Starting phenix.real_space_refine on Tue Aug 4 17:48:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u0j_41781/08_2026/8u0j_41781.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u0j_41781/08_2026/8u0j_41781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u0j_41781/08_2026/8u0j_41781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u0j_41781/08_2026/8u0j_41781.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u0j_41781/08_2026/8u0j_41781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u0j_41781/08_2026/8u0j_41781.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.000 sd= 0.061 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 48 5.49 5 Mg 1 5.21 5 S 10 5.16 5 C 3466 2.51 5 N 963 2.21 5 O 1169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5657 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4669 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 540} Chain breaks: 1 Chain: "B" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'DNA': 14} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 13} Chain: "D" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 471 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "F" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 226 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.33, per 1000 atoms: 0.24 Number of scatterers: 5657 At special positions: 0 Unit cell: (83.32, 81.6536, 102.484, 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 10 16.00 P 48 15.00 Mg 1 11.99 O 1169 8.00 N 963 7.00 C 3466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 107.5 milliseconds 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1074 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 6 sheets defined 36.7% alpha, 13.2% beta 9 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 249 through 266 Processing helix chain 'A' and resid 285 through 301 Processing helix chain 'A' and resid 317 through 328 removed outlier: 3.618A pdb=" N THR A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.701A pdb=" N TYR A 355 " --> pdb=" O LYS A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.834A pdb=" N VAL A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG A 367 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.529A pdb=" N TRP A 384 " --> pdb=" O GLU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 410 removed outlier: 4.174A pdb=" N VAL A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 4.015A pdb=" N ARG A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 473 removed outlier: 3.729A pdb=" N LEU A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 480 removed outlier: 4.310A pdb=" N ARG A 478 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS A 479 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 528 removed outlier: 3.772A pdb=" N GLU A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 542 Processing helix chain 'A' and resid 547 through 558 Processing helix chain 'A' and resid 565 through 572 removed outlier: 3.535A pdb=" N GLU A 568 " --> pdb=" O PRO A 565 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR A 571 " --> pdb=" O GLU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 589 Processing helix chain 'A' and resid 649 through 657 removed outlier: 3.909A pdb=" N LEU A 655 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE A 656 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 657 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.808A pdb=" N LYS A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS A 675 " --> pdb=" O TYR A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 684 No H-bonds generated for 'chain 'A' and resid 682 through 684' Processing sheet with id=AA1, first strand: chain 'A' and resid 136 through 144 removed outlier: 5.757A pdb=" N TYR A 137 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE A 159 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU A 139 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 157 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AA4, first strand: chain 'A' and resid 334 through 336 removed outlier: 7.052A pdb=" N LEU A 305 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ALA A 336 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE A 307 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASN A 345 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N CYS A 378 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU A 347 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 455 through 460 removed outlier: 7.228A pdb=" N LEU A 638 " --> pdb=" O THR A 504 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 506 " --> pdb=" O SER A 636 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N SER A 636 " --> pdb=" O ILE A 506 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 612 through 613 removed outlier: 3.917A pdb=" N PHE A 621 " --> pdb=" O PHE A 612 " (cutoff:3.500A) 154 hydrogen bonds defined for protein. 411 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 940 1.32 - 1.44: 1776 1.44 - 1.57: 3064 1.57 - 1.69: 93 1.69 - 1.81: 16 Bond restraints: 5889 Sorted by residual: bond pdb=" C3' DG B 5 " pdb=" O3' DG B 5 " ideal model delta sigma weight residual 1.435 1.382 0.053 1.30e-02 5.92e+03 1.67e+01 bond pdb=" C3' DA D 9 " pdb=" O3' DA D 9 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.42e+01 bond pdb=" C3' DC B 7 " pdb=" O3' DC B 7 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.41e+01 bond pdb=" C3' DT D 7 " pdb=" C2' DT D 7 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" O4' DG B 5 " pdb=" C1' DG B 5 " ideal model delta sigma weight residual 1.420 1.385 0.035 1.10e-02 8.26e+03 1.03e+01 ... (remaining 5884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 7711 2.00 - 3.99: 401 3.99 - 5.99: 43 5.99 - 7.98: 12 7.98 - 9.98: 2 Bond angle restraints: 8169 Sorted by residual: angle pdb=" C TYR A 363 " pdb=" N GLN A 364 " pdb=" CA GLN A 364 " ideal model delta sigma weight residual 121.54 131.52 -9.98 1.91e+00 2.74e-01 2.73e+01 angle pdb=" N3 DT B 9 " pdb=" C4 DT B 9 " pdb=" O4 DT B 9 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT B 2 " pdb=" C4 DT B 2 " pdb=" O4 DT B 2 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT B 10 " pdb=" C4 DT B 10 " pdb=" O4 DT B 10 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT B 14 " pdb=" C4 DT B 14 " pdb=" O4 DT B 14 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 ... (remaining 8164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 2770 17.94 - 35.88: 404 35.88 - 53.82: 189 53.82 - 71.76: 47 71.76 - 89.70: 9 Dihedral angle restraints: 3419 sinusoidal: 1749 harmonic: 1670 Sorted by residual: dihedral pdb=" CA SER A 437 " pdb=" C SER A 437 " pdb=" N GLU A 438 " pdb=" CA GLU A 438 " ideal model delta harmonic sigma weight residual -180.00 -125.52 -54.48 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA GLU A 435 " pdb=" C GLU A 435 " pdb=" N SER A 436 " pdb=" CA SER A 436 " ideal model delta harmonic sigma weight residual -180.00 -140.41 -39.59 0 5.00e+00 4.00e-02 6.27e+01 dihedral pdb=" CA TYR A 220 " pdb=" C TYR A 220 " pdb=" N ILE A 221 " pdb=" CA ILE A 221 " ideal model delta harmonic sigma weight residual 180.00 -158.53 -21.47 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 3416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 608 0.051 - 0.102: 211 0.102 - 0.153: 47 0.153 - 0.204: 11 0.204 - 0.255: 1 Chirality restraints: 878 Sorted by residual: chirality pdb=" CA PHE A 656 " pdb=" N PHE A 656 " pdb=" C PHE A 656 " pdb=" CB PHE A 656 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA GLN A 364 " pdb=" N GLN A 364 " pdb=" C GLN A 364 " pdb=" CB GLN A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C3' DG B 5 " pdb=" C4' DG B 5 " pdb=" O3' DG B 5 " pdb=" C2' DG B 5 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.35e-01 ... (remaining 875 not shown) Planarity restraints: 889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 364 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C GLN A 364 " 0.058 2.00e-02 2.50e+03 pdb=" O GLN A 364 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL A 365 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 428 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.12e+00 pdb=" N PRO A 429 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 429 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 429 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 363 " 0.015 2.00e-02 2.50e+03 1.39e-02 3.84e+00 pdb=" CG TYR A 363 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 363 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 363 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 363 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 363 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 363 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 363 " -0.000 2.00e-02 2.50e+03 ... (remaining 886 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 313 2.72 - 3.26: 5253 3.26 - 3.81: 9454 3.81 - 4.35: 11941 4.35 - 4.90: 19173 Nonbonded interactions: 46134 Sorted by model distance: nonbonded pdb=" OP1 DT B 3 " pdb="MG MG B 101 " model vdw 2.170 2.170 nonbonded pdb=" OH TYR A 620 " pdb=" O VAL A 668 " model vdw 2.204 3.040 nonbonded pdb=" OG SER A 576 " pdb=" OP1 DA D 23 " model vdw 2.250 3.040 nonbonded pdb=" NH1 ARG A 202 " pdb=" O GLY A 218 " model vdw 2.256 3.120 nonbonded pdb=" O2 DT D 20 " pdb=" N2 DG F 9 " model vdw 2.300 3.120 ... (remaining 46129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.900 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 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 : 0.008 0.103 5889 Z= 0.481 Angle : 0.964 9.980 8169 Z= 0.640 Chirality : 0.055 0.255 878 Planarity : 0.006 0.057 889 Dihedral : 20.282 89.698 2345 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.34), residues: 565 helix: 0.11 (0.40), residues: 154 sheet: -0.19 (0.53), residues: 90 loop : -1.30 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 367 TYR 0.034 0.003 TYR A 363 PHE 0.025 0.003 PHE A 685 TRP 0.011 0.001 TRP A 444 HIS 0.006 0.002 HIS A 660 Details of bonding type rmsd/Z covalent geometry : bond 0.00793 / 0.48 ( 5889) covalent geometry : angle 0.96358 / 0.64 ( 8169) hydrogen bonds : bond 0.16015 / 10.55 ( 174) hydrogen bonds : angle 6.45238 / 4.27 ( 451) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.113 Fit side-chains REVERT: A 302 GLU cc_start: 0.7306 (tp30) cc_final: 0.6769 (tm-30) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0816 time to fit residues: 8.7553 Evaluate side-chains 72 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 643 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.230999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.184135 restraints weight = 6518.397| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 3.23 r_work: 0.3963 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5889 Z= 0.155 Angle : 0.693 7.976 8169 Z= 0.382 Chirality : 0.047 0.204 878 Planarity : 0.006 0.042 889 Dihedral : 23.302 87.684 1166 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.39 % Allowed : 8.24 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.35), residues: 565 helix: 0.65 (0.41), residues: 157 sheet: -0.08 (0.52), residues: 91 loop : -1.27 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 382 TYR 0.017 0.002 TYR A 220 PHE 0.022 0.002 PHE A 611 TRP 0.008 0.001 TRP A 585 HIS 0.003 0.001 HIS A 660 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 ( 5889) covalent geometry : angle 0.69316 / 0.38 ( 8169) hydrogen bonds : bond 0.05231 / 3.28 ( 174) hydrogen bonds : angle 4.89067 / 3.23 ( 451) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.110 Fit side-chains REVERT: A 302 GLU cc_start: 0.7821 (tp30) cc_final: 0.7307 (tm-30) REVERT: A 440 ARG cc_start: 0.6733 (mmm160) cc_final: 0.5852 (mmm160) outliers start: 2 outliers final: 0 residues processed: 81 average time/residue: 0.0791 time to fit residues: 8.2392 Evaluate side-chains 76 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 0.3980 chunk 50 optimal weight: 0.5980 chunk 58 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.230293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.183277 restraints weight = 6522.982| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 3.26 r_work: 0.3959 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5889 Z= 0.161 Angle : 0.641 7.065 8169 Z= 0.354 Chirality : 0.045 0.158 878 Planarity : 0.005 0.042 889 Dihedral : 23.261 72.466 1166 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.18 % Allowed : 11.37 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.35), residues: 565 helix: 0.98 (0.41), residues: 157 sheet: -0.13 (0.52), residues: 95 loop : -1.26 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 367 TYR 0.015 0.002 TYR A 293 PHE 0.017 0.002 PHE A 685 TRP 0.004 0.001 TRP A 585 HIS 0.004 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 5889) covalent geometry : angle 0.64121 / 0.35 ( 8169) hydrogen bonds : bond 0.04602 / 3.00 ( 174) hydrogen bonds : angle 4.63860 / 3.01 ( 451) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.118 Fit side-chains REVERT: A 302 GLU cc_start: 0.7895 (tp30) cc_final: 0.7196 (tm-30) REVERT: A 440 ARG cc_start: 0.6709 (mmm160) cc_final: 0.5699 (mmm160) REVERT: A 619 MET cc_start: 0.5805 (mtm) cc_final: 0.5494 (mtm) outliers start: 6 outliers final: 4 residues processed: 80 average time/residue: 0.0853 time to fit residues: 8.6650 Evaluate side-chains 76 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 55 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.228021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.183187 restraints weight = 6390.984| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 3.03 r_work: 0.3959 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5889 Z= 0.172 Angle : 0.642 7.054 8169 Z= 0.352 Chirality : 0.044 0.154 878 Planarity : 0.005 0.042 889 Dihedral : 23.244 72.931 1166 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.16 % Allowed : 13.14 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.36), residues: 565 helix: 1.18 (0.41), residues: 156 sheet: 0.12 (0.54), residues: 88 loop : -1.22 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.017 0.002 TYR A 491 PHE 0.029 0.002 PHE A 611 TRP 0.004 0.001 TRP A 456 HIS 0.006 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 5889) covalent geometry : angle 0.64234 / 0.35 ( 8169) hydrogen bonds : bond 0.04291 / 2.75 ( 174) hydrogen bonds : angle 4.66645 / 3.02 ( 451) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.171 Fit side-chains REVERT: A 302 GLU cc_start: 0.7810 (tp30) cc_final: 0.7239 (tm-30) REVERT: A 310 LEU cc_start: 0.7761 (mm) cc_final: 0.7561 (mm) REVERT: A 371 GLN cc_start: 0.8251 (mt0) cc_final: 0.8017 (mt0) REVERT: A 440 ARG cc_start: 0.6741 (mmm160) cc_final: 0.5706 (mmm160) REVERT: A 540 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8329 (tm-30) REVERT: A 619 MET cc_start: 0.5869 (mtm) cc_final: 0.5531 (mtm) outliers start: 11 outliers final: 5 residues processed: 86 average time/residue: 0.0688 time to fit residues: 7.5890 Evaluate side-chains 82 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 597 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.8980 chunk 26 optimal weight: 0.0470 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.230591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.183806 restraints weight = 6550.023| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 3.24 r_work: 0.3960 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5889 Z= 0.147 Angle : 0.607 5.886 8169 Z= 0.334 Chirality : 0.043 0.152 878 Planarity : 0.005 0.040 889 Dihedral : 23.141 70.710 1166 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.98 % Allowed : 15.10 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.36), residues: 565 helix: 1.34 (0.41), residues: 156 sheet: -0.03 (0.52), residues: 92 loop : -1.18 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 615 TYR 0.013 0.001 TYR A 671 PHE 0.015 0.002 PHE A 685 TRP 0.006 0.001 TRP A 444 HIS 0.005 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 5889) covalent geometry : angle 0.60658 / 0.33 ( 8169) hydrogen bonds : bond 0.04108 / 2.67 ( 174) hydrogen bonds : angle 4.48523 / 2.91 ( 451) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.131 Fit side-chains REVERT: A 302 GLU cc_start: 0.7857 (tp30) cc_final: 0.7276 (tm-30) REVERT: A 371 GLN cc_start: 0.8289 (mt0) cc_final: 0.7981 (mm-40) REVERT: A 440 ARG cc_start: 0.6642 (mmm160) cc_final: 0.5784 (mmm160) REVERT: A 619 MET cc_start: 0.5781 (mtm) cc_final: 0.5446 (mtm) outliers start: 5 outliers final: 3 residues processed: 83 average time/residue: 0.0764 time to fit residues: 8.4140 Evaluate side-chains 75 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 GLN A 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.225569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.178060 restraints weight = 6502.843| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 3.22 r_work: 0.3908 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 5889 Z= 0.224 Angle : 0.677 6.123 8169 Z= 0.363 Chirality : 0.045 0.153 878 Planarity : 0.005 0.041 889 Dihedral : 23.279 75.422 1166 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.16 % Allowed : 15.10 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.35), residues: 565 helix: 1.14 (0.41), residues: 156 sheet: -0.27 (0.51), residues: 92 loop : -1.26 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.018 0.002 TYR A 620 PHE 0.036 0.003 PHE A 611 TRP 0.004 0.001 TRP A 444 HIS 0.008 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.22 ( 5889) covalent geometry : angle 0.67710 / 0.36 ( 8169) hydrogen bonds : bond 0.04392 / 2.80 ( 174) hydrogen bonds : angle 4.77699 / 3.09 ( 451) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.175 Fit side-chains REVERT: A 302 GLU cc_start: 0.7879 (tp30) cc_final: 0.7313 (tm-30) REVERT: A 371 GLN cc_start: 0.8303 (mt0) cc_final: 0.7983 (mm-40) REVERT: A 440 ARG cc_start: 0.6782 (mmm160) cc_final: 0.5827 (mmm160) REVERT: A 619 MET cc_start: 0.5952 (mtm) cc_final: 0.5556 (mtm) outliers start: 11 outliers final: 9 residues processed: 85 average time/residue: 0.0710 time to fit residues: 8.0507 Evaluate side-chains 82 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 57 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.229662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.182534 restraints weight = 6513.211| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 3.25 r_work: 0.3946 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5889 Z= 0.152 Angle : 0.612 6.032 8169 Z= 0.336 Chirality : 0.043 0.151 878 Planarity : 0.005 0.039 889 Dihedral : 23.129 71.492 1166 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.37 % Allowed : 16.47 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.36), residues: 565 helix: 1.39 (0.41), residues: 156 sheet: -0.20 (0.51), residues: 92 loop : -1.20 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 486 TYR 0.013 0.001 TYR A 671 PHE 0.016 0.002 PHE A 685 TRP 0.004 0.001 TRP A 444 HIS 0.004 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 5889) covalent geometry : angle 0.61183 / 0.34 ( 8169) hydrogen bonds : bond 0.04064 / 2.64 ( 174) hydrogen bonds : angle 4.56985 / 2.97 ( 451) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.145 Fit side-chains REVERT: A 302 GLU cc_start: 0.7839 (tp30) cc_final: 0.7283 (tm-30) REVERT: A 371 GLN cc_start: 0.8290 (mt0) cc_final: 0.8046 (mt0) REVERT: A 440 ARG cc_start: 0.6598 (mmm160) cc_final: 0.5689 (mmm160) REVERT: A 619 MET cc_start: 0.5757 (mtm) cc_final: 0.5418 (mtm) outliers start: 7 outliers final: 3 residues processed: 80 average time/residue: 0.0579 time to fit residues: 6.1057 Evaluate side-chains 73 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 0.0770 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 53 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.237432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.190967 restraints weight = 6461.465| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 3.12 r_work: 0.4081 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5889 Z= 0.138 Angle : 0.587 5.979 8169 Z= 0.323 Chirality : 0.042 0.151 878 Planarity : 0.005 0.040 889 Dihedral : 23.039 66.521 1166 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.98 % Allowed : 18.04 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.36), residues: 565 helix: 1.51 (0.41), residues: 157 sheet: 0.07 (0.52), residues: 88 loop : -1.14 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 382 TYR 0.013 0.001 TYR A 671 PHE 0.015 0.002 PHE A 685 TRP 0.004 0.001 TRP A 456 HIS 0.003 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 5889) covalent geometry : angle 0.58718 / 0.32 ( 8169) hydrogen bonds : bond 0.03918 / 2.56 ( 174) hydrogen bonds : angle 4.39964 / 2.85 ( 451) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.179 Fit side-chains REVERT: A 302 GLU cc_start: 0.7809 (tp30) cc_final: 0.7270 (tm-30) REVERT: A 417 TYR cc_start: 0.7718 (m-80) cc_final: 0.7496 (m-80) REVERT: A 440 ARG cc_start: 0.6701 (mmm160) cc_final: 0.5719 (mmm160) REVERT: A 619 MET cc_start: 0.5839 (mtm) cc_final: 0.5512 (mtm) outliers start: 5 outliers final: 3 residues processed: 78 average time/residue: 0.0755 time to fit residues: 7.7924 Evaluate side-chains 72 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 0.0370 chunk 4 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.231286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.184419 restraints weight = 6431.676| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 3.21 r_work: 0.3969 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5889 Z= 0.151 Angle : 0.609 6.754 8169 Z= 0.332 Chirality : 0.042 0.151 878 Planarity : 0.005 0.042 889 Dihedral : 23.050 69.234 1166 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.37 % Allowed : 18.43 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.36), residues: 565 helix: 1.58 (0.41), residues: 157 sheet: -0.07 (0.51), residues: 92 loop : -1.15 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 686 TYR 0.014 0.002 TYR A 370 PHE 0.019 0.002 PHE A 621 TRP 0.004 0.001 TRP A 456 HIS 0.003 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 5889) covalent geometry : angle 0.60902 / 0.33 ( 8169) hydrogen bonds : bond 0.03878 / 2.53 ( 174) hydrogen bonds : angle 4.43055 / 2.88 ( 451) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.133 Fit side-chains REVERT: A 302 GLU cc_start: 0.7887 (tp30) cc_final: 0.7280 (tm-30) REVERT: A 347 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7854 (mt) REVERT: A 440 ARG cc_start: 0.6569 (mmm160) cc_final: 0.5552 (mmm160) REVERT: A 578 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8060 (t0) REVERT: A 619 MET cc_start: 0.5778 (mtm) cc_final: 0.5411 (mtm) outliers start: 7 outliers final: 4 residues processed: 76 average time/residue: 0.0645 time to fit residues: 6.4749 Evaluate side-chains 75 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 578 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.234284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.187233 restraints weight = 6554.759| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 3.16 r_work: 0.4049 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5889 Z= 0.191 Angle : 0.640 7.586 8169 Z= 0.345 Chirality : 0.044 0.153 878 Planarity : 0.005 0.041 889 Dihedral : 23.119 72.869 1166 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.76 % Allowed : 17.84 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.36), residues: 565 helix: 1.43 (0.41), residues: 157 sheet: -0.87 (0.48), residues: 105 loop : -1.19 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 684 TYR 0.015 0.002 TYR A 639 PHE 0.023 0.002 PHE A 621 TRP 0.003 0.001 TRP A 444 HIS 0.003 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 ( 5889) covalent geometry : angle 0.64029 / 0.35 ( 8169) hydrogen bonds : bond 0.04051 / 2.63 ( 174) hydrogen bonds : angle 4.58349 / 2.97 ( 451) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.167 Fit side-chains REVERT: A 302 GLU cc_start: 0.7814 (tp30) cc_final: 0.7261 (tm-30) REVERT: A 347 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7890 (mt) REVERT: A 417 TYR cc_start: 0.7762 (m-80) cc_final: 0.7500 (m-80) REVERT: A 440 ARG cc_start: 0.6717 (mmm160) cc_final: 0.5728 (mmm160) REVERT: A 578 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8046 (t0) REVERT: A 619 MET cc_start: 0.5909 (mtm) cc_final: 0.5534 (mtm) outliers start: 9 outliers final: 6 residues processed: 81 average time/residue: 0.0600 time to fit residues: 6.4278 Evaluate side-chains 78 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 597 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 0.0980 chunk 53 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.236383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.189860 restraints weight = 6405.642| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 3.12 r_work: 0.4074 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5889 Z= 0.151 Angle : 0.607 5.894 8169 Z= 0.331 Chirality : 0.042 0.150 878 Planarity : 0.005 0.041 889 Dihedral : 23.031 70.106 1166 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 1.57 % Allowed : 18.43 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.36), residues: 565 helix: 1.61 (0.41), residues: 156 sheet: -0.05 (0.51), residues: 92 loop : -1.13 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 684 TYR 0.013 0.001 TYR A 671 PHE 0.024 0.002 PHE A 621 TRP 0.004 0.001 TRP A 456 HIS 0.003 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 5889) covalent geometry : angle 0.60735 / 0.33 ( 8169) hydrogen bonds : bond 0.03827 / 2.50 ( 174) hydrogen bonds : angle 4.47018 / 2.90 ( 451) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1245.17 seconds wall clock time: 21 minutes 57.21 seconds (1317.21 seconds total)