Starting phenix.real_space_refine on Thu Mar 6 09:28:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8i_44346/03_2025/9b8i_44346.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8i_44346/03_2025/9b8i_44346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b8i_44346/03_2025/9b8i_44346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8i_44346/03_2025/9b8i_44346.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8i_44346/03_2025/9b8i_44346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8i_44346/03_2025/9b8i_44346.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.053 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 3551 2.51 5 N 968 2.21 5 O 1067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5610 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 5610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5610 Classifications: {'peptide': 719} Link IDs: {'PCIS': 3, 'PTRANS': 51, 'TRANS': 664} Chain breaks: 3 Time building chain proxies: 4.91, per 1000 atoms: 0.88 Number of scatterers: 5610 At special positions: 0 Unit cell: (92.88, 82.08, 97.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1067 8.00 N 968 7.00 C 3551 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: 1.43 Conformation dependent library (CDL) restraints added in 965.9 milliseconds 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1344 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 11 sheets defined 23.5% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'C' and resid 26 through 42 Processing helix chain 'C' and resid 43 through 58 removed outlier: 3.589A pdb=" N VAL C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 71 removed outlier: 3.712A pdb=" N VAL C 65 " --> pdb=" O ASN C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 90 removed outlier: 3.804A pdb=" N LEU C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 212 removed outlier: 3.560A pdb=" N ALA C 212 " --> pdb=" O PHE C 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 208 through 212' Processing helix chain 'C' and resid 276 through 280 Processing helix chain 'C' and resid 291 through 295 Processing helix chain 'C' and resid 371 through 390 Processing helix chain 'C' and resid 391 through 393 No H-bonds generated for 'chain 'C' and resid 391 through 393' Processing helix chain 'C' and resid 452 through 465 Processing helix chain 'C' and resid 503 through 507 Processing helix chain 'C' and resid 509 through 512 Processing helix chain 'C' and resid 662 through 670 removed outlier: 3.906A pdb=" N PHE C 666 " --> pdb=" O ASP C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 709 Processing helix chain 'C' and resid 774 through 779 Processing helix chain 'C' and resid 815 through 828 Processing helix chain 'C' and resid 828 through 833 Processing sheet with id=AA1, first strand: chain 'C' and resid 201 through 207 removed outlier: 3.640A pdb=" N VAL C 204 " --> pdb=" O LEU C 333 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU C 333 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 206 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS C 241 " --> pdb=" O THR C 334 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN C 336 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL C 239 " --> pdb=" O GLN C 336 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP C 324 " --> pdb=" O THR C 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 201 through 207 removed outlier: 3.640A pdb=" N VAL C 204 " --> pdb=" O LEU C 333 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU C 333 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 206 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS C 241 " --> pdb=" O THR C 334 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN C 336 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL C 239 " --> pdb=" O GLN C 336 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA C 242 " --> pdb=" O ILE C 290 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 226 through 232 removed outlier: 3.704A pdb=" N VAL C 263 " --> pdb=" O GLY C 271 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLY C 271 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU C 265 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 398 through 400 removed outlier: 3.596A pdb=" N ALA C 408 " --> pdb=" O LYS C 444 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY C 450 " --> pdb=" O ALA C 412 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 501 through 502 removed outlier: 3.806A pdb=" N ASP C 542 " --> pdb=" O ASP C 650 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 501 through 502 removed outlier: 3.806A pdb=" N ASP C 542 " --> pdb=" O ASP C 650 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 523 through 528 removed outlier: 3.590A pdb=" N ASN C 611 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN C 570 " --> pdb=" O ILE C 562 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU C 564 " --> pdb=" O PHE C 568 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N PHE C 568 " --> pdb=" O LEU C 564 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 533 through 534 removed outlier: 3.554A pdb=" N ILE C 658 " --> pdb=" O VAL C 858 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 625 through 626 Processing sheet with id=AB1, first strand: chain 'C' and resid 717 through 719 removed outlier: 6.776A pdb=" N THR C 682 " --> pdb=" O THR C 717 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N THR C 719 " --> pdb=" O THR C 682 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THR C 684 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE C 683 " --> pdb=" O MET C 733 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE C 735 " --> pdb=" O ILE C 683 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C 685 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE C 732 " --> pdb=" O ILE C 809 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU C 811 " --> pdb=" O ILE C 732 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE C 734 " --> pdb=" O LEU C 811 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ALA C 813 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C 841 " --> pdb=" O ASN C 848 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 750 through 753 removed outlier: 3.737A pdb=" N TRP C 758 " --> pdb=" O LEU C 751 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER C 757 " --> pdb=" O THR C 785 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR C 785 " --> pdb=" O SER C 757 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL C 759 " --> pdb=" O ARG C 783 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ARG C 783 " --> pdb=" O VAL C 759 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C 761 " --> pdb=" O GLU C 781 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1888 1.35 - 1.46: 1143 1.46 - 1.58: 2655 1.58 - 1.70: 0 1.70 - 1.82: 46 Bond restraints: 5732 Sorted by residual: bond pdb=" N ILE C 295 " pdb=" CA ILE C 295 " ideal model delta sigma weight residual 1.459 1.495 -0.037 1.24e-02 6.50e+03 8.86e+00 bond pdb=" N ASN C 827 " pdb=" CA ASN C 827 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.31e-02 5.83e+03 8.50e+00 bond pdb=" N VAL C 718 " pdb=" CA VAL C 718 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.59e+00 bond pdb=" N ILE C 714 " pdb=" CA ILE C 714 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.30e-02 5.92e+03 7.49e+00 bond pdb=" N LYS C 653 " pdb=" CA LYS C 653 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.26e-02 6.30e+03 7.29e+00 ... (remaining 5727 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 7394 1.19 - 2.38: 288 2.38 - 3.57: 96 3.57 - 4.76: 8 4.76 - 5.94: 7 Bond angle restraints: 7793 Sorted by residual: angle pdb=" N ILE C 223 " pdb=" CA ILE C 223 " pdb=" C ILE C 223 " ideal model delta sigma weight residual 112.96 109.14 3.82 1.00e+00 1.00e+00 1.46e+01 angle pdb=" CA VAL C 47 " pdb=" C VAL C 47 " pdb=" O VAL C 47 " ideal model delta sigma weight residual 120.95 117.32 3.63 1.04e+00 9.25e-01 1.22e+01 angle pdb=" CA THR C 719 " pdb=" CB THR C 719 " pdb=" OG1 THR C 719 " ideal model delta sigma weight residual 109.60 104.65 4.95 1.50e+00 4.44e-01 1.09e+01 angle pdb=" N ARG C 817 " pdb=" CA ARG C 817 " pdb=" C ARG C 817 " ideal model delta sigma weight residual 111.07 107.61 3.46 1.07e+00 8.73e-01 1.05e+01 angle pdb=" CA THR C 717 " pdb=" CB THR C 717 " pdb=" OG1 THR C 717 " ideal model delta sigma weight residual 109.60 104.83 4.77 1.50e+00 4.44e-01 1.01e+01 ... (remaining 7788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 3076 16.90 - 33.80: 321 33.80 - 50.70: 66 50.70 - 67.60: 32 67.60 - 84.50: 5 Dihedral angle restraints: 3500 sinusoidal: 1422 harmonic: 2078 Sorted by residual: dihedral pdb=" CA ASP C 616 " pdb=" CB ASP C 616 " pdb=" CG ASP C 616 " pdb=" OD1 ASP C 616 " ideal model delta sinusoidal sigma weight residual -30.00 -89.86 59.86 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP C 324 " pdb=" CB ASP C 324 " pdb=" CG ASP C 324 " pdb=" OD1 ASP C 324 " ideal model delta sinusoidal sigma weight residual -30.00 -83.15 53.15 1 2.00e+01 2.50e-03 9.61e+00 dihedral pdb=" CA LYS C 487 " pdb=" CB LYS C 487 " pdb=" CG LYS C 487 " pdb=" CD LYS C 487 " ideal model delta sinusoidal sigma weight residual -180.00 -121.09 -58.91 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 3497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 619 0.039 - 0.077: 148 0.077 - 0.116: 87 0.116 - 0.155: 16 0.155 - 0.193: 3 Chirality restraints: 873 Sorted by residual: chirality pdb=" CA VAL C 718 " pdb=" N VAL C 718 " pdb=" C VAL C 718 " pdb=" CB VAL C 718 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CA LEU C 51 " pdb=" N LEU C 51 " pdb=" C LEU C 51 " pdb=" CB LEU C 51 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.43e-01 chirality pdb=" CA ILE C 714 " pdb=" N ILE C 714 " pdb=" C ILE C 714 " pdb=" CB ILE C 714 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 870 not shown) Planarity restraints: 1035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 451 " -0.261 9.50e-02 1.11e+02 1.17e-01 8.40e+00 pdb=" NE ARG C 451 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 451 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG C 451 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 451 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 224 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.10e+00 pdb=" C ASN C 224 " -0.043 2.00e-02 2.50e+03 pdb=" O ASN C 224 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO C 225 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 53 " 0.204 9.50e-02 1.11e+02 9.13e-02 5.16e+00 pdb=" NE ARG C 53 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG C 53 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 53 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 53 " 0.009 2.00e-02 2.50e+03 ... (remaining 1032 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1647 2.82 - 3.34: 4962 3.34 - 3.86: 8833 3.86 - 4.38: 9901 4.38 - 4.90: 17552 Nonbonded interactions: 42895 Sorted by model distance: nonbonded pdb=" ND2 ASN C 342 " pdb=" O MET C 434 " model vdw 2.302 3.120 nonbonded pdb=" O PRO C 441 " pdb=" NZ LYS C 444 " model vdw 2.349 3.120 nonbonded pdb=" O THR C 361 " pdb=" OG1 THR C 361 " model vdw 2.362 3.040 nonbonded pdb=" N GLU C 230 " pdb=" OE1 GLU C 230 " model vdw 2.366 3.120 nonbonded pdb=" NE2 GLN C 28 " pdb=" OD2 ASP C 58 " model vdw 2.379 3.120 ... (remaining 42890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.460 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.160 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5732 Z= 0.238 Angle : 0.590 5.945 7793 Z= 0.375 Chirality : 0.046 0.193 873 Planarity : 0.007 0.117 1035 Dihedral : 15.418 84.495 2156 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.96 % Allowed : 18.91 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.32), residues: 711 helix: 0.72 (0.43), residues: 147 sheet: 0.51 (0.37), residues: 208 loop : -0.01 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 384 HIS 0.001 0.000 HIS C 437 PHE 0.010 0.001 PHE C 704 TYR 0.007 0.001 TYR C 335 ARG 0.005 0.000 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.598 Fit side-chains REVERT: C 235 SER cc_start: 0.9045 (m) cc_final: 0.8833 (t) REVERT: C 355 SER cc_start: 0.9640 (m) cc_final: 0.9409 (t) REVERT: C 519 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8053 (mm-30) REVERT: C 676 MET cc_start: 0.7843 (mmm) cc_final: 0.7578 (mmt) outliers start: 6 outliers final: 6 residues processed: 88 average time/residue: 0.1616 time to fit residues: 19.0067 Evaluate side-chains 79 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 704 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 0.0010 chunk 41 optimal weight: 0.0870 chunk 64 optimal weight: 3.9990 overall best weight: 0.4966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 ASN C 578 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.119156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.093714 restraints weight = 9567.366| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.19 r_work: 0.3059 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5732 Z= 0.144 Angle : 0.509 6.022 7793 Z= 0.259 Chirality : 0.043 0.198 873 Planarity : 0.004 0.042 1035 Dihedral : 5.005 56.498 783 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.56 % Allowed : 19.23 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.31), residues: 711 helix: 1.68 (0.44), residues: 142 sheet: 0.53 (0.36), residues: 206 loop : 0.00 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 384 HIS 0.002 0.000 HIS C 437 PHE 0.010 0.001 PHE C 704 TYR 0.007 0.001 TYR C 619 ARG 0.004 0.000 ARG C 451 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.724 Fit side-chains REVERT: C 235 SER cc_start: 0.9080 (m) cc_final: 0.8768 (t) REVERT: C 355 SER cc_start: 0.9703 (m) cc_final: 0.9371 (t) REVERT: C 452 ASP cc_start: 0.6914 (p0) cc_final: 0.6704 (p0) REVERT: C 519 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8059 (mm-30) outliers start: 16 outliers final: 8 residues processed: 92 average time/residue: 0.1523 time to fit residues: 19.3256 Evaluate side-chains 84 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 704 PHE Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 785 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 45 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 GLN C 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.112649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.087393 restraints weight = 9735.504| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.15 r_work: 0.2963 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 5732 Z= 0.383 Angle : 0.601 6.059 7793 Z= 0.305 Chirality : 0.046 0.193 873 Planarity : 0.005 0.044 1035 Dihedral : 5.260 54.517 779 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.37 % Allowed : 18.91 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.31), residues: 711 helix: 1.61 (0.44), residues: 142 sheet: 0.24 (0.34), residues: 228 loop : -0.07 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 384 HIS 0.005 0.001 HIS C 437 PHE 0.019 0.002 PHE C 704 TYR 0.014 0.002 TYR C 619 ARG 0.004 0.000 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.698 Fit side-chains REVERT: C 53 ARG cc_start: 0.8791 (ttm-80) cc_final: 0.8480 (ttm-80) REVERT: C 254 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8121 (pp) REVERT: C 311 ASP cc_start: 0.8916 (t0) cc_final: 0.8594 (t0) REVERT: C 449 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8116 (t80) REVERT: C 542 ASP cc_start: 0.8103 (m-30) cc_final: 0.7730 (m-30) REVERT: C 726 GLN cc_start: 0.8814 (tp-100) cc_final: 0.8601 (tp40) outliers start: 21 outliers final: 12 residues processed: 92 average time/residue: 0.1558 time to fit residues: 19.7894 Evaluate side-chains 85 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 704 PHE Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 785 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 12 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 0.1980 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.089699 restraints weight = 9773.736| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.18 r_work: 0.3001 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5732 Z= 0.190 Angle : 0.527 6.073 7793 Z= 0.266 Chirality : 0.044 0.185 873 Planarity : 0.004 0.044 1035 Dihedral : 5.145 56.455 779 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.21 % Allowed : 18.91 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.31), residues: 711 helix: 1.73 (0.43), residues: 142 sheet: 0.15 (0.34), residues: 222 loop : 0.06 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 384 HIS 0.003 0.001 HIS C 437 PHE 0.012 0.001 PHE C 704 TYR 0.008 0.001 TYR C 619 ARG 0.003 0.000 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.672 Fit side-chains REVERT: C 53 ARG cc_start: 0.8775 (ttm-80) cc_final: 0.8387 (ttm-80) REVERT: C 311 ASP cc_start: 0.8861 (t0) cc_final: 0.8503 (t0) REVERT: C 361 THR cc_start: 0.9177 (p) cc_final: 0.8845 (t) REVERT: C 449 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.7957 (t80) outliers start: 20 outliers final: 12 residues processed: 92 average time/residue: 0.1596 time to fit residues: 20.0562 Evaluate side-chains 84 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 704 PHE Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 785 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 43 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.086890 restraints weight = 9701.655| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.23 r_work: 0.2954 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5732 Z= 0.323 Angle : 0.582 7.697 7793 Z= 0.292 Chirality : 0.046 0.178 873 Planarity : 0.004 0.046 1035 Dihedral : 5.333 56.006 779 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.69 % Allowed : 18.43 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.31), residues: 711 helix: 1.85 (0.44), residues: 136 sheet: 0.17 (0.34), residues: 228 loop : -0.06 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 863 HIS 0.004 0.001 HIS C 437 PHE 0.018 0.002 PHE C 704 TYR 0.011 0.001 TYR C 619 ARG 0.003 0.000 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.664 Fit side-chains REVERT: C 311 ASP cc_start: 0.8883 (t0) cc_final: 0.8528 (t0) REVERT: C 410 VAL cc_start: 0.9313 (OUTLIER) cc_final: 0.9004 (m) REVERT: C 449 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8069 (t80) REVERT: C 452 ASP cc_start: 0.7171 (p0) cc_final: 0.6942 (p0) outliers start: 23 outliers final: 15 residues processed: 92 average time/residue: 0.1566 time to fit residues: 19.6531 Evaluate side-chains 89 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 704 PHE Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 785 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 27 optimal weight: 0.0980 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 ASN C 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.089854 restraints weight = 9518.248| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.15 r_work: 0.3006 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5732 Z= 0.169 Angle : 0.536 7.153 7793 Z= 0.267 Chirality : 0.044 0.174 873 Planarity : 0.004 0.047 1035 Dihedral : 5.189 57.358 779 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.21 % Allowed : 19.23 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.31), residues: 711 helix: 1.97 (0.44), residues: 136 sheet: 0.18 (0.35), residues: 212 loop : 0.10 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 384 HIS 0.002 0.001 HIS C 437 PHE 0.012 0.001 PHE C 704 TYR 0.008 0.001 TYR C 619 ARG 0.003 0.000 ARG C 582 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.664 Fit side-chains REVERT: C 311 ASP cc_start: 0.8851 (t0) cc_final: 0.8517 (t0) REVERT: C 410 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.9010 (m) REVERT: C 449 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.7937 (t80) REVERT: C 452 ASP cc_start: 0.7056 (p0) cc_final: 0.6785 (p0) outliers start: 20 outliers final: 12 residues processed: 93 average time/residue: 0.1619 time to fit residues: 20.4381 Evaluate side-chains 89 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 704 PHE Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 785 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 9 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.089239 restraints weight = 9631.249| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.15 r_work: 0.2995 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5732 Z= 0.204 Angle : 0.545 6.853 7793 Z= 0.270 Chirality : 0.044 0.165 873 Planarity : 0.004 0.047 1035 Dihedral : 5.188 57.541 779 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.53 % Allowed : 19.71 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.31), residues: 711 helix: 1.97 (0.44), residues: 136 sheet: 0.24 (0.35), residues: 210 loop : 0.08 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 384 HIS 0.003 0.001 HIS C 437 PHE 0.012 0.001 PHE C 704 TYR 0.008 0.001 TYR C 619 ARG 0.003 0.000 ARG C 582 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.604 Fit side-chains REVERT: C 311 ASP cc_start: 0.8852 (t0) cc_final: 0.8509 (t0) REVERT: C 410 VAL cc_start: 0.9326 (OUTLIER) cc_final: 0.9004 (m) REVERT: C 449 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.7866 (t80) REVERT: C 452 ASP cc_start: 0.7108 (p0) cc_final: 0.6823 (p0) outliers start: 22 outliers final: 16 residues processed: 91 average time/residue: 0.1686 time to fit residues: 20.6440 Evaluate side-chains 92 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 704 PHE Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 785 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 56 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 ASN C 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.116228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.090038 restraints weight = 9582.956| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.23 r_work: 0.3010 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5732 Z= 0.162 Angle : 0.523 6.572 7793 Z= 0.259 Chirality : 0.043 0.163 873 Planarity : 0.004 0.047 1035 Dihedral : 5.111 58.754 779 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.72 % Allowed : 20.35 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.31), residues: 711 helix: 2.08 (0.45), residues: 136 sheet: 0.26 (0.36), residues: 200 loop : 0.08 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 384 HIS 0.002 0.000 HIS C 437 PHE 0.010 0.001 PHE C 704 TYR 0.006 0.001 TYR C 619 ARG 0.003 0.000 ARG C 422 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.646 Fit side-chains REVERT: C 311 ASP cc_start: 0.8853 (t0) cc_final: 0.8513 (t0) REVERT: C 410 VAL cc_start: 0.9353 (OUTLIER) cc_final: 0.9012 (m) REVERT: C 452 ASP cc_start: 0.7038 (p0) cc_final: 0.6750 (p0) REVERT: C 519 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7928 (mm-30) REVERT: C 554 VAL cc_start: 0.8153 (OUTLIER) cc_final: 0.7903 (p) REVERT: C 864 PHE cc_start: 0.7562 (p90) cc_final: 0.7126 (p90) outliers start: 17 outliers final: 14 residues processed: 92 average time/residue: 0.1683 time to fit residues: 21.1057 Evaluate side-chains 88 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 704 PHE Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 785 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.115939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.090603 restraints weight = 9563.998| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.18 r_work: 0.3016 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5732 Z= 0.174 Angle : 0.553 11.810 7793 Z= 0.267 Chirality : 0.043 0.163 873 Planarity : 0.004 0.047 1035 Dihedral : 5.120 58.866 779 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.04 % Allowed : 20.35 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.31), residues: 711 helix: 2.07 (0.45), residues: 136 sheet: 0.32 (0.36), residues: 200 loop : 0.07 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 384 HIS 0.002 0.001 HIS C 437 PHE 0.010 0.001 PHE C 704 TYR 0.007 0.001 TYR C 619 ARG 0.003 0.000 ARG C 582 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.729 Fit side-chains REVERT: C 311 ASP cc_start: 0.8852 (t0) cc_final: 0.8513 (t0) REVERT: C 361 THR cc_start: 0.9120 (p) cc_final: 0.8837 (t) REVERT: C 410 VAL cc_start: 0.9359 (OUTLIER) cc_final: 0.9033 (m) REVERT: C 452 ASP cc_start: 0.7083 (p0) cc_final: 0.6714 (p0) REVERT: C 519 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7930 (mm-30) REVERT: C 554 VAL cc_start: 0.8162 (OUTLIER) cc_final: 0.7912 (p) REVERT: C 864 PHE cc_start: 0.7567 (p90) cc_final: 0.7128 (p90) outliers start: 19 outliers final: 17 residues processed: 88 average time/residue: 0.2056 time to fit residues: 25.2906 Evaluate side-chains 91 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 543 MET Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 704 PHE Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 785 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 34 optimal weight: 0.0470 chunk 65 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.0484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.115794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.089673 restraints weight = 9756.355| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.26 r_work: 0.3002 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5732 Z= 0.209 Angle : 0.567 11.431 7793 Z= 0.279 Chirality : 0.044 0.179 873 Planarity : 0.004 0.047 1035 Dihedral : 5.150 58.544 779 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.21 % Allowed : 20.35 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.31), residues: 711 helix: 2.06 (0.45), residues: 136 sheet: 0.33 (0.37), residues: 187 loop : -0.05 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 384 HIS 0.002 0.001 HIS C 437 PHE 0.011 0.001 PHE C 704 TYR 0.008 0.001 TYR C 619 ARG 0.004 0.000 ARG C 582 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.612 Fit side-chains REVERT: C 311 ASP cc_start: 0.8858 (t0) cc_final: 0.8523 (t0) REVERT: C 452 ASP cc_start: 0.7153 (p0) cc_final: 0.6768 (p0) REVERT: C 519 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7945 (mm-30) REVERT: C 554 VAL cc_start: 0.8127 (OUTLIER) cc_final: 0.7885 (p) REVERT: C 749 ASP cc_start: 0.8824 (m-30) cc_final: 0.8611 (m-30) REVERT: C 777 ASP cc_start: 0.8944 (m-30) cc_final: 0.8597 (t70) REVERT: C 864 PHE cc_start: 0.7572 (p90) cc_final: 0.7174 (p90) outliers start: 20 outliers final: 16 residues processed: 86 average time/residue: 0.1555 time to fit residues: 18.3651 Evaluate side-chains 89 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 543 MET Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 704 PHE Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 785 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 7 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.089356 restraints weight = 9725.460| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.24 r_work: 0.2997 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5732 Z= 0.219 Angle : 0.568 11.278 7793 Z= 0.278 Chirality : 0.044 0.165 873 Planarity : 0.004 0.047 1035 Dihedral : 5.187 58.632 779 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.88 % Allowed : 20.99 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.31), residues: 711 helix: 2.05 (0.45), residues: 136 sheet: 0.31 (0.35), residues: 212 loop : -0.03 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 384 HIS 0.003 0.001 HIS C 437 PHE 0.012 0.001 PHE C 704 TYR 0.008 0.001 TYR C 619 ARG 0.004 0.000 ARG C 582 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3234.68 seconds wall clock time: 57 minutes 3.37 seconds (3423.37 seconds total)