Starting phenix.real_space_refine on Tue Feb 13 11:16:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvp_26815/02_2024/7uvp_26815_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvp_26815/02_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_26815/02_2024/7uvp_26815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvp_26815/02_2024/7uvp_26815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvp_26815/02_2024/7uvp_26815_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvp_26815/02_2024/7uvp_26815_updated.pdb" } 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-5238/modules/chem_data/mon_lib" Total number of atoms: 5671 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5671 Unusual residues: {' MG': 1, 'GTP': 1} Inner-chain residues flagged as termini: ['pdbres="GLU A 718 "'] Classifications: {'peptide': 718, 'undetermined': 2, 'water': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 685, None: 3} Not linked: pdbres="GLU A 718 " pdbres="GTP A 901 " Not linked: pdbres="GTP A 901 " pdbres=" MG A 902 " Not linked: pdbres=" MG A 902 " pdbres="HOH A1001 " Time building chain proxies: 3.68, per 1000 atoms: 0.65 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: 2.18 Conformation dependent library (CDL) restraints added in 992.8 milliseconds 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... running ksdssp... Secondary structure from input PDB file: 17 helices and 10 sheets defined 27.6% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 88 through 97 removed outlier: 3.531A pdb=" N VAL A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.649A pdb=" N TYR A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 153 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 199 through 217 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) Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 237 through 248 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 265 through 274 Processing helix chain 'A' and resid 412 through 425 Processing helix chain 'A' and resid 447 through 459 Processing helix chain 'A' and resid 559 through 572 removed outlier: 3.830A pdb=" N GLN A 572 " --> pdb=" O SER A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 616 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 637 through 646 Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 675 through 683 Processing helix chain 'A' and resid 701 through 717 removed outlier: 3.859A pdb=" N GLU A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 158 through 160 removed outlier: 6.059A pdb=" N PHE A 252 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL A 129 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N PHE A 255 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE A 131 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N THR A 100 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN A 11 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE A 102 " --> pdb=" O ASN A 11 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA A 13 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU A 104 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU A 15 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N ASN A 106 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LYS A 75 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE A 12 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASN A 77 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU A 14 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 79 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N GLY A 16 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A 65 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing sheet with id= B, 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= C, first strand: chain 'A' and resid 380 through 382 removed outlier: 4.494A pdb=" N SER A 324 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N TYR A 304 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL A 322 " --> pdb=" O TYR A 304 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 326 through 328 Processing sheet with id= E, first strand: chain 'A' and resid 348 through 350 Processing sheet with id= F, first strand: chain 'A' and resid 465 through 468 removed outlier: 4.610A pdb=" N THR A 440 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A 439 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 434 " --> pdb=" O GLN A 439 " (cutoff:3.500A) Processing sheet with id= G, 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) Processing sheet with id= H, 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: 3.516A pdb=" N GLU A 500 " --> pdb=" O LYS A 591 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 589 " --> pdb=" O HIS A 502 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 504 " --> pdb=" O VAL A 587 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL A 587 " --> pdb=" O ILE A 504 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLU A 506 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL A 585 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing sheet with id= I, 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= I Processing sheet with id= J, first strand: chain 'A' and resid 691 through 693 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) 184 hydrogen bonds defined for protein. 531 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: 1.98 Time building geometry restraints manager: 2.36 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: 39 2.53 - 3.13: 4322 3.13 - 3.72: 8576 3.72 - 4.31: 11874 4.31 - 4.90: 19847 Nonbonded interactions: 44658 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 44653 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: 0.750 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: 3.020 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 19.910 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.730 ------------------------------------------------------------------------------- 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= 0.163 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 : 0.652 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: 0.1860 time to fit residues: 34.5511 Evaluate side-chains 119 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.7513 moved from start: 0.1261 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= 0.205 Angle : 0.528 6.648 7795 Z= 0.274 Chirality : 0.045 0.131 846 Planarity : 0.004 0.052 1012 Dihedral : 10.503 175.739 787 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.79 % Allowed : 12.40 % Favored : 85.81 % 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: -1.05 (0.32), residues: 716 helix: 1.19 (0.37), residues: 212 sheet: -1.26 (0.42), residues: 177 loop : -1.62 (0.31), residues: 327 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 0.029 0.002 PHE A 693 TYR 0.030 0.002 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 146 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 0.650 Fit side-chains REVERT: A 224 MET cc_start: 0.6719 (tmm) cc_final: 0.6416 (tpt) REVERT: A 328 ARG cc_start: 0.7410 (tpp80) cc_final: 0.7068 (tpp80) REVERT: A 558 PHE cc_start: 0.6372 (m-10) cc_final: 0.6170 (m-10) outliers start: 11 outliers final: 7 residues processed: 138 average time/residue: 0.2005 time to fit residues: 35.0200 Evaluate side-chains 129 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 505 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: 72 random chunks: chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN A 274 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 5779 Z= 0.412 Angle : 0.638 7.752 7795 Z= 0.330 Chirality : 0.047 0.169 846 Planarity : 0.005 0.057 1012 Dihedral : 10.729 170.915 787 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.40 % Allowed : 15.33 % Favored : 80.26 % 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: -1.43 (0.31), residues: 716 helix: 0.79 (0.35), residues: 212 sheet: -1.61 (0.38), residues: 199 loop : -1.67 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 185 HIS 0.003 0.001 HIS A 443 PHE 0.020 0.002 PHE A 614 TYR 0.033 0.002 TYR A 319 ARG 0.004 0.000 ARG A 39 *********************** 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 152 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 0.676 Fit side-chains REVERT: A 96 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8125 (m110) REVERT: A 124 LYS cc_start: 0.8026 (tmtt) cc_final: 0.7728 (tmtt) REVERT: A 138 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.7538 (m110) REVERT: A 224 MET cc_start: 0.6935 (tmm) cc_final: 0.6547 (tpt) REVERT: A 240 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7279 (tp30) REVERT: A 592 MET cc_start: 0.6256 (tmm) cc_final: 0.5581 (tmm) outliers start: 27 outliers final: 13 residues processed: 136 average time/residue: 0.1899 time to fit residues: 33.0037 Evaluate side-chains 135 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 96 ASN 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 337 ASP Chi-restraints excluded: chain A residue 505 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 Chi-restraints excluded: chain A residue 690 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 0.1980 chunk 31 optimal weight: 0.3980 chunk 43 optimal weight: 0.0270 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 overall best weight: 0.2838 ------------------------------------------------------------------------------- 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: 0.7513 moved from start: 0.1805 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= 0.150 Angle : 0.494 6.217 7795 Z= 0.256 Chirality : 0.044 0.130 846 Planarity : 0.004 0.054 1012 Dihedral : 10.667 178.747 787 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.77 % Allowed : 18.60 % Favored : 78.63 % 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: 1.32 (0.37), residues: 213 sheet: -1.38 (0.38), residues: 199 loop : -1.44 (0.33), residues: 304 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 0.036 0.001 PHE A 693 TYR 0.032 0.002 TYR A 163 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 148 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 0.663 Fit side-chains REVERT: A 224 MET cc_start: 0.6790 (tmm) cc_final: 0.6462 (tpt) REVERT: A 328 ARG cc_start: 0.7421 (tpp80) cc_final: 0.7152 (tpp80) outliers start: 17 outliers final: 9 residues processed: 137 average time/residue: 0.1929 time to fit residues: 33.6968 Evaluate side-chains 131 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 126 ASN 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 428 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 658 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 0.0970 chunk 48 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.0050 chunk 62 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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: 0.7520 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5779 Z= 0.183 Angle : 0.521 8.872 7795 Z= 0.262 Chirality : 0.044 0.129 846 Planarity : 0.004 0.052 1012 Dihedral : 10.547 178.069 787 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.10 % Allowed : 19.90 % Favored : 77.00 % 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: 1.42 (0.37), residues: 213 sheet: -1.37 (0.38), residues: 199 loop : -1.39 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 185 HIS 0.004 0.001 HIS A 443 PHE 0.010 0.001 PHE A 614 TYR 0.027 0.002 TYR A 163 ARG 0.006 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 150 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 0.753 Fit side-chains REVERT: A 224 MET cc_start: 0.6787 (tmm) cc_final: 0.6443 (tpt) REVERT: A 238 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.6391 (ppp) REVERT: A 461 GLU cc_start: 0.8133 (mp0) cc_final: 0.7884 (mp0) REVERT: A 539 TRP cc_start: 0.7697 (p90) cc_final: 0.6910 (p90) REVERT: A 592 MET cc_start: 0.6159 (tmm) cc_final: 0.5561 (tmm) outliers start: 19 outliers final: 11 residues processed: 138 average time/residue: 0.1837 time to fit residues: 32.6734 Evaluate side-chains 137 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 228 PHE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 658 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.0470 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- 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: 0.7509 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5779 Z= 0.169 Angle : 0.503 7.548 7795 Z= 0.256 Chirality : 0.044 0.129 846 Planarity : 0.004 0.051 1012 Dihedral : 10.488 178.418 787 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.75 % Allowed : 20.72 % 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: -0.76 (0.32), residues: 716 helix: 1.49 (0.37), residues: 213 sheet: -1.28 (0.38), residues: 199 loop : -1.34 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 185 HIS 0.004 0.001 HIS A 443 PHE 0.015 0.001 PHE A 271 TYR 0.023 0.001 TYR A 163 ARG 0.005 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 151 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 0.695 Fit side-chains REVERT: A 10 LYS cc_start: 0.7331 (ptpt) cc_final: 0.6940 (ptpt) REVERT: A 224 MET cc_start: 0.6757 (tmm) cc_final: 0.6417 (tpt) REVERT: A 238 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.6374 (ppp) REVERT: A 328 ARG cc_start: 0.7305 (tpp80) cc_final: 0.7080 (tpp80) REVERT: A 329 GLU cc_start: 0.7658 (pm20) cc_final: 0.7367 (pm20) REVERT: A 461 GLU cc_start: 0.8069 (mp0) cc_final: 0.7857 (mp0) REVERT: A 637 MET cc_start: 0.7419 (tpt) cc_final: 0.7021 (tpt) outliers start: 23 outliers final: 16 residues processed: 137 average time/residue: 0.1858 time to fit residues: 33.2092 Evaluate side-chains 142 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 126 ASN 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 337 ASP Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 604 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 0.0020 chunk 32 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7544 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5779 Z= 0.223 Angle : 0.527 7.370 7795 Z= 0.270 Chirality : 0.044 0.129 846 Planarity : 0.004 0.049 1012 Dihedral : 10.480 175.146 787 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.08 % Allowed : 20.88 % 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: -0.93 (0.32), residues: 716 helix: 1.44 (0.37), residues: 213 sheet: -1.45 (0.37), residues: 202 loop : -1.46 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 185 HIS 0.003 0.001 HIS A 502 PHE 0.009 0.001 PHE A 271 TYR 0.022 0.002 TYR A 163 ARG 0.006 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 150 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 0.677 Fit side-chains REVERT: A 10 LYS cc_start: 0.7392 (ptpt) cc_final: 0.7170 (ptpt) REVERT: A 224 MET cc_start: 0.6801 (tmm) cc_final: 0.6424 (tpt) REVERT: A 238 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.6516 (ppp) REVERT: A 328 ARG cc_start: 0.7314 (tpp80) cc_final: 0.7093 (tpp80) REVERT: A 461 GLU cc_start: 0.8130 (mp0) cc_final: 0.7837 (mp0) REVERT: A 637 MET cc_start: 0.7300 (tpt) cc_final: 0.6971 (tpt) outliers start: 25 outliers final: 19 residues processed: 135 average time/residue: 0.1950 time to fit residues: 33.6657 Evaluate side-chains 140 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 66 VAL Chi-restraints excluded: chain A residue 126 ASN 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 269 MET Chi-restraints excluded: chain A residue 297 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7558 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5779 Z= 0.251 Angle : 0.551 7.408 7795 Z= 0.280 Chirality : 0.044 0.130 846 Planarity : 0.004 0.048 1012 Dihedral : 10.524 174.834 787 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.40 % Allowed : 20.72 % Favored : 74.88 % 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: -1.02 (0.32), residues: 716 helix: 1.38 (0.37), residues: 213 sheet: -1.51 (0.37), residues: 204 loop : -1.52 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 185 HIS 0.004 0.001 HIS A 502 PHE 0.010 0.001 PHE A 614 TYR 0.021 0.002 TYR A 163 ARG 0.006 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 148 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 121 time to evaluate : 0.652 Fit side-chains REVERT: A 224 MET cc_start: 0.6858 (tmm) cc_final: 0.6448 (tpt) REVERT: A 236 ASP cc_start: 0.7046 (t70) cc_final: 0.6761 (t0) REVERT: A 238 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.6654 (ppp) REVERT: A 461 GLU cc_start: 0.8144 (mp0) cc_final: 0.7874 (mp0) REVERT: A 637 MET cc_start: 0.7291 (tpt) cc_final: 0.6970 (tpt) outliers start: 27 outliers final: 22 residues processed: 132 average time/residue: 0.1851 time to fit residues: 31.6307 Evaluate side-chains 139 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 66 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 269 MET Chi-restraints excluded: chain A residue 297 VAL 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 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 663 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 0.0970 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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: 0.7543 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5779 Z= 0.209 Angle : 0.527 6.923 7795 Z= 0.269 Chirality : 0.044 0.130 846 Planarity : 0.004 0.049 1012 Dihedral : 10.507 174.500 787 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.75 % Allowed : 21.70 % 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: -1.01 (0.31), residues: 716 helix: 1.39 (0.37), residues: 213 sheet: -1.54 (0.37), residues: 204 loop : -1.48 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 185 HIS 0.004 0.001 HIS A 502 PHE 0.015 0.001 PHE A 520 TYR 0.021 0.002 TYR A 163 ARG 0.006 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 144 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 0.623 Fit side-chains REVERT: A 224 MET cc_start: 0.6803 (tmm) cc_final: 0.6422 (tpt) REVERT: A 236 ASP cc_start: 0.7023 (t70) cc_final: 0.6711 (t0) REVERT: A 238 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.6696 (ppp) outliers start: 23 outliers final: 22 residues processed: 129 average time/residue: 0.1901 time to fit residues: 31.4718 Evaluate side-chains 142 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 66 VAL Chi-restraints excluded: chain A residue 126 ASN 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 269 MET Chi-restraints excluded: chain A residue 297 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 0.0270 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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: 0.7523 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5779 Z= 0.180 Angle : 0.517 6.679 7795 Z= 0.265 Chirality : 0.044 0.129 846 Planarity : 0.004 0.048 1012 Dihedral : 10.454 175.610 787 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.92 % Allowed : 21.70 % Favored : 74.39 % 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 (0.32), residues: 716 helix: 1.48 (0.37), residues: 213 sheet: -1.49 (0.37), residues: 204 loop : -1.43 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 185 HIS 0.004 0.001 HIS A 502 PHE 0.037 0.002 PHE A 693 TYR 0.020 0.001 TYR A 163 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 144 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 0.682 Fit side-chains REVERT: A 224 MET cc_start: 0.6765 (tmm) cc_final: 0.6412 (tpt) REVERT: A 236 ASP cc_start: 0.6986 (t70) cc_final: 0.6681 (t0) REVERT: A 238 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.6646 (ppp) outliers start: 24 outliers final: 21 residues processed: 128 average time/residue: 0.1797 time to fit residues: 29.8818 Evaluate side-chains 139 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 126 ASN 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 269 MET Chi-restraints excluded: chain A residue 297 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.170796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.136560 restraints weight = 7124.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.139621 restraints weight = 4226.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.141857 restraints weight = 2999.051| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5779 Z= 0.298 Angle : 0.574 7.323 7795 Z= 0.295 Chirality : 0.045 0.132 846 Planarity : 0.004 0.049 1012 Dihedral : 10.562 172.985 787 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.08 % Allowed : 21.86 % Favored : 74.06 % 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: -1.16 (0.31), residues: 716 helix: 1.24 (0.37), residues: 213 sheet: -1.58 (0.37), residues: 204 loop : -1.59 (0.32), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 185 HIS 0.006 0.001 HIS A 502 PHE 0.037 0.002 PHE A 693 TYR 0.020 0.002 TYR A 163 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: 1521.12 seconds wall clock time: 28 minutes 25.26 seconds (1705.26 seconds total)