Starting phenix.real_space_refine on Thu Mar 6 10:15:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uvp_26815/03_2025/7uvp_26815.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uvp_26815/03_2025/7uvp_26815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uvp_26815/03_2025/7uvp_26815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uvp_26815/03_2025/7uvp_26815.map" model { file = "/net/cci-nas-00/data/ceres_data/7uvp_26815/03_2025/7uvp_26815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uvp_26815/03_2025/7uvp_26815.cif" } resolution = 3.7 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= 0.001 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 3589 2.51 5 N 951 2.21 5 O 1094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5671 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5637 Classifications: {'peptide': 718} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 685} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Time building chain proxies: 3.82, per 1000 atoms: 0.67 Number of scatterers: 5671 At special positions: 0 Unit cell: (73.692, 73.692, 128.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 3 15.00 Mg 1 11.99 O 1094 8.00 N 951 7.00 C 3589 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: 1.51 Conformation dependent library (CDL) restraints added in 1.0 seconds 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1312 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 10 sheets defined 31.9% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 22 through 33 Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.758A pdb=" N GLY A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 98 removed outlier: 3.805A pdb=" N THR A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.519A pdb=" N GLN A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 154 removed outlier: 4.217A pdb=" N GLU A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 218 removed outlier: 3.981A pdb=" N ASP A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLU A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N MET A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 231 Processing helix chain 'A' and resid 236 through 249 removed outlier: 3.583A pdb=" N GLU A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE A 242 " --> pdb=" O MET A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 411 through 426 Processing helix chain 'A' and resid 446 through 460 removed outlier: 3.542A pdb=" N LEU A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 573 removed outlier: 4.087A pdb=" N ILE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN A 572 " --> pdb=" O SER A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 617 removed outlier: 3.523A pdb=" N ALA A 613 " --> pdb=" O ALA A 609 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'A' and resid 670 through 673 Processing helix chain 'A' and resid 674 through 684 removed outlier: 3.515A pdb=" N ALA A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 716 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 70 removed outlier: 3.551A pdb=" N THR A 65 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA A 101 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LEU A 132 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE A 103 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASN A 134 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU A 105 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 164 removed outlier: 4.027A pdb=" N LYS A 181 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 285 through 286 removed outlier: 3.522A pdb=" N VAL A 285 " --> pdb=" O VAL A 293 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 334 through 335 removed outlier: 7.276A pdb=" N SER A 302 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N ILE A 366 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL A 350 " --> pdb=" O ILE A 366 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.808A pdb=" N SER A 434 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A 439 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR A 440 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.575A pdb=" N ARG A 475 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A 657 " --> pdb=" O PHE A 660 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 664 " --> pdb=" O GLY A 653 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A 653 " --> pdb=" O VAL A 664 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.575A pdb=" N ARG A 475 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU A 623 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TYR A 696 " --> pdb=" O GLU A 623 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE A 625 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 482 through 488 removed outlier: 3.682A pdb=" N ALA A 484 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 503 " --> pdb=" O ALA A 484 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 486 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLU A 500 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY A 590 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N HIS A 502 " --> pdb=" O TYR A 588 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS A 542 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL A 585 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL A 544 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL A 587 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE A 546 " --> pdb=" O VAL A 587 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N ASP A 589 " --> pdb=" O ILE A 546 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 517 through 519 removed outlier: 3.982A pdb=" N TYR A 518 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE A 525 " --> pdb=" O TYR A 518 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 224 hydrogen bonds defined for protein. 651 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: 1.70 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1864 1.34 - 1.46: 1135 1.46 - 1.58: 2714 1.58 - 1.69: 5 1.69 - 1.81: 61 Bond restraints: 5779 Sorted by residual: bond pdb=" CB PHE A 255 " pdb=" CG PHE A 255 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 8.08e-01 bond pdb=" C LYS A 471 " pdb=" N ILE A 472 " ideal model delta sigma weight residual 1.329 1.323 0.006 7.30e-03 1.88e+04 5.97e-01 bond pdb=" CA LYS A 405 " pdb=" C LYS A 405 " ideal model delta sigma weight residual 1.517 1.525 -0.008 1.07e-02 8.73e+03 5.04e-01 bond pdb=" C2' GTP A 901 " pdb=" C3' GTP A 901 " ideal model delta sigma weight residual 1.524 1.511 0.013 2.00e-02 2.50e+03 4.15e-01 bond pdb=" CE1 PHE A 255 " pdb=" CZ PHE A 255 " ideal model delta sigma weight residual 1.382 1.363 0.019 3.00e-02 1.11e+03 3.90e-01 ... (remaining 5774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 7583 1.30 - 2.60: 164 2.60 - 3.89: 41 3.89 - 5.19: 4 5.19 - 6.49: 3 Bond angle restraints: 7795 Sorted by residual: angle pdb=" C GLU A 534 " pdb=" N ILE A 535 " pdb=" CA ILE A 535 " ideal model delta sigma weight residual 122.59 120.56 2.03 7.20e-01 1.93e+00 7.98e+00 angle pdb=" C1' GTP A 901 " pdb=" C2' GTP A 901 " pdb=" C3' GTP A 901 " ideal model delta sigma weight residual 111.00 104.51 6.49 3.00e+00 1.11e-01 4.68e+00 angle pdb=" N VAL A 275 " pdb=" CA VAL A 275 " pdb=" C VAL A 275 " ideal model delta sigma weight residual 106.42 109.51 -3.09 1.51e+00 4.39e-01 4.19e+00 angle pdb=" CA MET A 282 " pdb=" CB MET A 282 " pdb=" CG MET A 282 " ideal model delta sigma weight residual 114.10 117.75 -3.65 2.00e+00 2.50e-01 3.33e+00 angle pdb=" CA LYS A 124 " pdb=" CB LYS A 124 " pdb=" CG LYS A 124 " ideal model delta sigma weight residual 114.10 117.42 -3.32 2.00e+00 2.50e-01 2.75e+00 ... (remaining 7790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 3424 35.29 - 70.58: 80 70.58 - 105.86: 8 105.86 - 141.15: 2 141.15 - 176.44: 1 Dihedral angle restraints: 3515 sinusoidal: 1461 harmonic: 2054 Sorted by residual: dihedral pdb=" C8 GTP A 901 " pdb=" C1' GTP A 901 " pdb=" N9 GTP A 901 " pdb=" O4' GTP A 901 " ideal model delta sinusoidal sigma weight residual 104.59 -78.97 -176.44 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GTP A 901 " pdb=" O3A GTP A 901 " pdb=" PB GTP A 901 " pdb=" PA GTP A 901 " ideal model delta sinusoidal sigma weight residual 291.08 179.75 111.33 1 2.00e+01 2.50e-03 3.27e+01 dihedral pdb=" C4' GTP A 901 " pdb=" C5' GTP A 901 " pdb=" O5' GTP A 901 " pdb=" PA GTP A 901 " ideal model delta sinusoidal sigma weight residual 260.87 150.29 110.58 1 2.00e+01 2.50e-03 3.24e+01 ... (remaining 3512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 514 0.031 - 0.062: 213 0.062 - 0.093: 67 0.093 - 0.124: 47 0.124 - 0.156: 5 Chirality restraints: 846 Sorted by residual: chirality pdb=" CB ILE A 535 " pdb=" CA ILE A 535 " pdb=" CG1 ILE A 535 " pdb=" CG2 ILE A 535 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CB VAL A 310 " pdb=" CA VAL A 310 " pdb=" CG1 VAL A 310 " pdb=" CG2 VAL A 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA VAL A 667 " pdb=" N VAL A 667 " pdb=" C VAL A 667 " pdb=" CB VAL A 667 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 843 not shown) Planarity restraints: 1012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 276 " 0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A 277 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 282 " 0.033 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO A 283 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 271 " 0.010 2.00e-02 2.50e+03 1.35e-02 3.19e+00 pdb=" CG PHE A 271 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 271 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 271 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 271 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 271 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 271 " 0.000 2.00e-02 2.50e+03 ... (remaining 1009 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 37 2.53 - 3.13: 4299 3.13 - 3.72: 8534 3.72 - 4.31: 11805 4.31 - 4.90: 19835 Nonbonded interactions: 44510 Sorted by model distance: nonbonded pdb=" O1B GTP A 901 " pdb="MG MG A 902 " model vdw 1.942 2.170 nonbonded pdb=" O3G GTP A 901 " pdb="MG MG A 902 " model vdw 1.987 2.170 nonbonded pdb=" O3B GTP A 901 " pdb="MG MG A 902 " model vdw 2.049 2.170 nonbonded pdb=" O LEU A 604 " pdb=" ND2 ASN A 608 " model vdw 2.203 3.120 nonbonded pdb=" NH1 ARG A 636 " pdb=" O THR A 683 " model vdw 2.260 3.120 ... (remaining 44505 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 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: 0.740 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.840 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 : 0.002 0.021 5779 Z= 0.161 Angle : 0.506 6.490 7795 Z= 0.265 Chirality : 0.043 0.156 846 Planarity : 0.004 0.052 1012 Dihedral : 15.709 176.438 2203 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.31), residues: 716 helix: 0.91 (0.39), residues: 193 sheet: -1.35 (0.40), residues: 196 loop : -1.26 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 185 HIS 0.003 0.001 HIS A 68 PHE 0.030 0.001 PHE A 271 TYR 0.011 0.001 TYR A 163 ARG 0.002 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.644 Fit side-chains REVERT: A 500 GLU cc_start: 0.4966 (tt0) cc_final: 0.4642 (tt0) REVERT: A 558 PHE cc_start: 0.6467 (m-10) cc_final: 0.6053 (m-10) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2170 time to fit residues: 40.5521 Evaluate side-chains 119 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 0.1980 chunk 55 optimal weight: 0.0370 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN A 219 ASN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.178033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.144136 restraints weight = 6918.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.147601 restraints weight = 3872.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.149859 restraints weight = 2632.105| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5779 Z= 0.191 Angle : 0.554 6.961 7795 Z= 0.291 Chirality : 0.046 0.163 846 Planarity : 0.004 0.052 1012 Dihedral : 10.400 177.395 787 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.31 % Allowed : 12.40 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.32), residues: 716 helix: 1.25 (0.37), residues: 214 sheet: -1.32 (0.39), residues: 195 loop : -1.45 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 185 HIS 0.003 0.001 HIS A 443 PHE 0.030 0.002 PHE A 693 TYR 0.029 0.001 TYR A 163 ARG 0.003 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.598 Fit side-chains REVERT: A 224 MET cc_start: 0.6708 (tmm) cc_final: 0.6357 (tmm) REVERT: A 500 GLU cc_start: 0.5133 (tt0) cc_final: 0.4899 (tt0) REVERT: A 558 PHE cc_start: 0.6098 (m-10) cc_final: 0.5849 (m-10) outliers start: 8 outliers final: 6 residues processed: 148 average time/residue: 0.2352 time to fit residues: 44.8537 Evaluate side-chains 138 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 683 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 0.0020 chunk 34 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN A 274 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.172098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.137075 restraints weight = 7112.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.140534 restraints weight = 4019.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.142840 restraints weight = 2746.090| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5779 Z= 0.284 Angle : 0.574 6.991 7795 Z= 0.299 Chirality : 0.046 0.145 846 Planarity : 0.005 0.057 1012 Dihedral : 10.429 174.961 787 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.92 % Allowed : 14.68 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.31), residues: 716 helix: 1.19 (0.37), residues: 213 sheet: -1.52 (0.37), residues: 197 loop : -1.53 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 185 HIS 0.003 0.001 HIS A 443 PHE 0.032 0.002 PHE A 693 TYR 0.022 0.002 TYR A 163 ARG 0.003 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.549 Fit side-chains REVERT: A 176 ASP cc_start: 0.8668 (t0) cc_final: 0.8309 (t0) REVERT: A 224 MET cc_start: 0.6807 (tmm) cc_final: 0.6510 (tpt) REVERT: A 706 LYS cc_start: 0.7642 (tptp) cc_final: 0.7396 (tptp) outliers start: 24 outliers final: 15 residues processed: 141 average time/residue: 0.1970 time to fit residues: 35.2542 Evaluate side-chains 138 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 648 ARG Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 683 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 49 optimal weight: 0.0670 chunk 38 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN A 362 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.174893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.140154 restraints weight = 7178.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.143576 restraints weight = 3982.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.146023 restraints weight = 2708.957| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5779 Z= 0.195 Angle : 0.518 6.616 7795 Z= 0.272 Chirality : 0.045 0.140 846 Planarity : 0.004 0.055 1012 Dihedral : 10.380 177.492 787 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.75 % Allowed : 17.29 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.31), residues: 716 helix: 1.41 (0.37), residues: 213 sheet: -1.55 (0.37), residues: 201 loop : -1.49 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 185 HIS 0.003 0.001 HIS A 443 PHE 0.034 0.002 PHE A 693 TYR 0.021 0.002 TYR A 319 ARG 0.003 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.832 Fit side-chains REVERT: A 176 ASP cc_start: 0.8550 (t0) cc_final: 0.8271 (t0) REVERT: A 224 MET cc_start: 0.6703 (tmm) cc_final: 0.6427 (tpt) REVERT: A 413 GLU cc_start: 0.7683 (pt0) cc_final: 0.7468 (pt0) REVERT: A 592 MET cc_start: 0.6309 (tmm) cc_final: 0.5685 (tmm) outliers start: 23 outliers final: 14 residues processed: 140 average time/residue: 0.3291 time to fit residues: 59.9204 Evaluate side-chains 134 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 683 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 68 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 0.0980 chunk 46 optimal weight: 0.0980 chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 53 optimal weight: 0.0030 chunk 17 optimal weight: 3.9990 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN A 449 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.176863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.142884 restraints weight = 7063.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.146184 restraints weight = 4067.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.148357 restraints weight = 2812.008| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5779 Z= 0.155 Angle : 0.505 7.154 7795 Z= 0.263 Chirality : 0.044 0.133 846 Planarity : 0.004 0.053 1012 Dihedral : 10.292 179.683 787 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.75 % Allowed : 18.76 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.32), residues: 716 helix: 1.55 (0.37), residues: 216 sheet: -1.35 (0.37), residues: 199 loop : -1.37 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 185 HIS 0.004 0.001 HIS A 443 PHE 0.026 0.001 PHE A 631 TYR 0.016 0.001 TYR A 163 ARG 0.003 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.722 Fit side-chains REVERT: A 141 CYS cc_start: 0.6313 (t) cc_final: 0.6100 (t) REVERT: A 224 MET cc_start: 0.6681 (tmm) cc_final: 0.6424 (tpt) REVERT: A 238 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.6212 (ppp) REVERT: A 539 TRP cc_start: 0.7576 (p90) cc_final: 0.7033 (p90) REVERT: A 592 MET cc_start: 0.6235 (tmm) cc_final: 0.5657 (tmm) outliers start: 23 outliers final: 15 residues processed: 137 average time/residue: 0.2194 time to fit residues: 38.7845 Evaluate side-chains 138 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 648 ARG Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 683 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 0.0000 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 274 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 = 0.3819 r_free = 0.3819 target = 0.176435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.141839 restraints weight = 7024.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.145403 restraints weight = 3916.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.147780 restraints weight = 2651.374| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5779 Z= 0.163 Angle : 0.508 6.287 7795 Z= 0.265 Chirality : 0.044 0.132 846 Planarity : 0.004 0.049 1012 Dihedral : 10.233 179.292 787 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.43 % Allowed : 19.09 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.32), residues: 716 helix: 1.63 (0.37), residues: 216 sheet: -1.19 (0.37), residues: 199 loop : -1.35 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 185 HIS 0.005 0.001 HIS A 449 PHE 0.034 0.001 PHE A 693 TYR 0.014 0.001 TYR A 163 ARG 0.003 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.682 Fit side-chains REVERT: A 141 CYS cc_start: 0.6345 (t) cc_final: 0.6142 (t) REVERT: A 224 MET cc_start: 0.6661 (tmm) cc_final: 0.6388 (tpt) REVERT: A 706 LYS cc_start: 0.7538 (tptp) cc_final: 0.7269 (tptp) outliers start: 21 outliers final: 14 residues processed: 130 average time/residue: 0.2816 time to fit residues: 46.5598 Evaluate side-chains 131 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 683 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 49 optimal weight: 0.0010 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 274 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 = 0.3797 r_free = 0.3797 target = 0.174177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.140061 restraints weight = 7087.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.143223 restraints weight = 4113.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.145464 restraints weight = 2879.763| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5779 Z= 0.208 Angle : 0.527 6.507 7795 Z= 0.274 Chirality : 0.044 0.135 846 Planarity : 0.004 0.048 1012 Dihedral : 10.269 178.055 787 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.73 % Allowed : 17.46 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.32), residues: 716 helix: 1.68 (0.37), residues: 215 sheet: -1.18 (0.38), residues: 198 loop : -1.38 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 185 HIS 0.005 0.001 HIS A 449 PHE 0.035 0.001 PHE A 693 TYR 0.014 0.001 TYR A 319 ARG 0.004 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.701 Fit side-chains REVERT: A 224 MET cc_start: 0.6603 (tmm) cc_final: 0.6345 (tpt) REVERT: A 238 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.6503 (ppp) outliers start: 29 outliers final: 17 residues processed: 142 average time/residue: 0.3331 time to fit residues: 60.9113 Evaluate side-chains 137 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 648 ARG Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 683 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 3 optimal weight: 0.0870 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 274 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 = 0.3772 r_free = 0.3772 target = 0.171845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.137892 restraints weight = 7013.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.141057 restraints weight = 4097.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.143192 restraints weight = 2871.405| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5779 Z= 0.261 Angle : 0.592 12.053 7795 Z= 0.304 Chirality : 0.046 0.157 846 Planarity : 0.004 0.049 1012 Dihedral : 10.345 177.130 787 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.24 % Allowed : 18.92 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.32), residues: 716 helix: 1.65 (0.37), residues: 213 sheet: -1.33 (0.37), residues: 200 loop : -1.44 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 185 HIS 0.005 0.001 HIS A 449 PHE 0.038 0.002 PHE A 693 TYR 0.018 0.002 TYR A 319 ARG 0.004 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.662 Fit side-chains REVERT: A 224 MET cc_start: 0.6764 (tmm) cc_final: 0.6395 (tpt) REVERT: A 236 ASP cc_start: 0.7002 (t70) cc_final: 0.6713 (t0) REVERT: A 238 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.6580 (ppp) REVERT: A 697 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6100 (mp0) outliers start: 26 outliers final: 20 residues processed: 142 average time/residue: 0.1991 time to fit residues: 35.9961 Evaluate side-chains 148 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 648 ARG Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 697 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.0470 chunk 16 optimal weight: 0.0870 chunk 55 optimal weight: 0.0670 chunk 3 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 274 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 = 0.3830 r_free = 0.3830 target = 0.177374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.143003 restraints weight = 7079.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.146535 restraints weight = 3960.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.148938 restraints weight = 2689.851| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5779 Z= 0.165 Angle : 0.559 11.215 7795 Z= 0.283 Chirality : 0.045 0.131 846 Planarity : 0.004 0.047 1012 Dihedral : 10.283 179.564 787 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.59 % Allowed : 20.72 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.32), residues: 716 helix: 1.70 (0.37), residues: 216 sheet: -1.19 (0.37), residues: 198 loop : -1.31 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 185 HIS 0.005 0.001 HIS A 449 PHE 0.037 0.001 PHE A 693 TYR 0.014 0.001 TYR A 508 ARG 0.004 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.582 Fit side-chains REVERT: A 224 MET cc_start: 0.6586 (tmm) cc_final: 0.6324 (tpt) REVERT: A 236 ASP cc_start: 0.6986 (t70) cc_final: 0.6676 (t0) REVERT: A 238 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.6472 (ppp) REVERT: A 539 TRP cc_start: 0.7574 (p90) cc_final: 0.6815 (p90) REVERT: A 697 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6014 (mp0) outliers start: 22 outliers final: 15 residues processed: 135 average time/residue: 0.1898 time to fit residues: 32.9736 Evaluate side-chains 137 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 648 ARG Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 697 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 59 optimal weight: 0.0060 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 274 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 = 0.3812 r_free = 0.3812 target = 0.175704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.141824 restraints weight = 7083.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.145218 restraints weight = 4075.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.147476 restraints weight = 2817.470| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5779 Z= 0.176 Angle : 0.562 11.212 7795 Z= 0.288 Chirality : 0.044 0.130 846 Planarity : 0.004 0.048 1012 Dihedral : 10.204 178.930 787 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.77 % Allowed : 21.70 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.32), residues: 716 helix: 1.77 (0.37), residues: 215 sheet: -1.08 (0.38), residues: 196 loop : -1.37 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 185 HIS 0.004 0.001 HIS A 449 PHE 0.035 0.001 PHE A 693 TYR 0.017 0.001 TYR A 508 ARG 0.005 0.000 ARG A 456 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.621 Fit side-chains REVERT: A 224 MET cc_start: 0.6571 (tmm) cc_final: 0.6314 (tpt) REVERT: A 236 ASP cc_start: 0.6938 (t70) cc_final: 0.6643 (t0) REVERT: A 238 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.6503 (ppp) REVERT: A 697 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6054 (mp0) outliers start: 17 outliers final: 14 residues processed: 133 average time/residue: 0.1927 time to fit residues: 32.6710 Evaluate side-chains 136 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 648 ARG Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 697 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 17 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 0.0570 chunk 70 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 274 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 = 0.3790 r_free = 0.3790 target = 0.173678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.139764 restraints weight = 7071.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.143077 restraints weight = 4104.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.145180 restraints weight = 2855.121| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5779 Z= 0.224 Angle : 0.580 11.210 7795 Z= 0.295 Chirality : 0.045 0.139 846 Planarity : 0.004 0.047 1012 Dihedral : 10.276 178.241 787 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.43 % Allowed : 21.53 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.32), residues: 716 helix: 1.71 (0.37), residues: 215 sheet: -1.22 (0.38), residues: 198 loop : -1.36 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 185 HIS 0.005 0.001 HIS A 449 PHE 0.037 0.002 PHE A 693 TYR 0.018 0.002 TYR A 508 ARG 0.006 0.000 ARG A 456 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2479.18 seconds wall clock time: 45 minutes 36.69 seconds (2736.69 seconds total)