Starting phenix.real_space_refine on Fri Jul 19 02:18:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvp_26815/07_2024/7uvp_26815_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvp_26815/07_2024/7uvp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvp_26815/07_2024/7uvp_26815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvp_26815/07_2024/7uvp_26815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvp_26815/07_2024/7uvp_26815_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvp_26815/07_2024/7uvp_26815_neut.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 Residue "A GLU 32": "OE1" <-> "OE2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A ASP 374": "OD1" <-> "OD2" Residue "A TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 629": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 3.95, per 1000 atoms: 0.70 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 - 3.50 Amino acid : False - 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: 2.24 Conformation dependent library (CDL) restraints added in 1.3 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: 0.80 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: 1.95 Time building geometry restraints manager: 2.40 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: 99.63 - 106.51: 166 106.51 - 113.39: 3108 113.39 - 120.27: 2018 120.27 - 127.16: 2457 127.16 - 134.04: 46 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 2.520 nonbonded pdb=" NH1 ARG A 636 " pdb=" O THR A 683 " model vdw 2.260 2.520 ... (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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.920 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.790 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.643 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: 0.1835 time to fit residues: 34.1439 Evaluate side-chains 119 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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: 0.9980 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 0.3980 chunk 36 optimal weight: 0.4980 chunk 28 optimal weight: 0.0060 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 219 ASN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1416 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= 0.192 Angle : 0.542 6.844 7795 Z= 0.284 Chirality : 0.045 0.160 846 Planarity : 0.004 0.052 1012 Dihedral : 10.501 176.339 787 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.63 % Allowed : 12.40 % Favored : 85.97 % 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: -0.92 (0.32), residues: 716 helix: 1.32 (0.37), residues: 214 sheet: -1.32 (0.39), residues: 198 loop : -1.45 (0.33), residues: 304 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 0.001 PHE A 693 TYR 0.030 0.001 TYR A 163 ARG 0.002 0.000 ARG A 120 *********************** 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 147 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 137 time to evaluate : 0.664 Fit side-chains REVERT: A 224 MET cc_start: 0.6686 (tmm) cc_final: 0.6341 (tmm) REVERT: A 328 ARG cc_start: 0.7429 (tpp80) cc_final: 0.7125 (tpp80) REVERT: A 500 GLU cc_start: 0.5126 (tt0) cc_final: 0.4900 (tt0) REVERT: A 558 PHE cc_start: 0.6116 (m-10) cc_final: 0.5864 (m-10) outliers start: 10 outliers final: 6 residues processed: 140 average time/residue: 0.1988 time to fit residues: 35.2972 Evaluate side-chains 132 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 337 ASP 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 35 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 0.3980 chunk 17 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 274 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5779 Z= 0.252 Angle : 0.548 7.009 7795 Z= 0.285 Chirality : 0.045 0.144 846 Planarity : 0.004 0.055 1012 Dihedral : 10.536 173.588 787 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.43 % Allowed : 15.17 % 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: -0.95 (0.32), residues: 716 helix: 1.42 (0.37), residues: 212 sheet: -1.45 (0.37), residues: 199 loop : -1.47 (0.33), residues: 305 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 0.031 0.002 PHE A 693 TYR 0.024 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 151 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 0.658 Fit side-chains REVERT: A 706 LYS cc_start: 0.7685 (tptp) cc_final: 0.7424 (tptp) outliers start: 21 outliers final: 12 residues processed: 140 average time/residue: 0.1945 time to fit residues: 35.0942 Evaluate side-chains 129 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 337 ASP 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 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 48 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 chunk 57 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1872 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= 0.224 Angle : 0.529 6.823 7795 Z= 0.278 Chirality : 0.045 0.142 846 Planarity : 0.004 0.055 1012 Dihedral : 10.541 174.129 787 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.26 % Allowed : 17.62 % Favored : 79.12 % 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: -0.86 (0.32), residues: 716 helix: 1.49 (0.37), residues: 213 sheet: -1.44 (0.37), residues: 199 loop : -1.39 (0.33), residues: 304 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 0.033 0.002 PHE A 693 TYR 0.025 0.002 TYR A 319 ARG 0.003 0.000 ARG A 249 *********************** 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 141 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 0.669 Fit side-chains REVERT: A 224 MET cc_start: 0.6741 (tmm) cc_final: 0.6453 (tpt) REVERT: A 328 ARG cc_start: 0.7586 (tpp80) cc_final: 0.7276 (tpp80) REVERT: A 592 MET cc_start: 0.6315 (tmm) cc_final: 0.5695 (tmm) outliers start: 20 outliers final: 14 residues processed: 129 average time/residue: 0.2018 time to fit residues: 33.2269 Evaluate side-chains 128 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 505 VAL 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 0 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 138 ASN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 5779 Z= 0.446 Angle : 0.675 8.035 7795 Z= 0.354 Chirality : 0.048 0.158 846 Planarity : 0.005 0.054 1012 Dihedral : 10.819 170.535 787 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 4.73 % Allowed : 19.09 % Favored : 76.18 % 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: -1.40 (0.31), residues: 716 helix: 0.95 (0.36), residues: 214 sheet: -1.63 (0.36), residues: 199 loop : -1.75 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 185 HIS 0.005 0.001 HIS A 502 PHE 0.016 0.002 PHE A 614 TYR 0.030 0.002 TYR A 319 ARG 0.004 0.001 ARG A 39 *********************** 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 158 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 0.641 Fit side-chains REVERT: A 124 LYS cc_start: 0.8063 (tmtt) cc_final: 0.7812 (tmtt) REVERT: A 224 MET cc_start: 0.6912 (tmm) cc_final: 0.6520 (tpt) REVERT: A 236 ASP cc_start: 0.7115 (t70) cc_final: 0.6836 (t0) REVERT: A 238 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.6724 (ppp) outliers start: 29 outliers final: 20 residues processed: 141 average time/residue: 0.1944 time to fit residues: 35.3168 Evaluate side-chains 139 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 138 ASN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 196 ASP 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 337 ASP 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 629 GLU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 676 SER 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: 0.5980 chunk 68 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 0.0670 chunk 5 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5779 Z= 0.185 Angle : 0.526 6.624 7795 Z= 0.278 Chirality : 0.045 0.142 846 Planarity : 0.004 0.050 1012 Dihedral : 10.752 177.653 787 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.75 % Allowed : 21.21 % 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: -1.05 (0.32), residues: 716 helix: 1.44 (0.37), residues: 214 sheet: -1.58 (0.36), residues: 204 loop : -1.57 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 185 HIS 0.003 0.001 HIS A 443 PHE 0.038 0.001 PHE A 693 TYR 0.035 0.002 TYR A 163 ARG 0.004 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 147 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.627 Fit side-chains REVERT: A 224 MET cc_start: 0.6856 (tmm) cc_final: 0.6514 (tpt) REVERT: A 238 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.6812 (ppp) REVERT: A 413 GLU cc_start: 0.7469 (pt0) cc_final: 0.7267 (pt0) REVERT: A 457 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8356 (tt) outliers start: 23 outliers final: 16 residues processed: 136 average time/residue: 0.1797 time to fit residues: 31.7457 Evaluate side-chains 138 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 457 LEU 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 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 702 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 0.0370 chunk 40 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2234 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= 0.187 Angle : 0.539 11.586 7795 Z= 0.275 Chirality : 0.044 0.151 846 Planarity : 0.004 0.050 1012 Dihedral : 10.628 177.233 787 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.08 % Allowed : 21.37 % Favored : 74.55 % 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: -0.84 (0.32), residues: 716 helix: 1.66 (0.37), residues: 214 sheet: -1.45 (0.36), residues: 204 loop : -1.51 (0.33), residues: 298 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 0.035 0.001 PHE A 693 TYR 0.030 0.002 TYR A 163 ARG 0.003 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 148 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 0.669 Fit side-chains REVERT: A 224 MET cc_start: 0.6799 (tmm) cc_final: 0.6445 (tpt) REVERT: A 238 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.6678 (ppp) REVERT: A 457 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8337 (tt) REVERT: A 539 TRP cc_start: 0.7654 (p90) cc_final: 0.7007 (p90) outliers start: 25 outliers final: 20 residues processed: 137 average time/residue: 0.1884 time to fit residues: 33.3318 Evaluate side-chains 142 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 297 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 457 LEU 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 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 702 ASP Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5779 Z= 0.233 Angle : 0.562 11.128 7795 Z= 0.287 Chirality : 0.045 0.138 846 Planarity : 0.004 0.049 1012 Dihedral : 10.619 175.320 787 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.73 % Allowed : 21.37 % Favored : 73.90 % 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 (0.31), residues: 716 helix: 1.57 (0.37), residues: 214 sheet: -1.52 (0.36), residues: 204 loop : -1.54 (0.33), residues: 298 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 0.036 0.001 PHE A 693 TYR 0.029 0.002 TYR A 163 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 146 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 0.740 Fit side-chains REVERT: A 224 MET cc_start: 0.6822 (tmm) cc_final: 0.6448 (tpt) REVERT: A 238 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.6796 (ppp) REVERT: A 457 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8359 (tt) REVERT: A 539 TRP cc_start: 0.7660 (p90) cc_final: 0.7003 (p90) REVERT: A 697 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6194 (mp0) REVERT: A 707 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8069 (mt) outliers start: 29 outliers final: 22 residues processed: 131 average time/residue: 0.1906 time to fit residues: 32.0536 Evaluate side-chains 141 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 196 ASP Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 457 LEU 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 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 Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5779 Z= 0.216 Angle : 0.558 10.827 7795 Z= 0.286 Chirality : 0.045 0.137 846 Planarity : 0.004 0.048 1012 Dihedral : 10.610 175.336 787 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.89 % Allowed : 21.70 % Favored : 73.41 % 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: -0.91 (0.31), residues: 716 helix: 1.59 (0.37), residues: 214 sheet: -1.50 (0.36), residues: 204 loop : -1.52 (0.32), residues: 298 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 0.037 0.001 PHE A 693 TYR 0.027 0.002 TYR A 163 ARG 0.003 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 fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 0.644 Fit side-chains REVERT: A 124 LYS cc_start: 0.7939 (tmtt) cc_final: 0.7676 (tmtt) REVERT: A 224 MET cc_start: 0.6786 (tmm) cc_final: 0.6431 (tpt) REVERT: A 238 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.6743 (ppp) REVERT: A 457 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8330 (tt) REVERT: A 539 TRP cc_start: 0.7652 (p90) cc_final: 0.7233 (p90) REVERT: A 697 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6239 (mp0) REVERT: A 707 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8006 (mt) outliers start: 30 outliers final: 24 residues processed: 131 average time/residue: 0.1928 time to fit residues: 32.7691 Evaluate side-chains 142 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 114 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 147 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 505 VAL 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 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 Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 0.2980 chunk 44 optimal weight: 0.0060 chunk 60 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 0.0870 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 overall best weight: 0.2172 ------------------------------------------------------------------------------- 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 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2545 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= 0.138 Angle : 0.517 10.497 7795 Z= 0.263 Chirality : 0.044 0.144 846 Planarity : 0.004 0.049 1012 Dihedral : 10.491 179.398 787 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.26 % Allowed : 23.16 % Favored : 73.57 % 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: 1.75 (0.37), residues: 216 sheet: -1.26 (0.37), residues: 202 loop : -1.38 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 185 HIS 0.004 0.001 HIS A 443 PHE 0.034 0.001 PHE A 693 TYR 0.026 0.001 TYR A 163 ARG 0.004 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 fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 0.514 Fit side-chains REVERT: A 141 CYS cc_start: 0.6280 (t) cc_final: 0.6075 (t) REVERT: A 224 MET cc_start: 0.6677 (tmm) cc_final: 0.6416 (tpt) REVERT: A 238 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.6392 (ppp) REVERT: A 539 TRP cc_start: 0.7579 (p90) cc_final: 0.7167 (p90) REVERT: A 697 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6163 (mp0) REVERT: A 707 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7913 (mt) outliers start: 20 outliers final: 13 residues processed: 130 average time/residue: 0.1880 time to fit residues: 31.9071 Evaluate side-chains 134 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 337 ASP 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 629 GLU Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 0.0970 chunk 40 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 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 = 0.3809 r_free = 0.3809 target = 0.175180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.141373 restraints weight = 6944.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.144450 restraints weight = 4076.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.146784 restraints weight = 2868.336| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2542 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= 0.194 Angle : 0.553 10.564 7795 Z= 0.282 Chirality : 0.044 0.139 846 Planarity : 0.004 0.047 1012 Dihedral : 10.465 178.857 787 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.77 % Allowed : 23.98 % Favored : 73.25 % 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: -0.67 (0.32), residues: 716 helix: 1.70 (0.37), residues: 216 sheet: -1.37 (0.37), residues: 204 loop : -1.32 (0.33), residues: 296 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 0.035 0.001 PHE A 693 TYR 0.026 0.002 TYR A 163 ARG 0.007 0.000 ARG A 456 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1597.26 seconds wall clock time: 28 minutes 53.57 seconds (1733.57 seconds total)