Starting phenix.real_space_refine on Thu Jul 2 02:02:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u0j_41781/07_2026/8u0j_41781.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u0j_41781/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8u0j_41781/07_2026/8u0j_41781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u0j_41781/07_2026/8u0j_41781.map" model { file = "/net/cci-nas-00/data/ceres_data/8u0j_41781/07_2026/8u0j_41781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u0j_41781/07_2026/8u0j_41781.cif" } 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-dev-6108/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: 1.29, per 1000 atoms: 0.23 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: 0.51 Conformation dependent library (CDL) restraints added in 162.4 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: 0.44 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: 0.74 Time building geometry restraints manager: 0.67 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: 2.050 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.250 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.540 ------------------------------------------------------------------------------- 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 : 0.962 9.980 8169 Z= 0.639 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 0.96194 / 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 : 0.110 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: 0.0697 time to fit residues: 7.6131 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 : 0.173 ------------------------------------------------------------------------------- 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: 0.5980 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 600 GLN A 643 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.229228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.181887 restraints weight = 6544.885| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 3.25 r_work: 0.3943 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5889 Z= 0.182 Angle : 0.707 8.104 8169 Z= 0.389 Chirality : 0.047 0.215 878 Planarity : 0.006 0.041 889 Dihedral : 23.394 88.443 1166 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.59 % Allowed : 8.82 % Favored : 90.59 % 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: -0.89 (0.34), residues: 565 helix: 0.58 (0.41), residues: 157 sheet: -0.27 (0.51), residues: 95 loop : -1.33 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 382 TYR 0.019 0.002 TYR A 220 PHE 0.021 0.002 PHE A 611 TRP 0.008 0.001 TRP A 585 HIS 0.004 0.001 HIS A 660 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 ( 5889) covalent geometry : angle 0.70745 / 0.39 ( 8169) hydrogen bonds : bond 0.05340 / 3.36 ( 174) hydrogen bonds : angle 4.94646 / 3.26 ( 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 80 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.141 Fit side-chains REVERT: A 302 GLU cc_start: 0.7843 (tp30) cc_final: 0.7324 (tm-30) REVERT: A 440 ARG cc_start: 0.6792 (mmm160) cc_final: 0.5861 (mmm160) outliers start: 3 outliers final: 2 residues processed: 78 average time/residue: 0.0732 time to fit residues: 7.4000 Evaluate side-chains 78 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain A residue 490 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 0.0370 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.0980 chunk 30 optimal weight: 0.0000 chunk 21 optimal weight: 2.9990 overall best weight: 0.3662 ------------------------------------------------------------------------------- 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 = 0.4572 r_free = 0.4572 target = 0.232952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.186539 restraints weight = 6525.657| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 3.26 r_work: 0.3987 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5889 Z= 0.136 Angle : 0.615 6.909 8169 Z= 0.342 Chirality : 0.044 0.154 878 Planarity : 0.005 0.043 889 Dihedral : 23.196 66.625 1166 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.18 % Allowed : 10.20 % Favored : 88.63 % 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: -0.51 (0.35), residues: 565 helix: 1.05 (0.41), residues: 158 sheet: 0.09 (0.53), residues: 91 loop : -1.23 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 615 TYR 0.013 0.001 TYR A 671 PHE 0.017 0.002 PHE A 685 TRP 0.007 0.001 TRP A 444 HIS 0.003 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 ( 5889) covalent geometry : angle 0.61544 / 0.34 ( 8169) hydrogen bonds : bond 0.04421 / 2.91 ( 174) hydrogen bonds : angle 4.47267 / 2.91 ( 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 92 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.128 Fit side-chains REVERT: A 302 GLU cc_start: 0.7855 (tp30) cc_final: 0.7168 (tm-30) REVERT: A 371 GLN cc_start: 0.8257 (mt0) cc_final: 0.7999 (mt0) REVERT: A 440 ARG cc_start: 0.6615 (mmm160) cc_final: 0.5762 (mmm160) REVERT: A 619 MET cc_start: 0.5710 (mtm) cc_final: 0.5456 (mtm) outliers start: 6 outliers final: 3 residues processed: 88 average time/residue: 0.0663 time to fit residues: 7.5748 Evaluate side-chains 79 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 57 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 6 optimal weight: 0.0270 chunk 4 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 48 optimal weight: 0.0370 chunk 36 optimal weight: 0.8980 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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 = 0.4571 r_free = 0.4571 target = 0.232897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.186354 restraints weight = 6485.737| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 3.23 r_work: 0.3993 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1715 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= 0.137 Angle : 0.603 6.943 8169 Z= 0.334 Chirality : 0.042 0.149 878 Planarity : 0.005 0.039 889 Dihedral : 23.185 67.635 1166 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.98 % Allowed : 13.14 % Favored : 85.88 % 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: -0.32 (0.36), residues: 565 helix: 1.26 (0.41), residues: 158 sheet: 0.13 (0.53), residues: 91 loop : -1.11 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 341 TYR 0.015 0.001 TYR A 491 PHE 0.015 0.002 PHE A 685 TRP 0.006 0.001 TRP A 444 HIS 0.003 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 5889) covalent geometry : angle 0.60330 / 0.33 ( 8169) hydrogen bonds : bond 0.04099 / 2.67 ( 174) hydrogen bonds : angle 4.42358 / 2.86 ( 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 86 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.192 Fit side-chains REVERT: A 302 GLU cc_start: 0.7844 (tp30) cc_final: 0.7184 (tm-30) REVERT: A 371 GLN cc_start: 0.8253 (mt0) cc_final: 0.8027 (mt0) REVERT: A 440 ARG cc_start: 0.6567 (mmm160) cc_final: 0.5796 (mmm160) REVERT: A 540 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8267 (tm-30) REVERT: A 619 MET cc_start: 0.5787 (mtm) cc_final: 0.5470 (mtm) outliers start: 5 outliers final: 2 residues processed: 84 average time/residue: 0.0774 time to fit residues: 8.2725 Evaluate side-chains 73 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 490 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.228834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.181804 restraints weight = 6556.044| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 3.23 r_work: 0.3942 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5889 Z= 0.181 Angle : 0.633 6.098 8169 Z= 0.345 Chirality : 0.045 0.180 878 Planarity : 0.005 0.043 889 Dihedral : 23.257 73.365 1166 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.76 % Allowed : 13.14 % Favored : 85.10 % 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: -0.43 (0.36), residues: 565 helix: 1.29 (0.41), residues: 156 sheet: -0.08 (0.52), residues: 92 loop : -1.19 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 367 TYR 0.015 0.002 TYR A 639 PHE 0.013 0.002 PHE A 685 TRP 0.006 0.001 TRP A 444 HIS 0.007 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 5889) covalent geometry : angle 0.63256 / 0.34 ( 8169) hydrogen bonds : bond 0.04281 / 2.77 ( 174) hydrogen bonds : angle 4.53727 / 2.95 ( 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 88 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.178 Fit side-chains REVERT: A 302 GLU cc_start: 0.7872 (tp30) cc_final: 0.7272 (tm-30) REVERT: A 371 GLN cc_start: 0.8266 (mt0) cc_final: 0.7967 (mm-40) REVERT: A 440 ARG cc_start: 0.6704 (mmm160) cc_final: 0.5843 (mmm160) REVERT: A 509 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8019 (mt) REVERT: A 619 MET cc_start: 0.5837 (mtm) cc_final: 0.5510 (mtm) outliers start: 9 outliers final: 7 residues processed: 83 average time/residue: 0.0743 time to fit residues: 7.9743 Evaluate side-chains 79 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 PHE 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: 0.7980 chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 654 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.226811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.179504 restraints weight = 6502.325| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 3.21 r_work: 0.3919 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1877 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= 0.211 Angle : 0.656 6.028 8169 Z= 0.356 Chirality : 0.045 0.157 878 Planarity : 0.005 0.044 889 Dihedral : 23.284 75.351 1166 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.35 % Allowed : 13.33 % Favored : 84.31 % 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: -0.57 (0.35), residues: 565 helix: 1.17 (0.41), residues: 157 sheet: -0.26 (0.51), residues: 92 loop : -1.25 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 486 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 0.00482 / 0.21 ( 5889) covalent geometry : angle 0.65648 / 0.36 ( 8169) hydrogen bonds : bond 0.04301 / 2.74 ( 174) hydrogen bonds : angle 4.69780 / 3.05 ( 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: 12 poor density : 78 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7884 (tp30) cc_final: 0.7320 (tm-30) REVERT: A 371 GLN cc_start: 0.8276 (mt0) cc_final: 0.7969 (mm-40) REVERT: A 440 ARG cc_start: 0.6783 (mmm160) cc_final: 0.5908 (mmm160) REVERT: A 509 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8022 (mt) REVERT: A 611 PHE cc_start: 0.7332 (t80) cc_final: 0.7096 (t80) REVERT: A 619 MET cc_start: 0.5860 (mtm) cc_final: 0.5497 (mtm) outliers start: 12 outliers final: 10 residues processed: 83 average time/residue: 0.0652 time to fit residues: 7.0122 Evaluate side-chains 84 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 241 GLU 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 468 ASP Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 632 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: 0.9990 chunk 41 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 39 optimal weight: 0.0570 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 = 0.229540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.182346 restraints weight = 6513.509| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 3.23 r_work: 0.3947 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5889 Z= 0.163 Angle : 0.613 6.228 8169 Z= 0.336 Chirality : 0.043 0.152 878 Planarity : 0.005 0.043 889 Dihedral : 23.179 70.991 1166 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.57 % Allowed : 15.88 % Favored : 82.55 % 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: -0.47 (0.35), residues: 565 helix: 1.31 (0.41), residues: 157 sheet: -0.16 (0.52), residues: 92 loop : -1.23 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 341 TYR 0.014 0.002 TYR A 671 PHE 0.027 0.002 PHE A 611 TRP 0.004 0.001 TRP A 456 HIS 0.004 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 5889) covalent geometry : angle 0.61297 / 0.34 ( 8169) hydrogen bonds : bond 0.04050 / 2.60 ( 174) hydrogen bonds : angle 4.53709 / 2.95 ( 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 90 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7857 (tp30) cc_final: 0.7294 (tm-30) REVERT: A 371 GLN cc_start: 0.8279 (mt0) cc_final: 0.8047 (mt0) REVERT: A 440 ARG cc_start: 0.6720 (mmm160) cc_final: 0.5787 (mmm160) REVERT: A 611 PHE cc_start: 0.7356 (t80) cc_final: 0.7089 (t80) REVERT: A 619 MET cc_start: 0.5844 (mtm) cc_final: 0.5488 (mtm) outliers start: 8 outliers final: 5 residues processed: 86 average time/residue: 0.0613 time to fit residues: 6.8327 Evaluate side-chains 81 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4632 r_free = 0.4632 target = 0.235061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.188230 restraints weight = 6456.019| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 3.11 r_work: 0.4053 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5889 Z= 0.169 Angle : 0.616 5.905 8169 Z= 0.337 Chirality : 0.043 0.154 878 Planarity : 0.005 0.044 889 Dihedral : 23.175 70.765 1166 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.76 % Allowed : 15.88 % Favored : 82.35 % 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: -0.44 (0.35), residues: 565 helix: 1.34 (0.41), residues: 157 sheet: -0.19 (0.52), residues: 92 loop : -1.20 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 341 TYR 0.013 0.002 TYR A 671 PHE 0.027 0.002 PHE A 611 TRP 0.004 0.001 TRP A 456 HIS 0.004 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 5889) covalent geometry : angle 0.61609 / 0.34 ( 8169) hydrogen bonds : bond 0.04047 / 2.61 ( 174) hydrogen bonds : angle 4.55647 / 2.96 ( 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 84 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7774 (tp30) cc_final: 0.7273 (tm-30) REVERT: A 440 ARG cc_start: 0.6798 (mmm160) cc_final: 0.5855 (mmm160) REVERT: A 611 PHE cc_start: 0.7315 (t80) cc_final: 0.7048 (t80) REVERT: A 619 MET cc_start: 0.5951 (mtm) cc_final: 0.5604 (mtm) outliers start: 9 outliers final: 6 residues processed: 82 average time/residue: 0.0607 time to fit residues: 6.4466 Evaluate side-chains 77 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 21 optimal weight: 0.8980 chunk 44 optimal weight: 0.0000 chunk 4 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 19 optimal weight: 0.0970 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 482 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.237346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.190989 restraints weight = 6404.035| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 3.10 r_work: 0.4082 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2228 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= 0.142 Angle : 0.607 6.920 8169 Z= 0.332 Chirality : 0.043 0.152 878 Planarity : 0.005 0.045 889 Dihedral : 23.099 68.756 1166 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.18 % Allowed : 17.25 % Favored : 81.57 % 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: -0.30 (0.36), residues: 565 helix: 1.52 (0.41), residues: 157 sheet: -0.04 (0.52), residues: 92 loop : -1.19 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 341 TYR 0.015 0.002 TYR A 370 PHE 0.024 0.002 PHE A 611 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 0.00310 / 0.14 ( 5889) covalent geometry : angle 0.60689 / 0.33 ( 8169) hydrogen bonds : bond 0.03855 / 2.50 ( 174) hydrogen bonds : angle 4.44835 / 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 83 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7765 (tp30) cc_final: 0.7258 (tm-30) REVERT: A 341 ARG cc_start: 0.7171 (mtm110) cc_final: 0.6553 (mtp180) REVERT: A 440 ARG cc_start: 0.6769 (mmm160) cc_final: 0.5719 (mmm160) REVERT: A 578 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8046 (t0) REVERT: A 611 PHE cc_start: 0.7275 (t80) cc_final: 0.7026 (t80) REVERT: A 619 MET cc_start: 0.5824 (mtm) cc_final: 0.5505 (mtm) outliers start: 6 outliers final: 5 residues processed: 80 average time/residue: 0.0771 time to fit residues: 7.8088 Evaluate side-chains 79 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 656 PHE 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: 1.9990 chunk 37 optimal weight: 0.0770 chunk 28 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 19 optimal weight: 0.0770 chunk 12 optimal weight: 0.8980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 482 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.237856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.191276 restraints weight = 6543.924| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 3.16 r_work: 0.4082 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5889 Z= 0.146 Angle : 0.602 6.752 8169 Z= 0.329 Chirality : 0.042 0.152 878 Planarity : 0.005 0.043 889 Dihedral : 23.074 68.596 1166 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 1.37 % Allowed : 17.84 % Favored : 80.78 % 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: 1.55 (0.41), residues: 157 sheet: 0.04 (0.52), residues: 92 loop : -1.14 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 686 TYR 0.012 0.001 TYR A 491 PHE 0.024 0.002 PHE A 611 TRP 0.004 0.001 TRP A 492 HIS 0.003 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 5889) covalent geometry : angle 0.60172 / 0.33 ( 8169) hydrogen bonds : bond 0.03814 / 2.48 ( 174) hydrogen bonds : angle 4.45471 / 2.87 ( 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 82 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.111 Fit side-chains REVERT: A 302 GLU cc_start: 0.7827 (tp30) cc_final: 0.7273 (tm-30) REVERT: A 341 ARG cc_start: 0.7202 (mtm110) cc_final: 0.6638 (mtp180) REVERT: A 440 ARG cc_start: 0.6734 (mmm160) cc_final: 0.5535 (mmm160) REVERT: A 578 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8078 (t0) REVERT: A 611 PHE cc_start: 0.7274 (t80) cc_final: 0.7070 (t80) REVERT: A 619 MET cc_start: 0.5793 (mtm) cc_final: 0.5463 (mtm) outliers start: 7 outliers final: 6 residues processed: 78 average time/residue: 0.0673 time to fit residues: 6.7739 Evaluate side-chains 77 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 0.0020 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 53 optimal weight: 0.0070 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 0.1980 overall best weight: 0.3206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 482 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.240929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.195128 restraints weight = 6411.320| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 3.11 r_work: 0.4124 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5889 Z= 0.125 Angle : 0.580 6.045 8169 Z= 0.318 Chirality : 0.041 0.150 878 Planarity : 0.005 0.043 889 Dihedral : 22.984 67.086 1166 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.37 % Allowed : 17.65 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.10 (0.36), residues: 565 helix: 1.70 (0.41), residues: 157 sheet: 0.01 (0.51), residues: 92 loop : -1.04 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 486 TYR 0.012 0.001 TYR A 137 PHE 0.021 0.002 PHE A 611 TRP 0.005 0.001 TRP A 456 HIS 0.002 0.000 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 5889) covalent geometry : angle 0.58008 / 0.32 ( 8169) hydrogen bonds : bond 0.03608 / 2.36 ( 174) hydrogen bonds : angle 4.30007 / 2.77 ( 451) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1177.04 seconds wall clock time: 20 minutes 52.60 seconds (1252.60 seconds total)