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: 0.68 (0.42), residues: 391 helix: 1.58 (0.50), residues: 120 sheet: 0.47 (0.61), residues: 71 loop : -0.19 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 162 HIS 0.002 0.001 HIS A 105 PHE 0.004 0.001 PHE A 454 TYR 0.024 0.002 TYR A 341 ARG 0.011 0.001 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 48 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.498 Fit side-chains REVERT: A 77 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7192 (tt0) REVERT: A 119 LYS cc_start: 0.8369 (mttt) cc_final: 0.8079 (mtmt) REVERT: A 126 GLU cc_start: 0.7466 (mm-30) cc_final: 0.6999 (mp0) REVERT: A 168 ASN cc_start: 0.8557 (m110) cc_final: 0.8065 (t0) REVERT: A 301 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7834 (m110) REVERT: A 484 GLN cc_start: 0.8625 (tp-100) cc_final: 0.8373 (tp40) outliers start: 7 outliers final: 6 residues processed: 44 average time/residue: 1.3560 time to fit residues: 63.1005 Evaluate side-chains 48 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 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 54 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1241 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= 0.305 Angle : 0.606 7.888 12445 Z= 0.326 Chirality : 0.037 0.148 1529 Planarity : 0.005 0.041 776 Dihedral : 22.135 170.234 3639 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.05 % Allowed : 13.16 % 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: 0.50 (0.42), residues: 391 helix: 1.31 (0.49), residues: 120 sheet: 0.46 (0.61), residues: 71 loop : -0.26 (0.41), 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 0.007 0.002 PHE A 315 TYR 0.023 0.003 TYR A 341 ARG 0.004 0.001 ARG A 152 ********************** 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 : 0.486 Fit side-chains REVERT: A 77 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7230 (tt0) REVERT: A 119 LYS cc_start: 0.8434 (mttt) cc_final: 0.8134 (mtmt) REVERT: A 168 ASN cc_start: 0.8608 (m110) cc_final: 0.8074 (t0) REVERT: A 301 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.7947 (m110) REVERT: A 484 GLN cc_start: 0.8622 (tp-100) cc_final: 0.8387 (tp40) outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 1.3144 time to fit residues: 61.2632 Evaluate side-chains 46 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 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: 0.8980 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: 0.0870 chunk 53 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 40 optimal weight: 0.0670 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.178796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.126420 restraints weight = 5493.795| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 0.73 r_work: 0.3139 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1228 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= 0.136 Angle : 0.498 7.263 12445 Z= 0.273 Chirality : 0.031 0.186 1529 Planarity : 0.004 0.043 776 Dihedral : 22.012 168.376 3639 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.75 % Allowed : 13.74 % Favored : 84.50 % 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: 0.70 (0.42), residues: 391 helix: 1.61 (0.49), residues: 120 sheet: 0.32 (0.61), residues: 70 loop : -0.12 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 162 HIS 0.004 0.001 HIS A 105 PHE 0.004 0.001 PHE A 41 TYR 0.023 0.001 TYR A 341 ARG 0.004 0.000 ARG A 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2431.82 seconds wall clock time: 44 minutes 44.21 seconds (2684.21 seconds total)