Starting phenix.real_space_refine on Thu Mar 6 05:53:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oua_20200/03_2025/6oua_20200.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oua_20200/03_2025/6oua_20200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oua_20200/03_2025/6oua_20200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oua_20200/03_2025/6oua_20200.map" model { file = "/net/cci-nas-00/data/ceres_data/6oua_20200/03_2025/6oua_20200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oua_20200/03_2025/6oua_20200.cif" } resolution = 4.18 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= 0.003 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 25 5.16 5 C 3340 2.51 5 N 885 2.21 5 O 958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 5208 Number of models: 1 Model: "" Number of chains: 3 Chain: "I" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3105 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "H" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1100 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "K" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1003 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Time building chain proxies: 3.75, per 1000 atoms: 0.72 Number of scatterers: 5208 At special positions: 0 Unit cell: (111.35, 88.4, 77.35, 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 25 16.00 O 958 8.00 N 885 7.00 C 3340 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: 1.16 Conformation dependent library (CDL) restraints added in 593.8 milliseconds 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 0 sheets defined 62.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'I' and resid 342 through 348 removed outlier: 4.690A pdb=" N ASN I 348 " --> pdb=" O ILE I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 368 removed outlier: 3.809A pdb=" N GLU I 358 " --> pdb=" O SER I 354 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE I 361 " --> pdb=" O TYR I 357 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE I 368 " --> pdb=" O LEU I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 377 removed outlier: 4.248A pdb=" N GLU I 377 " --> pdb=" O THR I 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 374 through 377' Processing helix chain 'I' and resid 378 through 386 Processing helix chain 'I' and resid 389 through 397 removed outlier: 5.069A pdb=" N ARG I 395 " --> pdb=" O LYS I 391 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE I 396 " --> pdb=" O LEU I 392 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE I 397 " --> pdb=" O SER I 393 " (cutoff:3.500A) Processing helix chain 'I' and resid 412 through 420 Processing helix chain 'I' and resid 432 through 448 removed outlier: 3.922A pdb=" N VAL I 437 " --> pdb=" O ARG I 433 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LYS I 438 " --> pdb=" O GLU I 434 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP I 446 " --> pdb=" O SER I 442 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR I 448 " --> pdb=" O PHE I 444 " (cutoff:3.500A) Processing helix chain 'I' and resid 458 through 475 removed outlier: 4.032A pdb=" N THR I 470 " --> pdb=" O LEU I 466 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN I 471 " --> pdb=" O GLN I 467 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP I 475 " --> pdb=" O ASN I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 494 removed outlier: 3.944A pdb=" N THR I 484 " --> pdb=" O ALA I 480 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N HIS I 487 " --> pdb=" O LEU I 483 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP I 488 " --> pdb=" O THR I 484 " (cutoff:3.500A) Processing helix chain 'I' and resid 508 through 525 removed outlier: 4.190A pdb=" N LEU I 519 " --> pdb=" O SER I 515 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN I 525 " --> pdb=" O GLN I 521 " (cutoff:3.500A) Processing helix chain 'I' and resid 531 through 535 Processing helix chain 'I' and resid 550 through 565 removed outlier: 3.908A pdb=" N LEU I 554 " --> pdb=" O ASP I 550 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU I 561 " --> pdb=" O ALA I 557 " (cutoff:3.500A) Processing helix chain 'I' and resid 578 through 593 removed outlier: 4.246A pdb=" N ASN I 590 " --> pdb=" O MET I 586 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 613 Processing helix chain 'I' and resid 614 through 618 removed outlier: 3.821A pdb=" N ASN I 617 " --> pdb=" O ILE I 614 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU I 618 " --> pdb=" O LEU I 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 614 through 618' Processing helix chain 'I' and resid 625 through 630 removed outlier: 3.868A pdb=" N LYS I 629 " --> pdb=" O PHE I 625 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE I 630 " --> pdb=" O LYS I 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 625 through 630' Processing helix chain 'I' and resid 641 through 653 removed outlier: 3.955A pdb=" N ARG I 649 " --> pdb=" O ILE I 645 " (cutoff:3.500A) Processing helix chain 'I' and resid 668 through 675 Processing helix chain 'I' and resid 692 through 697 Processing helix chain 'I' and resid 697 through 705 removed outlier: 4.891A pdb=" N HIS I 703 " --> pdb=" O LYS I 699 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER I 705 " --> pdb=" O LEU I 701 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 39 removed outlier: 3.669A pdb=" N ILE H 28 " --> pdb=" O ARG H 24 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP H 31 " --> pdb=" O LEU H 27 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR H 34 " --> pdb=" O LEU H 30 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU H 35 " --> pdb=" O ASP H 31 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS H 39 " --> pdb=" O LEU H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 66 removed outlier: 4.148A pdb=" N ARG H 56 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS H 57 " --> pdb=" O LEU H 53 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE H 61 " --> pdb=" O HIS H 57 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR H 66 " --> pdb=" O ASN H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 90 Processing helix chain 'H' and resid 102 through 129 removed outlier: 3.802A pdb=" N SER H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU H 120 " --> pdb=" O GLU H 116 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU H 123 " --> pdb=" O ALA H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'K' and resid 6 through 32 removed outlier: 4.036A pdb=" N LYS K 13 " --> pdb=" O ASP K 9 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN K 18 " --> pdb=" O ASN K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 38 removed outlier: 3.693A pdb=" N THR K 37 " --> pdb=" O ASP K 34 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS K 38 " --> pdb=" O GLU K 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 34 through 38' Processing helix chain 'K' and resid 49 through 57 removed outlier: 3.515A pdb=" N THR K 54 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N GLU K 55 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU K 56 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU K 57 " --> pdb=" O PHE K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 75 removed outlier: 3.554A pdb=" N LEU K 74 " --> pdb=" O GLY K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 107 removed outlier: 4.432A pdb=" N SER K 91 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU K 106 " --> pdb=" O ALA K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 128 removed outlier: 3.595A pdb=" N ASP K 113 " --> pdb=" O ASN K 109 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS K 115 " --> pdb=" O ASN K 111 " (cutoff:3.500A) 218 hydrogen bonds defined for protein. 645 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: 1.10 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1546 1.34 - 1.45: 867 1.45 - 1.57: 2850 1.57 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 5305 Sorted by residual: bond pdb=" CA PHE I 630 " pdb=" CB PHE I 630 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.33e-02 5.65e+03 1.08e+01 bond pdb=" CB GLU H 16 " pdb=" CG GLU H 16 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.49e+00 bond pdb=" C LYS K 46 " pdb=" N PRO K 47 " ideal model delta sigma weight residual 1.334 1.386 -0.053 2.34e-02 1.83e+03 5.04e+00 bond pdb=" N ASP I 351 " pdb=" CA ASP I 351 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.76e+00 bond pdb=" CB LEU I 466 " pdb=" CG LEU I 466 " ideal model delta sigma weight residual 1.530 1.490 0.040 2.00e-02 2.50e+03 4.02e+00 ... (remaining 5300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 6900 3.18 - 6.35: 206 6.35 - 9.53: 46 9.53 - 12.71: 6 12.71 - 15.88: 1 Bond angle restraints: 7159 Sorted by residual: angle pdb=" C CYS I 401 " pdb=" N ASN I 402 " pdb=" CA ASN I 402 " ideal model delta sigma weight residual 121.54 130.86 -9.32 1.91e+00 2.74e-01 2.38e+01 angle pdb=" C ASP I 389 " pdb=" N ASN I 390 " pdb=" CA ASN I 390 " ideal model delta sigma weight residual 121.54 130.30 -8.76 1.91e+00 2.74e-01 2.11e+01 angle pdb=" CA LEU H 90 " pdb=" CB LEU H 90 " pdb=" CG LEU H 90 " ideal model delta sigma weight residual 116.30 132.18 -15.88 3.50e+00 8.16e-02 2.06e+01 angle pdb=" CA ILE I 620 " pdb=" CB ILE I 620 " pdb=" CG2 ILE I 620 " ideal model delta sigma weight residual 110.50 118.10 -7.60 1.70e+00 3.46e-01 2.00e+01 angle pdb=" C HIS H 41 " pdb=" N ALA H 42 " pdb=" CA ALA H 42 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.97e+01 ... (remaining 7154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 2859 15.45 - 30.90: 297 30.90 - 46.36: 71 46.36 - 61.81: 14 61.81 - 77.26: 6 Dihedral angle restraints: 3247 sinusoidal: 1354 harmonic: 1893 Sorted by residual: dihedral pdb=" CA ILE I 636 " pdb=" C ILE I 636 " pdb=" N PRO I 637 " pdb=" CA PRO I 637 " ideal model delta harmonic sigma weight residual -180.00 -119.27 -60.73 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA ASP K 68 " pdb=" C ASP K 68 " pdb=" N PRO K 69 " pdb=" CA PRO K 69 " ideal model delta harmonic sigma weight residual 180.00 152.87 27.13 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA TYR I 340 " pdb=" C TYR I 340 " pdb=" N SER I 341 " pdb=" CA SER I 341 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 3244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 679 0.088 - 0.177: 125 0.177 - 0.265: 17 0.265 - 0.353: 2 0.353 - 0.442: 1 Chirality restraints: 824 Sorted by residual: chirality pdb=" CB ILE K 36 " pdb=" CA ILE K 36 " pdb=" CG1 ILE K 36 " pdb=" CG2 ILE K 36 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" CB ILE I 636 " pdb=" CA ILE I 636 " pdb=" CG1 ILE I 636 " pdb=" CG2 ILE I 636 " both_signs ideal model delta sigma weight residual False 2.64 2.98 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB ILE H 44 " pdb=" CA ILE H 44 " pdb=" CG1 ILE H 44 " pdb=" CG2 ILE H 44 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 821 not shown) Planarity restraints: 898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE I 636 " 0.060 5.00e-02 4.00e+02 9.20e-02 1.36e+01 pdb=" N PRO I 637 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO I 637 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO I 637 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP K 68 " 0.044 5.00e-02 4.00e+02 6.54e-02 6.85e+00 pdb=" N PRO K 69 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO K 69 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO K 69 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 550 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO I 551 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO I 551 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO I 551 " 0.035 5.00e-02 4.00e+02 ... (remaining 895 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1512 2.82 - 3.34: 4911 3.34 - 3.86: 7947 3.86 - 4.38: 8702 4.38 - 4.90: 14301 Nonbonded interactions: 37373 Sorted by model distance: nonbonded pdb=" O LEU I 552 " pdb=" OG SER I 555 " model vdw 2.294 3.040 nonbonded pdb=" NH2 ARG H 118 " pdb=" OE1 GLN K 107 " model vdw 2.309 3.120 nonbonded pdb=" OD1 ASP I 549 " pdb=" OG1 THR I 634 " model vdw 2.312 3.040 nonbonded pdb=" OD2 ASP H 31 " pdb=" NH2 ARG H 56 " model vdw 2.322 3.120 nonbonded pdb=" NH2 ARG H 71 " pdb=" OD2 ASP K 68 " model vdw 2.331 3.120 ... (remaining 37368 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 group one per residue 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: 3.770 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.570 Find NCS groups from input model: 0.050 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 0.076 5305 Z= 0.496 Angle : 1.373 15.883 7159 Z= 0.694 Chirality : 0.071 0.442 824 Planarity : 0.008 0.092 898 Dihedral : 13.972 77.258 2007 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.32 % Allowed : 17.43 % Favored : 82.25 % Rotamer: Outliers : 2.35 % Allowed : 10.42 % Favored : 87.23 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -5.89 (0.23), residues: 631 helix: -3.43 (0.17), residues: 371 sheet: None (None), residues: 0 loop : -4.59 (0.31), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP I 446 HIS 0.007 0.002 HIS I 678 PHE 0.033 0.003 PHE I 604 TYR 0.022 0.003 TYR I 464 ARG 0.005 0.001 ARG I 697 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 367 CYS cc_start: 0.8447 (p) cc_final: 0.8057 (p) REVERT: I 668 GLU cc_start: 0.8605 (pp20) cc_final: 0.8396 (pp20) REVERT: I 677 HIS cc_start: 0.8516 (t70) cc_final: 0.8257 (t-90) REVERT: H 34 TYR cc_start: 0.8464 (t80) cc_final: 0.8257 (t80) REVERT: H 99 GLU cc_start: 0.7937 (pm20) cc_final: 0.7598 (mt-10) REVERT: H 100 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7817 (tm) REVERT: K 38 LYS cc_start: 0.8380 (pttp) cc_final: 0.8048 (mttm) REVERT: K 77 ASN cc_start: 0.8172 (t0) cc_final: 0.7668 (t0) outliers start: 14 outliers final: 4 residues processed: 147 average time/residue: 0.2021 time to fit residues: 36.8318 Evaluate side-chains 103 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 371 GLN I 501 ASN I 581 GLN I 666 ASN H 13 GLN H 58 GLN ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN H 111 HIS K 107 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.139435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.117978 restraints weight = 9436.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.121017 restraints weight = 5890.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.123119 restraints weight = 4155.786| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5305 Z= 0.208 Angle : 0.777 7.154 7159 Z= 0.404 Chirality : 0.048 0.226 824 Planarity : 0.006 0.101 898 Dihedral : 6.864 51.708 682 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.15 % Favored : 86.85 % Rotamer: Outliers : 0.34 % Allowed : 5.04 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -4.37 (0.28), residues: 631 helix: -2.00 (0.23), residues: 376 sheet: None (None), residues: 0 loop : -4.32 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 472 HIS 0.002 0.001 HIS H 19 PHE 0.022 0.002 PHE I 604 TYR 0.012 0.001 TYR I 584 ARG 0.005 0.001 ARG K 119 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 434 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8020 (mp0) REVERT: I 668 GLU cc_start: 0.8790 (pp20) cc_final: 0.8528 (pp20) REVERT: I 677 HIS cc_start: 0.8200 (t70) cc_final: 0.7693 (t-90) REVERT: I 691 ASN cc_start: 0.8310 (t0) cc_final: 0.8093 (t0) REVERT: H 37 ARG cc_start: 0.7939 (ttm170) cc_final: 0.7324 (mtt180) REVERT: H 99 GLU cc_start: 0.7898 (pm20) cc_final: 0.7463 (mt-10) REVERT: K 21 ASN cc_start: 0.7024 (m110) cc_final: 0.6820 (m-40) REVERT: K 35 GLU cc_start: 0.8633 (tp30) cc_final: 0.7754 (tp30) REVERT: K 77 ASN cc_start: 0.8137 (t0) cc_final: 0.7669 (t0) REVERT: K 93 MET cc_start: 0.7276 (mmp) cc_final: 0.6714 (ttm) REVERT: K 103 MET cc_start: 0.7363 (mmp) cc_final: 0.6484 (tmm) outliers start: 2 outliers final: 0 residues processed: 152 average time/residue: 0.2614 time to fit residues: 50.9079 Evaluate side-chains 103 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 47 optimal weight: 0.0010 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.0970 chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 487 HIS H 57 HIS ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 GLN K 123 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.143319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.123172 restraints weight = 9320.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.126183 restraints weight = 5707.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128333 restraints weight = 3973.818| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5305 Z= 0.177 Angle : 0.738 9.997 7159 Z= 0.373 Chirality : 0.046 0.299 824 Planarity : 0.005 0.097 898 Dihedral : 6.201 48.131 682 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.00 % Favored : 87.00 % Rotamer: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -3.48 (0.31), residues: 631 helix: -1.20 (0.25), residues: 379 sheet: None (None), residues: 0 loop : -4.12 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 89 HIS 0.001 0.000 HIS I 694 PHE 0.019 0.001 PHE I 604 TYR 0.023 0.001 TYR I 619 ARG 0.003 0.000 ARG K 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 434 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7998 (mp0) REVERT: I 677 HIS cc_start: 0.7830 (t70) cc_final: 0.7582 (t-90) REVERT: I 691 ASN cc_start: 0.8315 (t0) cc_final: 0.8073 (t0) REVERT: H 52 LEU cc_start: 0.8641 (mm) cc_final: 0.8233 (tp) REVERT: H 78 ASN cc_start: 0.5960 (m-40) cc_final: 0.5752 (m-40) REVERT: H 80 ASN cc_start: 0.7180 (t0) cc_final: 0.6848 (t0) REVERT: H 99 GLU cc_start: 0.7732 (pm20) cc_final: 0.7507 (mt-10) REVERT: H 100 LEU cc_start: 0.7931 (tp) cc_final: 0.7676 (tt) REVERT: K 21 ASN cc_start: 0.6915 (m110) cc_final: 0.6698 (m110) REVERT: K 61 MET cc_start: 0.8170 (ptp) cc_final: 0.7886 (ptp) REVERT: K 77 ASN cc_start: 0.8070 (t0) cc_final: 0.7531 (t0) REVERT: K 93 MET cc_start: 0.7146 (mmp) cc_final: 0.6413 (ttm) REVERT: K 103 MET cc_start: 0.7383 (mmp) cc_final: 0.6611 (tmm) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2929 time to fit residues: 54.2307 Evaluate side-chains 104 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 18 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 501 ASN H 58 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.151778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.133911 restraints weight = 8902.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.136403 restraints weight = 5814.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.138375 restraints weight = 4249.942| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5305 Z= 0.212 Angle : 0.734 7.705 7159 Z= 0.374 Chirality : 0.048 0.241 824 Planarity : 0.005 0.090 898 Dihedral : 5.958 46.762 682 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.63 % Favored : 86.37 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -3.01 (0.32), residues: 631 helix: -0.78 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -4.01 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 686 HIS 0.002 0.001 HIS H 57 PHE 0.016 0.002 PHE K 25 TYR 0.015 0.001 TYR H 34 ARG 0.002 0.000 ARG K 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 668 GLU cc_start: 0.8593 (pp20) cc_final: 0.8284 (pp20) REVERT: I 699 LYS cc_start: 0.7120 (mmpt) cc_final: 0.5872 (tptt) REVERT: H 8 GLN cc_start: 0.8007 (pp30) cc_final: 0.7423 (pp30) REVERT: H 52 LEU cc_start: 0.8751 (mm) cc_final: 0.8404 (tp) REVERT: H 80 ASN cc_start: 0.6703 (t0) cc_final: 0.6438 (t0) REVERT: K 21 ASN cc_start: 0.6899 (m110) cc_final: 0.6679 (m110) REVERT: K 25 PHE cc_start: 0.8060 (m-80) cc_final: 0.7859 (m-80) REVERT: K 77 ASN cc_start: 0.8066 (t0) cc_final: 0.7529 (t0) REVERT: K 103 MET cc_start: 0.7650 (mmp) cc_final: 0.6960 (tmm) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.3004 time to fit residues: 50.8838 Evaluate side-chains 102 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 677 HIS ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.145954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.125762 restraints weight = 8854.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.128963 restraints weight = 5466.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.131204 restraints weight = 3812.575| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5305 Z= 0.199 Angle : 0.722 8.373 7159 Z= 0.364 Chirality : 0.047 0.241 824 Planarity : 0.005 0.092 898 Dihedral : 5.805 48.525 682 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.00 % Favored : 87.00 % Rotamer: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -2.76 (0.33), residues: 631 helix: -0.55 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -3.95 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 89 HIS 0.007 0.001 HIS I 677 PHE 0.013 0.001 PHE K 72 TYR 0.015 0.001 TYR I 711 ARG 0.006 0.000 ARG H 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 699 LYS cc_start: 0.6754 (mmpt) cc_final: 0.5613 (tptt) REVERT: H 52 LEU cc_start: 0.8723 (mm) cc_final: 0.8340 (tp) REVERT: H 80 ASN cc_start: 0.6967 (t0) cc_final: 0.6684 (t0) REVERT: K 21 ASN cc_start: 0.6871 (m110) cc_final: 0.6641 (m110) REVERT: K 61 MET cc_start: 0.8189 (ptp) cc_final: 0.7857 (ptp) REVERT: K 77 ASN cc_start: 0.8089 (t0) cc_final: 0.7563 (t0) REVERT: K 103 MET cc_start: 0.7448 (mmp) cc_final: 0.6848 (tmm) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2581 time to fit residues: 40.2723 Evaluate side-chains 99 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 39 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 0.0370 chunk 38 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 0.0980 chunk 58 optimal weight: 3.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 581 GLN ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.155348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.138237 restraints weight = 8735.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.140846 restraints weight = 5716.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.142747 restraints weight = 4150.233| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5305 Z= 0.212 Angle : 0.742 12.364 7159 Z= 0.374 Chirality : 0.048 0.344 824 Planarity : 0.005 0.094 898 Dihedral : 5.791 49.558 682 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.31 % Favored : 86.69 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -2.55 (0.33), residues: 631 helix: -0.39 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -3.89 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 89 HIS 0.003 0.001 HIS H 57 PHE 0.019 0.001 PHE K 25 TYR 0.013 0.001 TYR I 619 ARG 0.003 0.000 ARG H 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 367 CYS cc_start: 0.8401 (p) cc_final: 0.7969 (p) REVERT: I 699 LYS cc_start: 0.6913 (mmpt) cc_final: 0.5692 (tptt) REVERT: H 52 LEU cc_start: 0.8749 (mm) cc_final: 0.8458 (tp) REVERT: H 80 ASN cc_start: 0.6736 (t0) cc_final: 0.6520 (t0) REVERT: K 21 ASN cc_start: 0.6808 (m110) cc_final: 0.6563 (m110) REVERT: K 61 MET cc_start: 0.8234 (ptp) cc_final: 0.7859 (ptp) REVERT: K 77 ASN cc_start: 0.8092 (t0) cc_final: 0.7490 (t0) REVERT: K 103 MET cc_start: 0.7704 (mmp) cc_final: 0.7032 (tmm) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2647 time to fit residues: 43.3253 Evaluate side-chains 103 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 51 optimal weight: 0.0020 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.160249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.141988 restraints weight = 9483.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.144309 restraints weight = 6396.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.145986 restraints weight = 4807.819| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5305 Z= 0.194 Angle : 0.740 11.224 7159 Z= 0.369 Chirality : 0.048 0.317 824 Planarity : 0.004 0.092 898 Dihedral : 5.655 48.250 682 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -2.35 (0.33), residues: 631 helix: -0.22 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -3.83 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 89 HIS 0.002 0.000 HIS H 57 PHE 0.017 0.001 PHE K 25 TYR 0.020 0.001 TYR I 340 ARG 0.006 0.000 ARG H 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 677 HIS cc_start: 0.7616 (t-90) cc_final: 0.7397 (t-90) REVERT: I 699 LYS cc_start: 0.6937 (mmpt) cc_final: 0.5708 (tptt) REVERT: K 21 ASN cc_start: 0.6712 (m110) cc_final: 0.6435 (m110) REVERT: K 61 MET cc_start: 0.8194 (ptp) cc_final: 0.7796 (ptp) REVERT: K 77 ASN cc_start: 0.8026 (t0) cc_final: 0.7412 (t0) REVERT: K 103 MET cc_start: 0.7476 (mmp) cc_final: 0.6927 (tmm) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1951 time to fit residues: 30.8016 Evaluate side-chains 105 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 51 optimal weight: 0.0170 chunk 54 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 55 optimal weight: 0.0980 chunk 53 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.163083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.144729 restraints weight = 9392.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.147075 restraints weight = 6266.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.148648 restraints weight = 4692.876| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5305 Z= 0.183 Angle : 0.728 10.400 7159 Z= 0.361 Chirality : 0.047 0.302 824 Planarity : 0.004 0.088 898 Dihedral : 5.524 47.435 682 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -2.20 (0.34), residues: 631 helix: -0.07 (0.28), residues: 378 sheet: None (None), residues: 0 loop : -3.78 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 89 HIS 0.002 0.000 HIS H 57 PHE 0.018 0.001 PHE K 25 TYR 0.018 0.001 TYR I 340 ARG 0.002 0.000 ARG K 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 677 HIS cc_start: 0.7558 (t-90) cc_final: 0.7349 (t-90) REVERT: I 699 LYS cc_start: 0.6916 (mmpt) cc_final: 0.5723 (tptt) REVERT: K 21 ASN cc_start: 0.6670 (m110) cc_final: 0.6409 (m110) REVERT: K 61 MET cc_start: 0.8139 (ptp) cc_final: 0.7679 (mpp) REVERT: K 77 ASN cc_start: 0.7960 (t0) cc_final: 0.7325 (t0) REVERT: K 103 MET cc_start: 0.7616 (mmp) cc_final: 0.6912 (tmm) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1889 time to fit residues: 31.0025 Evaluate side-chains 105 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 47 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 0.0010 chunk 18 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 35 optimal weight: 0.0050 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 581 GLN ** I 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 GLN ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.159462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.140665 restraints weight = 9589.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.143142 restraints weight = 6253.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.144776 restraints weight = 4608.812| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5305 Z= 0.181 Angle : 0.741 10.855 7159 Z= 0.364 Chirality : 0.048 0.297 824 Planarity : 0.004 0.086 898 Dihedral : 5.408 46.056 682 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.52 % Favored : 87.48 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.34), residues: 631 helix: 0.10 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -3.60 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 686 HIS 0.002 0.000 HIS H 57 PHE 0.018 0.001 PHE K 25 TYR 0.017 0.001 TYR I 340 ARG 0.004 0.000 ARG H 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 532 ILE cc_start: 0.8218 (mp) cc_final: 0.7821 (mt) REVERT: I 542 MET cc_start: 0.6983 (tmm) cc_final: 0.6521 (tmm) REVERT: I 677 HIS cc_start: 0.7533 (t-90) cc_final: 0.7320 (t-90) REVERT: I 699 LYS cc_start: 0.6919 (mmpt) cc_final: 0.5744 (tptt) REVERT: K 21 ASN cc_start: 0.6666 (m110) cc_final: 0.6400 (m110) REVERT: K 61 MET cc_start: 0.8112 (ptp) cc_final: 0.7685 (mpp) REVERT: K 77 ASN cc_start: 0.7892 (t0) cc_final: 0.7309 (t0) REVERT: K 103 MET cc_start: 0.7583 (mmp) cc_final: 0.6990 (tmm) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2024 time to fit residues: 32.3822 Evaluate side-chains 106 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 0.0870 chunk 34 optimal weight: 9.9990 chunk 16 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.161405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.143304 restraints weight = 9646.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.145771 restraints weight = 6443.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.147498 restraints weight = 4814.151| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5305 Z= 0.191 Angle : 0.744 10.604 7159 Z= 0.367 Chirality : 0.048 0.292 824 Planarity : 0.004 0.085 898 Dihedral : 5.393 45.885 682 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.15 % Favored : 86.85 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.34), residues: 631 helix: 0.16 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -3.61 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 359 HIS 0.002 0.000 HIS H 57 PHE 0.020 0.002 PHE K 25 TYR 0.017 0.001 TYR I 340 ARG 0.006 0.000 ARG H 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 367 CYS cc_start: 0.8412 (p) cc_final: 0.7994 (p) REVERT: I 542 MET cc_start: 0.6996 (tmm) cc_final: 0.6745 (tmm) REVERT: I 677 HIS cc_start: 0.7584 (t-90) cc_final: 0.7350 (t-90) REVERT: I 699 LYS cc_start: 0.6911 (mmpt) cc_final: 0.5723 (tptt) REVERT: K 21 ASN cc_start: 0.6667 (m110) cc_final: 0.6404 (m110) REVERT: K 61 MET cc_start: 0.8155 (ptp) cc_final: 0.7722 (mpp) REVERT: K 77 ASN cc_start: 0.7940 (t0) cc_final: 0.7325 (t0) REVERT: K 103 MET cc_start: 0.7526 (mmp) cc_final: 0.6935 (tmm) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2827 time to fit residues: 45.5809 Evaluate side-chains 105 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 0.0470 chunk 21 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.155115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.137339 restraints weight = 8617.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.139969 restraints weight = 5637.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.141886 restraints weight = 4096.640| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5305 Z= 0.183 Angle : 0.747 10.793 7159 Z= 0.366 Chirality : 0.048 0.291 824 Planarity : 0.004 0.084 898 Dihedral : 5.361 44.948 682 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.04 % Favored : 87.96 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.34), residues: 631 helix: 0.22 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -3.56 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 89 HIS 0.001 0.000 HIS H 57 PHE 0.019 0.001 PHE K 25 TYR 0.016 0.001 TYR I 340 ARG 0.004 0.000 ARG H 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2496.33 seconds wall clock time: 46 minutes 33.53 seconds (2793.53 seconds total)