Starting phenix.real_space_refine on Mon May 12 07:37:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wgr_37515/05_2025/8wgr_37515_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wgr_37515/05_2025/8wgr_37515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wgr_37515/05_2025/8wgr_37515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wgr_37515/05_2025/8wgr_37515.map" model { file = "/net/cci-nas-00/data/ceres_data/8wgr_37515/05_2025/8wgr_37515_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wgr_37515/05_2025/8wgr_37515_trim.cif" } resolution = 2.75 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= 0.002 sd= 0.159 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: 7 Type Number sf(0) Gaussians K 1 8.98 5 S 20 5.16 5 Cl 1 4.86 5 C 2981 2.51 5 N 683 2.21 5 O 773 1.98 5 H 4371 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8830 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8754 Classifications: {'peptide': 548} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 528} Chain breaks: 1 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 76 Unusual residues: {' K': 1, ' CL': 1, 'DSM': 2} Classifications: {'undetermined': 4, 'water': 34} Link IDs: {None: 37} Time building chain proxies: 4.85, per 1000 atoms: 0.55 Number of scatterers: 8830 At special positions: 0 Unit cell: (70.3625, 70.3625, 99.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 Cl 1 17.00 S 20 16.00 O 773 8.00 N 683 7.00 C 2981 6.00 H 4371 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.03 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: 2.58 Conformation dependent library (CDL) restraints added in 810.7 milliseconds 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1008 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 1 sheets defined 84.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.719A pdb=" N VAL A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.611A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.774A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 removed outlier: 3.619A pdb=" N GLY A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 226 through 230 removed outlier: 4.158A pdb=" N ILE A 230 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 262 through 267 removed outlier: 3.664A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 283 removed outlier: 3.796A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.630A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.746A pdb=" N LYS A 303 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU A 304 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 320 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.689A pdb=" N ALA A 328 " --> pdb=" O GLY A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 373 Processing helix chain 'A' and resid 375 through 379 removed outlier: 4.000A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 Proline residue: A 392 - end of helix removed outlier: 3.617A pdb=" N THR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.581A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.800A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 497 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.521A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 592 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 599 through 604 removed outlier: 4.333A pdb=" N GLN A 603 " --> pdb=" O HIS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 616 removed outlier: 3.879A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 295 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.42 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4364 1.03 - 1.23: 19 1.23 - 1.42: 2021 1.42 - 1.62: 2505 1.62 - 1.81: 31 Bond restraints: 8940 Sorted by residual: bond pdb=" C ALA A 73 " pdb=" O ALA A 73 " ideal model delta sigma weight residual 1.235 1.161 0.075 1.26e-02 6.30e+03 3.50e+01 bond pdb=" C VAL A 74 " pdb=" O VAL A 74 " ideal model delta sigma weight residual 1.236 1.169 0.067 1.19e-02 7.06e+03 3.18e+01 bond pdb=" C ASN A 78 " pdb=" O ASN A 78 " ideal model delta sigma weight residual 1.236 1.176 0.061 1.18e-02 7.18e+03 2.63e+01 bond pdb=" C ASP A 75 " pdb=" O ASP A 75 " ideal model delta sigma weight residual 1.233 1.178 0.055 1.17e-02 7.31e+03 2.20e+01 bond pdb=" C ASP A 75 " pdb=" N LEU A 76 " ideal model delta sigma weight residual 1.335 1.277 0.058 1.34e-02 5.57e+03 1.88e+01 ... (remaining 8935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.06: 16083 7.06 - 14.12: 12 14.12 - 21.18: 0 21.18 - 28.24: 0 28.24 - 35.30: 3 Bond angle restraints: 16098 Sorted by residual: angle pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 109.00 73.70 35.30 3.00e+00 1.11e-01 1.38e+02 angle pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 110.00 76.58 33.42 3.00e+00 1.11e-01 1.24e+02 angle pdb=" CB TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 109.00 76.12 32.88 3.00e+00 1.11e-01 1.20e+02 angle pdb=" CA ASP A 75 " pdb=" CB ASP A 75 " pdb=" CG ASP A 75 " ideal model delta sigma weight residual 112.60 119.52 -6.92 1.00e+00 1.00e+00 4.79e+01 angle pdb=" O GLY A 71 " pdb=" C GLY A 71 " pdb=" N PHE A 72 " ideal model delta sigma weight residual 122.24 115.98 6.26 1.06e+00 8.90e-01 3.49e+01 ... (remaining 16093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 3745 17.77 - 35.55: 337 35.55 - 53.32: 103 53.32 - 71.10: 41 71.10 - 88.87: 7 Dihedral angle restraints: 4233 sinusoidal: 2150 harmonic: 2083 Sorted by residual: dihedral pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta harmonic sigma weight residual -180.00 -157.65 -22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" C TYR A 205 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual -122.60 -132.22 9.62 0 2.50e+00 1.60e-01 1.48e+01 dihedral pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual 122.80 132.02 -9.22 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 4230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 663 0.083 - 0.165: 25 0.165 - 0.248: 1 0.248 - 0.331: 0 0.331 - 0.413: 1 Chirality restraints: 690 Sorted by residual: chirality pdb=" CA TYR A 205 " pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CB TYR A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CB VAL A 74 " pdb=" CA VAL A 74 " pdb=" CG1 VAL A 74 " pdb=" CG2 VAL A 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.96e-01 chirality pdb=" CA ILE A 103 " pdb=" N ILE A 103 " pdb=" C ILE A 103 " pdb=" CB ILE A 103 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 687 not shown) Planarity restraints: 1281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 78 " 0.029 2.00e-02 2.50e+03 3.78e-02 2.14e+01 pdb=" CG ASN A 78 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 78 " -0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN A 78 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN A 78 " -0.057 2.00e-02 2.50e+03 pdb="HD22 ASN A 78 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ILE A 103 " -0.057 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 75 " -0.015 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" CG ASP A 75 " 0.055 2.00e-02 2.50e+03 pdb=" OD1 ASP A 75 " -0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP A 75 " -0.020 2.00e-02 2.50e+03 ... (remaining 1278 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.24: 839 2.24 - 2.96: 23151 2.96 - 3.69: 33227 3.69 - 4.41: 50817 4.41 - 5.14: 80780 Nonbonded interactions: 188814 Sorted by model distance: nonbonded pdb=" OE1 GLN A 612 " pdb=" H GLN A 612 " model vdw 1.509 2.450 nonbonded pdb=" OE1 GLU A 425 " pdb="HH22 ARG A 442 " model vdw 1.629 2.450 nonbonded pdb=" H HIS A 178 " pdb=" OD1 ASN A 181 " model vdw 1.631 2.450 nonbonded pdb=" O ILE A 561 " pdb=" HG SER A 564 " model vdw 1.676 2.450 nonbonded pdb=" O ALA A 476 " pdb=" HG SER A 480 " model vdw 1.681 2.450 ... (remaining 188809 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: 0.430 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: 0.160 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.210 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 4570 Z= 0.274 Angle : 0.709 9.254 6233 Z= 0.369 Chirality : 0.041 0.413 690 Planarity : 0.005 0.050 754 Dihedral : 17.038 88.869 1537 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.12 % Favored : 96.69 % Rotamer: Outliers : 2.38 % Allowed : 22.08 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.38), residues: 544 helix: 1.68 (0.28), residues: 376 sheet: None (None), residues: 0 loop : -0.10 (0.52), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.003 0.001 HIS A 598 PHE 0.027 0.001 PHE A 72 TYR 0.014 0.001 TYR A 271 ARG 0.001 0.000 ARG A 512 Details of bonding type rmsd hydrogen bonds : bond 0.11994 ( 295) hydrogen bonds : angle 5.10887 ( 852) SS BOND : bond 0.00027 ( 1) SS BOND : angle 1.50410 ( 2) covalent geometry : bond 0.00439 ( 4569) covalent geometry : angle 0.70851 ( 6231) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7184 (mm) cc_final: 0.6769 (mt) REVERT: A 113 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7836 (mt-10) REVERT: A 174 THR cc_start: 0.8224 (m) cc_final: 0.7983 (p) REVERT: A 301 ARG cc_start: 0.7514 (tpt90) cc_final: 0.7312 (tpt90) REVERT: A 376 ILE cc_start: 0.8183 (tt) cc_final: 0.7397 (mp) REVERT: A 458 LEU cc_start: 0.7707 (tt) cc_final: 0.7494 (tt) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 1.2365 time to fit residues: 120.0954 Evaluate side-chains 58 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 493 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.131806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.110540 restraints weight = 15273.971| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.81 r_work: 0.3321 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4570 Z= 0.192 Angle : 0.622 7.983 6233 Z= 0.317 Chirality : 0.043 0.439 690 Planarity : 0.005 0.040 754 Dihedral : 11.451 141.998 618 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.25 % Allowed : 20.13 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.37), residues: 544 helix: 1.37 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.27 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 614 HIS 0.005 0.001 HIS A 598 PHE 0.016 0.002 PHE A 316 TYR 0.020 0.002 TYR A 84 ARG 0.003 0.000 ARG A 512 Details of bonding type rmsd hydrogen bonds : bond 0.05730 ( 295) hydrogen bonds : angle 4.96945 ( 852) SS BOND : bond 0.00009 ( 1) SS BOND : angle 2.50801 ( 2) covalent geometry : bond 0.00461 ( 4569) covalent geometry : angle 0.62088 ( 6231) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7167 (mm) cc_final: 0.6730 (mt) REVERT: A 376 ILE cc_start: 0.8298 (tt) cc_final: 0.7456 (mp) REVERT: A 439 LYS cc_start: 0.7724 (ttmt) cc_final: 0.7387 (ttmp) REVERT: A 440 ARG cc_start: 0.7450 (mtp85) cc_final: 0.7215 (ttm-80) REVERT: A 528 PHE cc_start: 0.7847 (m-80) cc_final: 0.7624 (m-80) outliers start: 15 outliers final: 5 residues processed: 67 average time/residue: 1.2882 time to fit residues: 92.9683 Evaluate side-chains 56 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 377 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 0.0070 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.134819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.113831 restraints weight = 15382.823| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.78 r_work: 0.3359 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4570 Z= 0.115 Angle : 0.533 8.839 6233 Z= 0.265 Chirality : 0.039 0.412 690 Planarity : 0.005 0.035 754 Dihedral : 10.960 139.662 611 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.16 % Allowed : 20.13 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.38), residues: 544 helix: 1.56 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -0.28 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 553 HIS 0.004 0.001 HIS A 598 PHE 0.009 0.001 PHE A 316 TYR 0.015 0.001 TYR A 84 ARG 0.004 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04459 ( 295) hydrogen bonds : angle 4.62338 ( 852) SS BOND : bond 0.00006 ( 1) SS BOND : angle 1.59567 ( 2) covalent geometry : bond 0.00250 ( 4569) covalent geometry : angle 0.53183 ( 6231) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7230 (mm) cc_final: 0.6818 (mt) REVERT: A 301 ARG cc_start: 0.7398 (tpt90) cc_final: 0.6552 (ttt180) REVERT: A 376 ILE cc_start: 0.8291 (tt) cc_final: 0.7464 (mp) REVERT: A 439 LYS cc_start: 0.7760 (ttmt) cc_final: 0.7400 (ttmp) outliers start: 10 outliers final: 4 residues processed: 57 average time/residue: 1.3659 time to fit residues: 83.6868 Evaluate side-chains 52 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 350 ASN A 539 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.131648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.110702 restraints weight = 15370.931| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.76 r_work: 0.3318 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4570 Z= 0.155 Angle : 0.565 8.834 6233 Z= 0.284 Chirality : 0.041 0.430 690 Planarity : 0.005 0.039 754 Dihedral : 10.930 137.482 611 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.60 % Allowed : 19.48 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.37), residues: 544 helix: 1.49 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -0.35 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 253 HIS 0.004 0.001 HIS A 598 PHE 0.013 0.001 PHE A 316 TYR 0.018 0.001 TYR A 84 ARG 0.004 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.05012 ( 295) hydrogen bonds : angle 4.75011 ( 852) SS BOND : bond 0.00031 ( 1) SS BOND : angle 2.15665 ( 2) covalent geometry : bond 0.00372 ( 4569) covalent geometry : angle 0.56350 ( 6231) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7209 (mm) cc_final: 0.6781 (mt) REVERT: A 301 ARG cc_start: 0.7412 (tpt90) cc_final: 0.6559 (ttt180) REVERT: A 376 ILE cc_start: 0.8295 (tt) cc_final: 0.7412 (mp) REVERT: A 439 LYS cc_start: 0.7826 (ttmt) cc_final: 0.7006 (ttpp) REVERT: A 528 PHE cc_start: 0.7921 (m-80) cc_final: 0.7649 (m-80) outliers start: 12 outliers final: 5 residues processed: 63 average time/residue: 1.3006 time to fit residues: 88.3776 Evaluate side-chains 54 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 588 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 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 170 ASN A 350 ASN A 539 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.133079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.112123 restraints weight = 15305.042| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.75 r_work: 0.3338 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4570 Z= 0.125 Angle : 0.546 8.931 6233 Z= 0.272 Chirality : 0.040 0.421 690 Planarity : 0.005 0.037 754 Dihedral : 10.928 138.373 611 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.95 % Allowed : 20.78 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.37), residues: 544 helix: 1.55 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -0.37 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 553 HIS 0.003 0.001 HIS A 598 PHE 0.011 0.001 PHE A 94 TYR 0.016 0.001 TYR A 84 ARG 0.003 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04629 ( 295) hydrogen bonds : angle 4.65692 ( 852) SS BOND : bond 0.00027 ( 1) SS BOND : angle 2.01886 ( 2) covalent geometry : bond 0.00285 ( 4569) covalent geometry : angle 0.54469 ( 6231) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7197 (mm) cc_final: 0.6755 (mt) REVERT: A 301 ARG cc_start: 0.7402 (tpt90) cc_final: 0.6567 (ttt180) REVERT: A 376 ILE cc_start: 0.8304 (tt) cc_final: 0.7453 (mp) REVERT: A 436 GLN cc_start: 0.7666 (pt0) cc_final: 0.6930 (mm110) REVERT: A 439 LYS cc_start: 0.7713 (ttmt) cc_final: 0.6885 (ttpp) REVERT: A 581 GLN cc_start: 0.7895 (tt0) cc_final: 0.7654 (mt0) outliers start: 9 outliers final: 4 residues processed: 60 average time/residue: 1.3065 time to fit residues: 84.4042 Evaluate side-chains 52 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.131702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.110719 restraints weight = 15288.260| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.76 r_work: 0.3318 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4570 Z= 0.143 Angle : 0.559 8.875 6233 Z= 0.279 Chirality : 0.040 0.428 690 Planarity : 0.005 0.039 754 Dihedral : 10.940 137.776 611 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.95 % Allowed : 19.91 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.37), residues: 544 helix: 1.56 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -0.39 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 80 HIS 0.003 0.001 HIS A 598 PHE 0.014 0.001 PHE A 316 TYR 0.017 0.001 TYR A 84 ARG 0.006 0.001 ARG A 440 Details of bonding type rmsd hydrogen bonds : bond 0.04839 ( 295) hydrogen bonds : angle 4.70129 ( 852) SS BOND : bond 0.00045 ( 1) SS BOND : angle 2.10889 ( 2) covalent geometry : bond 0.00337 ( 4569) covalent geometry : angle 0.55780 ( 6231) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6751 (mt) REVERT: A 303 LYS cc_start: 0.8161 (ptmt) cc_final: 0.7296 (ptmm) REVERT: A 376 ILE cc_start: 0.8342 (tt) cc_final: 0.7466 (mp) REVERT: A 436 GLN cc_start: 0.7670 (pt0) cc_final: 0.7032 (mm110) REVERT: A 439 LYS cc_start: 0.7690 (ttmt) cc_final: 0.6879 (ttpp) REVERT: A 440 ARG cc_start: 0.7748 (ttp-110) cc_final: 0.6860 (mtt90) REVERT: A 528 PHE cc_start: 0.7921 (m-80) cc_final: 0.7675 (m-80) REVERT: A 581 GLN cc_start: 0.7916 (tt0) cc_final: 0.7692 (mt0) outliers start: 9 outliers final: 4 residues processed: 58 average time/residue: 1.4936 time to fit residues: 92.3932 Evaluate side-chains 57 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 588 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.132597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.111631 restraints weight = 15407.487| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.76 r_work: 0.3331 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4570 Z= 0.130 Angle : 0.545 8.948 6233 Z= 0.272 Chirality : 0.040 0.425 690 Planarity : 0.005 0.042 754 Dihedral : 10.934 138.178 611 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.16 % Allowed : 19.48 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.37), residues: 544 helix: 1.62 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -0.36 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 80 HIS 0.003 0.001 HIS A 598 PHE 0.012 0.001 PHE A 316 TYR 0.016 0.001 TYR A 84 ARG 0.008 0.001 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04616 ( 295) hydrogen bonds : angle 4.63871 ( 852) SS BOND : bond 0.00084 ( 1) SS BOND : angle 1.85245 ( 2) covalent geometry : bond 0.00302 ( 4569) covalent geometry : angle 0.54365 ( 6231) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6739 (mt) REVERT: A 301 ARG cc_start: 0.7461 (tpt90) cc_final: 0.6604 (ttt180) REVERT: A 303 LYS cc_start: 0.8160 (ptmt) cc_final: 0.7303 (ptmm) REVERT: A 436 GLN cc_start: 0.7730 (pt0) cc_final: 0.6980 (mm110) REVERT: A 439 LYS cc_start: 0.7680 (ttmt) cc_final: 0.7014 (ttpp) REVERT: A 528 PHE cc_start: 0.7907 (m-80) cc_final: 0.7666 (m-80) REVERT: A 581 GLN cc_start: 0.7879 (tt0) cc_final: 0.7672 (mt0) outliers start: 10 outliers final: 4 residues processed: 58 average time/residue: 1.4794 time to fit residues: 91.7131 Evaluate side-chains 56 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 450 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.132959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.111962 restraints weight = 15558.173| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.78 r_work: 0.3335 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4570 Z= 0.125 Angle : 0.547 8.889 6233 Z= 0.271 Chirality : 0.039 0.425 690 Planarity : 0.005 0.045 754 Dihedral : 10.927 138.366 611 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.30 % Allowed : 20.78 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.37), residues: 544 helix: 1.65 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -0.36 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 553 HIS 0.003 0.001 HIS A 598 PHE 0.014 0.001 PHE A 316 TYR 0.016 0.001 TYR A 84 ARG 0.009 0.001 ARG A 440 Details of bonding type rmsd hydrogen bonds : bond 0.04509 ( 295) hydrogen bonds : angle 4.61100 ( 852) SS BOND : bond 0.00131 ( 1) SS BOND : angle 1.75581 ( 2) covalent geometry : bond 0.00288 ( 4569) covalent geometry : angle 0.54626 ( 6231) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.729 Fit side-chains REVERT: A 66 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6755 (mt) REVERT: A 205 TYR cc_start: 0.4364 (OUTLIER) cc_final: 0.3210 (t80) REVERT: A 206 LYS cc_start: 0.7164 (ptpp) cc_final: 0.6558 (pmmt) REVERT: A 301 ARG cc_start: 0.7415 (tpt90) cc_final: 0.6568 (ttt180) REVERT: A 303 LYS cc_start: 0.8151 (ptmt) cc_final: 0.7286 (ptmm) REVERT: A 376 ILE cc_start: 0.8247 (tt) cc_final: 0.7443 (mp) REVERT: A 436 GLN cc_start: 0.7723 (pt0) cc_final: 0.7005 (mm110) REVERT: A 439 LYS cc_start: 0.7679 (ttmt) cc_final: 0.6836 (ttpp) REVERT: A 528 PHE cc_start: 0.7906 (m-80) cc_final: 0.7665 (m-80) REVERT: A 541 LYS cc_start: 0.7955 (mmmm) cc_final: 0.7737 (mtmt) REVERT: A 543 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8056 (tt) outliers start: 6 outliers final: 2 residues processed: 56 average time/residue: 1.6016 time to fit residues: 95.7239 Evaluate side-chains 57 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 543 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.132561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.111609 restraints weight = 15495.258| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.77 r_work: 0.3329 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4570 Z= 0.130 Angle : 0.550 8.893 6233 Z= 0.273 Chirality : 0.040 0.428 690 Planarity : 0.005 0.043 754 Dihedral : 10.918 138.198 611 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.73 % Allowed : 20.56 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.37), residues: 544 helix: 1.63 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -0.39 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 553 HIS 0.003 0.001 HIS A 598 PHE 0.014 0.001 PHE A 316 TYR 0.016 0.001 TYR A 84 ARG 0.010 0.001 ARG A 440 Details of bonding type rmsd hydrogen bonds : bond 0.04575 ( 295) hydrogen bonds : angle 4.62032 ( 852) SS BOND : bond 0.00144 ( 1) SS BOND : angle 1.78442 ( 2) covalent geometry : bond 0.00303 ( 4569) covalent geometry : angle 0.54952 ( 6231) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6742 (mt) REVERT: A 205 TYR cc_start: 0.4319 (OUTLIER) cc_final: 0.3185 (t80) REVERT: A 206 LYS cc_start: 0.7165 (ptpp) cc_final: 0.6567 (pmmt) REVERT: A 301 ARG cc_start: 0.7415 (tpt90) cc_final: 0.6567 (ttt180) REVERT: A 376 ILE cc_start: 0.8326 (tt) cc_final: 0.7487 (mp) REVERT: A 436 GLN cc_start: 0.7721 (pt0) cc_final: 0.7008 (mm110) REVERT: A 439 LYS cc_start: 0.7690 (ttmt) cc_final: 0.6849 (ttpp) REVERT: A 528 PHE cc_start: 0.7909 (m-80) cc_final: 0.7673 (m-80) REVERT: A 541 LYS cc_start: 0.7837 (mmmm) cc_final: 0.7588 (mtmt) REVERT: A 543 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8045 (tt) outliers start: 8 outliers final: 3 residues processed: 58 average time/residue: 1.4473 time to fit residues: 90.0372 Evaluate side-chains 58 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 543 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.133539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.112621 restraints weight = 15379.392| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.78 r_work: 0.3349 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4570 Z= 0.119 Angle : 0.540 8.893 6233 Z= 0.267 Chirality : 0.039 0.424 690 Planarity : 0.005 0.039 754 Dihedral : 10.900 138.587 611 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.52 % Allowed : 21.43 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.37), residues: 544 helix: 1.70 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -0.36 (0.53), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 553 HIS 0.002 0.001 HIS A 598 PHE 0.011 0.001 PHE A 316 TYR 0.015 0.001 TYR A 84 ARG 0.008 0.001 ARG A 440 Details of bonding type rmsd hydrogen bonds : bond 0.04355 ( 295) hydrogen bonds : angle 4.55525 ( 852) SS BOND : bond 0.00116 ( 1) SS BOND : angle 1.67694 ( 2) covalent geometry : bond 0.00271 ( 4569) covalent geometry : angle 0.53927 ( 6231) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6739 (mt) REVERT: A 107 MET cc_start: 0.8117 (ttp) cc_final: 0.7501 (ttp) REVERT: A 205 TYR cc_start: 0.4306 (OUTLIER) cc_final: 0.3554 (t80) REVERT: A 266 THR cc_start: 0.8091 (m) cc_final: 0.7367 (t) REVERT: A 301 ARG cc_start: 0.7389 (tpt90) cc_final: 0.6547 (ttt180) REVERT: A 376 ILE cc_start: 0.8324 (tt) cc_final: 0.7505 (mp) REVERT: A 436 GLN cc_start: 0.7691 (pt0) cc_final: 0.7002 (mm110) REVERT: A 439 LYS cc_start: 0.7675 (ttmt) cc_final: 0.6839 (ttpp) outliers start: 7 outliers final: 3 residues processed: 58 average time/residue: 1.5178 time to fit residues: 93.8518 Evaluate side-chains 58 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 508 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.133126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.112424 restraints weight = 15467.408| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.74 r_work: 0.3338 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4570 Z= 0.122 Angle : 0.551 8.870 6233 Z= 0.273 Chirality : 0.039 0.425 690 Planarity : 0.005 0.037 754 Dihedral : 10.853 138.579 610 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.08 % Allowed : 22.08 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.37), residues: 544 helix: 1.68 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -0.35 (0.53), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 553 HIS 0.002 0.001 HIS A 598 PHE 0.012 0.001 PHE A 316 TYR 0.015 0.001 TYR A 84 ARG 0.008 0.001 ARG A 440 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 295) hydrogen bonds : angle 4.54537 ( 852) SS BOND : bond 0.00111 ( 1) SS BOND : angle 1.66510 ( 2) covalent geometry : bond 0.00281 ( 4569) covalent geometry : angle 0.54998 ( 6231) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5594.37 seconds wall clock time: 96 minutes 21.89 seconds (5781.89 seconds total)