Starting phenix.real_space_refine on Sun Mar 10 21:39:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e50_27899/03_2024/8e50_27899_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e50_27899/03_2024/8e50_27899.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e50_27899/03_2024/8e50_27899_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e50_27899/03_2024/8e50_27899_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e50_27899/03_2024/8e50_27899_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e50_27899/03_2024/8e50_27899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e50_27899/03_2024/8e50_27899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e50_27899/03_2024/8e50_27899_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e50_27899/03_2024/8e50_27899_updated.pdb" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 24 5.16 5 C 3394 2.51 5 N 905 2.21 5 O 950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A GLU 302": "OE1" <-> "OE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 425": "OE1" <-> "OE2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A GLU 629": "OE1" <-> "OE2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A GLU 750": "OE1" <-> "OE2" Residue "A GLU 772": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5277 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5277 Unusual residues: {'COA': 1, 'NKO': 1} Classifications: {'peptide': 651, 'undetermined': 2} Link IDs: {'PTRANS': 21, 'TRANS': 629, None: 2} Not linked: pdbres="LEU A 828 " pdbres="COA A 901 " Not linked: pdbres="COA A 901 " pdbres="NKO A 902 " Chain breaks: 5 Time building chain proxies: 3.61, per 1000 atoms: 0.68 Number of scatterers: 5277 At special positions: 0 Unit cell: (69.72, 93.24, 99.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 4 15.00 O 950 8.00 N 905 7.00 C 3394 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: 1.95 Conformation dependent library (CDL) restraints added in 993.0 milliseconds 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1242 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 6 sheets defined 55.9% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 110 through 116 Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 137 through 148 removed outlier: 3.551A pdb=" N VAL A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 177 removed outlier: 3.872A pdb=" N ASN A 164 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 167 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A 171 " --> pdb=" O LYS A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 200 removed outlier: 3.706A pdb=" N ASN A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 218 removed outlier: 3.692A pdb=" N VAL A 214 " --> pdb=" O GLN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 246 removed outlier: 4.383A pdb=" N LEU A 239 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A 240 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE A 242 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 244 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS A 245 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 264 through 271 removed outlier: 3.596A pdb=" N LYS A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 305 Processing helix chain 'A' and resid 331 through 340 removed outlier: 3.672A pdb=" N LEU A 339 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 368 No H-bonds generated for 'chain 'A' and resid 365 through 368' Processing helix chain 'A' and resid 380 through 389 Processing helix chain 'A' and resid 406 through 415 removed outlier: 3.842A pdb=" N SER A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 431 Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 457 through 477 removed outlier: 4.009A pdb=" N ARG A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 502 through 519 removed outlier: 3.547A pdb=" N ARG A 519 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 539 removed outlier: 3.652A pdb=" N GLN A 538 " --> pdb=" O MET A 534 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 539 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 594 removed outlier: 3.586A pdb=" N LEU A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL A 576 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N HIS A 578 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL A 579 " --> pdb=" O GLY A 575 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE A 580 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N MET A 582 " --> pdb=" O HIS A 578 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLU A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 625 removed outlier: 3.745A pdb=" N SER A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 653 removed outlier: 3.577A pdb=" N GLN A 652 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 739 removed outlier: 3.901A pdb=" N LEU A 725 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY A 726 " --> pdb=" O GLN A 722 " (cutoff:3.500A) Proline residue: A 727 - end of helix removed outlier: 4.227A pdb=" N TYR A 732 " --> pdb=" O LEU A 728 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 764 removed outlier: 4.194A pdb=" N GLN A 753 " --> pdb=" O PRO A 749 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A 754 " --> pdb=" O GLU A 750 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR A 758 " --> pdb=" O LYS A 754 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 774 Processing helix chain 'A' and resid 776 through 789 Processing helix chain 'A' and resid 807 through 809 No H-bonds generated for 'chain 'A' and resid 807 through 809' Processing helix chain 'A' and resid 813 through 825 removed outlier: 3.684A pdb=" N ILE A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE A 825 " --> pdb=" O TYR A 821 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 88 through 90 Processing sheet with id= B, first strand: chain 'A' and resid 223 through 228 Processing sheet with id= C, first strand: chain 'A' and resid 254 through 256 removed outlier: 6.030A pdb=" N PHE A 274 " --> pdb=" O SER A 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 544 through 548 Processing sheet with id= E, first strand: chain 'A' and resid 656 through 658 Processing sheet with id= F, first strand: chain 'A' and resid 792 through 794 220 hydrogen bonds defined for protein. 606 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: 1.39 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.73: 5343 1.73 - 2.26: 34 2.26 - 2.79: 0 2.79 - 3.32: 1 3.32 - 3.85: 1 Bond restraints: 5379 Sorted by residual: bond pdb=" AO6 COA A 901 " pdb=" AP2 COA A 901 " ideal model delta sigma weight residual 1.610 3.850 -2.240 2.00e-02 2.50e+03 1.25e+04 bond pdb=" AP1 COA A 901 " pdb="AO5* COA A 901 " ideal model delta sigma weight residual 1.610 3.240 -1.630 2.00e-02 2.50e+03 6.64e+03 bond pdb=" PC9 COA A 901 " pdb=" PO9 COA A 901 " ideal model delta sigma weight residual 1.410 1.228 0.182 2.00e-02 2.50e+03 8.24e+01 bond pdb=" N VAL A 800 " pdb=" CA VAL A 800 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.14e-02 7.69e+03 1.40e+01 bond pdb=" N VAL A 418 " pdb=" CA VAL A 418 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.14e-02 7.69e+03 1.26e+01 ... (remaining 5374 not shown) Histogram of bond angle deviations from ideal: 25.80 - 50.75: 2 50.75 - 75.71: 1 75.71 - 100.66: 1 100.66 - 125.62: 7087 125.62 - 150.57: 191 Bond angle restraints: 7282 Sorted by residual: angle pdb=" AO3 COA A 901 " pdb=" AP2 COA A 901 " pdb=" AO6 COA A 901 " ideal model delta sigma weight residual 102.60 25.80 76.80 3.00e+00 1.11e-01 6.55e+02 angle pdb=" AO3 COA A 901 " pdb=" AP1 COA A 901 " pdb="AO5* COA A 901 " ideal model delta sigma weight residual 102.60 46.67 55.93 3.00e+00 1.11e-01 3.48e+02 angle pdb=" AO2 COA A 901 " pdb=" AP1 COA A 901 " pdb="AO5* COA A 901 " ideal model delta sigma weight residual 109.50 150.57 -41.07 3.00e+00 1.11e-01 1.87e+02 angle pdb=" AO1 COA A 901 " pdb=" AP1 COA A 901 " pdb="AO5* COA A 901 " ideal model delta sigma weight residual 108.20 68.35 39.85 3.00e+00 1.11e-01 1.76e+02 angle pdb=" AP1 COA A 901 " pdb="AO5* COA A 901 " pdb="AC5* COA A 901 " ideal model delta sigma weight residual 120.50 139.57 -19.07 3.00e+00 1.11e-01 4.04e+01 ... (remaining 7277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.79: 3130 32.79 - 65.58: 94 65.58 - 98.38: 2 98.38 - 131.17: 5 131.17 - 163.96: 2 Dihedral angle restraints: 3233 sinusoidal: 1324 harmonic: 1909 Sorted by residual: dihedral pdb=" AO7 COA A 901 " pdb="AO3* COA A 901 " pdb="AP3* COA A 901 " pdb="AC3* COA A 901 " ideal model delta sinusoidal sigma weight residual 196.54 32.58 163.96 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" AO3 COA A 901 " pdb=" AP1 COA A 901 " pdb="AO5* COA A 901 " pdb="AC5* COA A 901 " ideal model delta sinusoidal sigma weight residual 291.94 137.37 154.57 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" PC9 COA A 901 " pdb="PC10 COA A 901 " pdb="PC11 COA A 901 " pdb="PC12 COA A 901 " ideal model delta sinusoidal sigma weight residual 177.72 -54.11 -128.17 1 2.00e+01 2.50e-03 3.88e+01 ... (remaining 3230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 257 0.043 - 0.086: 250 0.086 - 0.129: 231 0.129 - 0.173: 89 0.173 - 0.216: 21 Chirality restraints: 848 Sorted by residual: chirality pdb=" CA ILE A 347 " pdb=" N ILE A 347 " pdb=" C ILE A 347 " pdb=" CB ILE A 347 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE A 206 " pdb=" N ILE A 206 " pdb=" C ILE A 206 " pdb=" CB ILE A 206 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE A 312 " pdb=" N ILE A 312 " pdb=" C ILE A 312 " pdb=" CB ILE A 312 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 845 not shown) Planarity restraints: 904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 292 " 0.019 2.00e-02 2.50e+03 1.04e-02 2.17e+00 pdb=" CG TYR A 292 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 292 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 292 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 292 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 292 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 292 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 292 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 200 " -0.011 2.00e-02 2.50e+03 9.81e-03 1.68e+00 pdb=" CG PHE A 200 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 200 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 200 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 200 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 200 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 200 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 197 " -0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C PHE A 197 " 0.020 2.00e-02 2.50e+03 pdb=" O PHE A 197 " -0.007 2.00e-02 2.50e+03 pdb=" N ASN A 198 " -0.007 2.00e-02 2.50e+03 ... (remaining 901 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 2 2.26 - 2.92: 1816 2.92 - 3.58: 7493 3.58 - 4.24: 11414 4.24 - 4.90: 20229 Nonbonded interactions: 40954 Sorted by model distance: nonbonded pdb=" AP2 COA A 901 " pdb="AO5* COA A 901 " model vdw 1.603 2.720 nonbonded pdb=" AO6 COA A 901 " pdb=" AP1 COA A 901 " model vdw 1.610 2.720 nonbonded pdb=" O ARG A 318 " pdb=" NH1 ARG A 320 " model vdw 2.345 2.520 nonbonded pdb="AO4* COA A 901 " pdb="AO5* COA A 901 " model vdw 2.472 2.432 nonbonded pdb=" O ILE A 760 " pdb=" OG1 THR A 763 " model vdw 2.494 2.440 ... (remaining 40949 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: 0.010 Normalize map: mean=0, sd=1: 5.270 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: 12.300 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.340 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 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 : 0.040 2.240 5379 Z= 2.221 Angle : 2.286 76.802 7282 Z= 1.451 Chirality : 0.088 0.216 848 Planarity : 0.003 0.014 904 Dihedral : 16.126 163.959 1991 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % 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: -4.32 (0.25), residues: 639 helix: -2.97 (0.18), residues: 376 sheet: -2.38 (0.65), residues: 46 loop : -2.36 (0.34), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 191 HIS 0.008 0.002 HIS A 496 PHE 0.023 0.002 PHE A 200 TYR 0.021 0.003 TYR A 292 ARG 0.004 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 127 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 101 HIS cc_start: 0.5843 (m90) cc_final: 0.5421 (m-70) REVERT: A 104 TRP cc_start: 0.7402 (m-90) cc_final: 0.6883 (m-10) REVERT: A 108 ARG cc_start: 0.6909 (mtt90) cc_final: 0.6379 (tpp80) REVERT: A 117 GLU cc_start: 0.6016 (mt-10) cc_final: 0.5775 (mt-10) REVERT: A 119 ASP cc_start: 0.6640 (t0) cc_final: 0.6161 (t70) REVERT: A 189 THR cc_start: 0.7376 (m) cc_final: 0.7061 (p) REVERT: A 293 ARG cc_start: 0.7075 (mtp180) cc_final: 0.6655 (mtt180) REVERT: A 326 CYS cc_start: 0.8107 (t) cc_final: 0.7507 (p) REVERT: A 328 ARG cc_start: 0.7187 (mtt-85) cc_final: 0.6970 (mmm-85) REVERT: A 356 TYR cc_start: 0.7860 (m-80) cc_final: 0.7629 (m-80) REVERT: A 426 GLN cc_start: 0.6445 (tp40) cc_final: 0.6031 (mt0) REVERT: A 478 LYS cc_start: 0.7108 (ttpt) cc_final: 0.6629 (mmtt) REVERT: A 535 HIS cc_start: 0.7342 (t-90) cc_final: 0.6853 (t70) REVERT: A 614 GLN cc_start: 0.8251 (mt0) cc_final: 0.7561 (tp40) REVERT: A 629 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7384 (mm-30) REVERT: A 632 ILE cc_start: 0.6916 (mt) cc_final: 0.6597 (mt) REVERT: A 657 THR cc_start: 0.6802 (p) cc_final: 0.6588 (p) REVERT: A 704 CYS cc_start: 0.6262 (m) cc_final: 0.5678 (t) REVERT: A 778 LEU cc_start: 0.6528 (mt) cc_final: 0.6139 (mt) REVERT: A 798 LYS cc_start: 0.6232 (mtmt) cc_final: 0.6017 (ttmt) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2079 time to fit residues: 32.6076 Evaluate side-chains 63 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 198 ASN A 363 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN A 614 GLN A 715 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5379 Z= 0.209 Angle : 0.609 8.630 7282 Z= 0.307 Chirality : 0.040 0.152 848 Planarity : 0.004 0.042 904 Dihedral : 14.891 175.898 745 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.59 % Allowed : 9.15 % Favored : 88.26 % 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: -1.19 (0.30), residues: 639 helix: -0.06 (0.25), residues: 383 sheet: -1.26 (0.70), residues: 46 loop : -1.91 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.005 0.001 HIS A 471 PHE 0.016 0.001 PHE A 809 TYR 0.016 0.002 TYR A 776 ARG 0.003 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 83 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 101 HIS cc_start: 0.5931 (m-70) cc_final: 0.5434 (m-70) REVERT: A 104 TRP cc_start: 0.7264 (m-90) cc_final: 0.6830 (m-10) REVERT: A 108 ARG cc_start: 0.6730 (mtt90) cc_final: 0.6343 (tpp-160) REVERT: A 293 ARG cc_start: 0.7178 (mtp180) cc_final: 0.6774 (mtt180) REVERT: A 326 CYS cc_start: 0.8089 (t) cc_final: 0.7421 (p) REVERT: A 328 ARG cc_start: 0.7138 (mtt-85) cc_final: 0.6917 (mmm-85) REVERT: A 356 TYR cc_start: 0.7889 (m-80) cc_final: 0.7365 (m-80) REVERT: A 426 GLN cc_start: 0.6515 (tp40) cc_final: 0.5825 (mt0) REVERT: A 478 LYS cc_start: 0.7222 (ttpt) cc_final: 0.6767 (mmtt) REVERT: A 535 HIS cc_start: 0.7406 (t-90) cc_final: 0.7099 (t70) REVERT: A 546 ILE cc_start: 0.7223 (OUTLIER) cc_final: 0.6920 (mp) REVERT: A 629 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7165 (tp30) REVERT: A 632 ILE cc_start: 0.6721 (mt) cc_final: 0.6378 (mt) REVERT: A 778 LEU cc_start: 0.6544 (mt) cc_final: 0.6290 (mt) REVERT: A 788 ASP cc_start: 0.7956 (t0) cc_final: 0.7687 (t0) outliers start: 15 outliers final: 5 residues processed: 80 average time/residue: 0.2017 time to fit residues: 20.5288 Evaluate side-chains 62 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 546 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.0370 chunk 16 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 52 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5379 Z= 0.187 Angle : 0.517 7.638 7282 Z= 0.260 Chirality : 0.039 0.143 848 Planarity : 0.004 0.037 904 Dihedral : 14.215 177.207 745 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.28 % Allowed : 10.54 % Favored : 86.18 % 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: 0.22 (0.33), residues: 639 helix: 1.17 (0.27), residues: 379 sheet: -0.73 (0.73), residues: 46 loop : -1.51 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 379 HIS 0.005 0.001 HIS A 471 PHE 0.013 0.001 PHE A 200 TYR 0.010 0.001 TYR A 776 ARG 0.003 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 85 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 0.677 Fit side-chains REVERT: A 101 HIS cc_start: 0.6166 (m-70) cc_final: 0.5665 (m-70) REVERT: A 104 TRP cc_start: 0.7203 (m-90) cc_final: 0.6856 (m-10) REVERT: A 108 ARG cc_start: 0.6740 (mtt90) cc_final: 0.6314 (tpp-160) REVERT: A 239 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7242 (tm) REVERT: A 293 ARG cc_start: 0.7156 (mtp180) cc_final: 0.6871 (mtt-85) REVERT: A 326 CYS cc_start: 0.8108 (t) cc_final: 0.7462 (p) REVERT: A 328 ARG cc_start: 0.7008 (mtt-85) cc_final: 0.6807 (mmm-85) REVERT: A 356 TYR cc_start: 0.7852 (m-80) cc_final: 0.7436 (m-80) REVERT: A 357 ASP cc_start: 0.8151 (t0) cc_final: 0.7887 (t0) REVERT: A 426 GLN cc_start: 0.6900 (tp40) cc_final: 0.6070 (mt0) REVERT: A 478 LYS cc_start: 0.7289 (ttpt) cc_final: 0.6821 (mmtt) REVERT: A 522 ASP cc_start: 0.7206 (m-30) cc_final: 0.6973 (m-30) REVERT: A 546 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7096 (mp) REVERT: A 629 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7255 (tp30) REVERT: A 788 ASP cc_start: 0.7989 (t0) cc_final: 0.7764 (t0) outliers start: 19 outliers final: 13 residues processed: 80 average time/residue: 0.2358 time to fit residues: 24.4825 Evaluate side-chains 68 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 53 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 795 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 GLN A 368 GLN A 552 ASN A 612 GLN A 756 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5379 Z= 0.235 Angle : 0.550 7.737 7282 Z= 0.270 Chirality : 0.039 0.150 848 Planarity : 0.004 0.037 904 Dihedral : 13.176 171.909 745 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.97 % Allowed : 11.92 % Favored : 84.11 % 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: 0.38 (0.33), residues: 639 helix: 1.27 (0.27), residues: 376 sheet: -0.64 (0.70), residues: 52 loop : -1.35 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 379 HIS 0.006 0.001 HIS A 471 PHE 0.020 0.002 PHE A 738 TYR 0.011 0.001 TYR A 776 ARG 0.008 0.001 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 74 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 51 time to evaluate : 0.653 Fit side-chains REVERT: A 101 HIS cc_start: 0.6278 (m-70) cc_final: 0.5927 (m-70) REVERT: A 104 TRP cc_start: 0.7141 (m-90) cc_final: 0.6801 (m-10) REVERT: A 108 ARG cc_start: 0.6724 (mtt90) cc_final: 0.6315 (tpp-160) REVERT: A 138 ARG cc_start: 0.6463 (mmp-170) cc_final: 0.6165 (tpt-90) REVERT: A 239 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7283 (tm) REVERT: A 287 ARG cc_start: 0.7636 (mtt180) cc_final: 0.6825 (mtm-85) REVERT: A 293 ARG cc_start: 0.7190 (mtp180) cc_final: 0.6982 (mtt-85) REVERT: A 326 CYS cc_start: 0.8143 (t) cc_final: 0.7367 (p) REVERT: A 356 TYR cc_start: 0.7947 (m-80) cc_final: 0.7449 (m-80) REVERT: A 357 ASP cc_start: 0.8203 (t0) cc_final: 0.7938 (t0) REVERT: A 426 GLN cc_start: 0.7189 (tp40) cc_final: 0.6130 (mt0) REVERT: A 478 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6850 (mmtt) REVERT: A 546 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7080 (mp) REVERT: A 552 ASN cc_start: 0.6271 (OUTLIER) cc_final: 0.6007 (m-40) REVERT: A 629 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7075 (tp30) REVERT: A 788 ASP cc_start: 0.7946 (t0) cc_final: 0.7738 (t0) REVERT: A 794 GLU cc_start: 0.7157 (tt0) cc_final: 0.6538 (pm20) outliers start: 23 outliers final: 16 residues processed: 72 average time/residue: 0.2122 time to fit residues: 19.3317 Evaluate side-chains 65 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 45 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 740 HIS Chi-restraints excluded: chain A residue 795 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 43 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 198 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5379 Z= 0.174 Angle : 0.500 8.741 7282 Z= 0.245 Chirality : 0.038 0.133 848 Planarity : 0.004 0.038 904 Dihedral : 12.001 164.369 745 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.63 % Allowed : 12.78 % Favored : 83.59 % 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: 0.72 (0.33), residues: 639 helix: 1.55 (0.27), residues: 376 sheet: 0.04 (0.79), residues: 46 loop : -1.34 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 191 HIS 0.004 0.001 HIS A 471 PHE 0.017 0.001 PHE A 738 TYR 0.009 0.001 TYR A 236 ARG 0.006 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 71 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 50 time to evaluate : 0.644 Fit side-chains REVERT: A 101 HIS cc_start: 0.6264 (m-70) cc_final: 0.5939 (m-70) REVERT: A 104 TRP cc_start: 0.7147 (m-90) cc_final: 0.6803 (m-10) REVERT: A 108 ARG cc_start: 0.6699 (mtt90) cc_final: 0.6306 (tpp-160) REVERT: A 138 ARG cc_start: 0.6639 (mmp-170) cc_final: 0.6371 (mmm160) REVERT: A 239 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7226 (tm) REVERT: A 287 ARG cc_start: 0.7802 (mtt180) cc_final: 0.6980 (mtm-85) REVERT: A 326 CYS cc_start: 0.8047 (t) cc_final: 0.7382 (p) REVERT: A 356 TYR cc_start: 0.7912 (m-80) cc_final: 0.7438 (m-80) REVERT: A 357 ASP cc_start: 0.8103 (t0) cc_final: 0.7800 (t0) REVERT: A 426 GLN cc_start: 0.7308 (tp40) cc_final: 0.6269 (mt0) REVERT: A 478 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6816 (mmtt) REVERT: A 546 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7131 (mp) REVERT: A 629 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7100 (tp30) REVERT: A 788 ASP cc_start: 0.7921 (t0) cc_final: 0.7704 (t0) REVERT: A 794 GLU cc_start: 0.7154 (tt0) cc_final: 0.6517 (pm20) outliers start: 21 outliers final: 17 residues processed: 66 average time/residue: 0.2173 time to fit residues: 18.0914 Evaluate side-chains 66 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 46 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 740 HIS Chi-restraints excluded: chain A residue 795 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.0040 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5379 Z= 0.256 Angle : 0.536 8.626 7282 Z= 0.263 Chirality : 0.039 0.134 848 Planarity : 0.004 0.038 904 Dihedral : 11.286 155.019 745 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.66 % Allowed : 12.61 % Favored : 82.73 % 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: 0.69 (0.33), residues: 639 helix: 1.53 (0.27), residues: 373 sheet: -0.38 (0.69), residues: 58 loop : -1.26 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 379 HIS 0.006 0.001 HIS A 471 PHE 0.017 0.002 PHE A 738 TYR 0.010 0.001 TYR A 776 ARG 0.005 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 73 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 46 time to evaluate : 0.567 Fit side-chains REVERT: A 101 HIS cc_start: 0.6147 (m-70) cc_final: 0.5812 (m-70) REVERT: A 104 TRP cc_start: 0.7190 (m-90) cc_final: 0.6836 (m-10) REVERT: A 108 ARG cc_start: 0.6694 (mtt90) cc_final: 0.6242 (tpp-160) REVERT: A 137 SER cc_start: 0.6465 (p) cc_final: 0.6237 (t) REVERT: A 138 ARG cc_start: 0.6796 (mmp-170) cc_final: 0.6491 (mmm160) REVERT: A 239 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7231 (tm) REVERT: A 287 ARG cc_start: 0.7743 (mtt180) cc_final: 0.6903 (mtm-85) REVERT: A 326 CYS cc_start: 0.8073 (t) cc_final: 0.7374 (p) REVERT: A 356 TYR cc_start: 0.7951 (m-80) cc_final: 0.7430 (m-80) REVERT: A 357 ASP cc_start: 0.8151 (t0) cc_final: 0.7791 (t0) REVERT: A 426 GLN cc_start: 0.7572 (tp40) cc_final: 0.6531 (mt0) REVERT: A 478 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6770 (mmtt) REVERT: A 546 ILE cc_start: 0.7414 (OUTLIER) cc_final: 0.7092 (mp) REVERT: A 629 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7150 (tp30) REVERT: A 788 ASP cc_start: 0.7855 (t0) cc_final: 0.7655 (t0) REVERT: A 794 GLU cc_start: 0.7238 (tt0) cc_final: 0.6606 (pm20) outliers start: 27 outliers final: 21 residues processed: 69 average time/residue: 0.1866 time to fit residues: 16.7058 Evaluate side-chains 69 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 45 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 740 HIS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 795 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 0.0670 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5379 Z= 0.180 Angle : 0.505 8.653 7282 Z= 0.244 Chirality : 0.038 0.167 848 Planarity : 0.004 0.038 904 Dihedral : 10.444 151.683 745 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.32 % Allowed : 12.78 % Favored : 82.90 % 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: 0.75 (0.33), residues: 639 helix: 1.51 (0.27), residues: 378 sheet: -0.25 (0.69), residues: 58 loop : -1.20 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 191 HIS 0.005 0.001 HIS A 471 PHE 0.017 0.001 PHE A 738 TYR 0.009 0.001 TYR A 236 ARG 0.005 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 74 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 49 time to evaluate : 0.669 Fit side-chains REVERT: A 101 HIS cc_start: 0.6107 (m-70) cc_final: 0.5756 (m-70) REVERT: A 104 TRP cc_start: 0.7174 (m-90) cc_final: 0.6811 (m-10) REVERT: A 108 ARG cc_start: 0.6731 (mtt90) cc_final: 0.6255 (tpp-160) REVERT: A 137 SER cc_start: 0.6441 (p) cc_final: 0.6227 (t) REVERT: A 138 ARG cc_start: 0.6788 (mmp-170) cc_final: 0.6479 (mmm160) REVERT: A 239 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7229 (tm) REVERT: A 287 ARG cc_start: 0.7758 (mtt180) cc_final: 0.6906 (mtm-85) REVERT: A 326 CYS cc_start: 0.8061 (t) cc_final: 0.7381 (p) REVERT: A 356 TYR cc_start: 0.7974 (m-80) cc_final: 0.7491 (m-80) REVERT: A 357 ASP cc_start: 0.8079 (t0) cc_final: 0.7695 (t0) REVERT: A 426 GLN cc_start: 0.7618 (tp40) cc_final: 0.6591 (mt0) REVERT: A 478 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6745 (mmtt) REVERT: A 546 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7104 (mp) REVERT: A 629 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7112 (tp30) REVERT: A 788 ASP cc_start: 0.7831 (t0) cc_final: 0.7622 (t0) REVERT: A 794 GLU cc_start: 0.7257 (tt0) cc_final: 0.6611 (pm20) outliers start: 25 outliers final: 20 residues processed: 69 average time/residue: 0.2188 time to fit residues: 19.1170 Evaluate side-chains 68 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 45 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 740 HIS Chi-restraints excluded: chain A residue 795 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 0.0570 chunk 42 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5379 Z= 0.177 Angle : 0.501 8.555 7282 Z= 0.242 Chirality : 0.038 0.186 848 Planarity : 0.004 0.038 904 Dihedral : 10.076 147.638 745 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.97 % Allowed : 13.82 % Favored : 82.21 % 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: 0.83 (0.34), residues: 639 helix: 1.61 (0.27), residues: 377 sheet: -0.17 (0.69), residues: 58 loop : -1.25 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 191 HIS 0.004 0.001 HIS A 471 PHE 0.015 0.001 PHE A 738 TYR 0.009 0.001 TYR A 236 ARG 0.005 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 69 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 46 time to evaluate : 0.579 Fit side-chains REVERT: A 101 HIS cc_start: 0.6130 (m-70) cc_final: 0.5791 (m-70) REVERT: A 104 TRP cc_start: 0.7170 (m-90) cc_final: 0.6810 (m-10) REVERT: A 108 ARG cc_start: 0.6727 (mtt90) cc_final: 0.6247 (tpp-160) REVERT: A 137 SER cc_start: 0.6469 (p) cc_final: 0.6241 (t) REVERT: A 138 ARG cc_start: 0.6769 (mmp-170) cc_final: 0.6442 (mmm160) REVERT: A 239 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7211 (tm) REVERT: A 287 ARG cc_start: 0.7795 (mtt180) cc_final: 0.6907 (mtm-85) REVERT: A 326 CYS cc_start: 0.8061 (t) cc_final: 0.7366 (p) REVERT: A 356 TYR cc_start: 0.7988 (m-80) cc_final: 0.7510 (m-80) REVERT: A 357 ASP cc_start: 0.8098 (t0) cc_final: 0.7715 (t0) REVERT: A 426 GLN cc_start: 0.7633 (tp40) cc_final: 0.6591 (mt0) REVERT: A 478 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6744 (mmtt) REVERT: A 546 ILE cc_start: 0.7417 (OUTLIER) cc_final: 0.7107 (mp) REVERT: A 629 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7071 (tp30) REVERT: A 788 ASP cc_start: 0.7842 (t0) cc_final: 0.7635 (t0) REVERT: A 794 GLU cc_start: 0.7286 (tt0) cc_final: 0.6613 (pm20) outliers start: 23 outliers final: 17 residues processed: 65 average time/residue: 0.1995 time to fit residues: 16.7940 Evaluate side-chains 65 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 45 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 740 HIS Chi-restraints excluded: chain A residue 795 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 58 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 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 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5379 Z= 0.190 Angle : 0.510 9.679 7282 Z= 0.245 Chirality : 0.038 0.197 848 Planarity : 0.004 0.038 904 Dihedral : 9.772 143.327 745 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.45 % Allowed : 14.34 % Favored : 82.21 % 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: 0.83 (0.33), residues: 639 helix: 1.62 (0.27), residues: 376 sheet: -0.11 (0.69), residues: 58 loop : -1.26 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 191 HIS 0.005 0.001 HIS A 471 PHE 0.016 0.001 PHE A 200 TYR 0.009 0.001 TYR A 236 ARG 0.004 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 66 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 46 time to evaluate : 0.606 Fit side-chains REVERT: A 101 HIS cc_start: 0.6104 (m-70) cc_final: 0.5738 (m-70) REVERT: A 104 TRP cc_start: 0.7203 (m-90) cc_final: 0.6842 (m-10) REVERT: A 108 ARG cc_start: 0.6710 (mtt90) cc_final: 0.6244 (tpp-160) REVERT: A 239 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7208 (tm) REVERT: A 287 ARG cc_start: 0.7799 (mtt180) cc_final: 0.6895 (mtm-85) REVERT: A 326 CYS cc_start: 0.8044 (t) cc_final: 0.7343 (p) REVERT: A 356 TYR cc_start: 0.8020 (m-80) cc_final: 0.7525 (m-80) REVERT: A 357 ASP cc_start: 0.8093 (t0) cc_final: 0.7877 (t0) REVERT: A 426 GLN cc_start: 0.7652 (tp40) cc_final: 0.6620 (mt0) REVERT: A 478 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6727 (mmtt) REVERT: A 546 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.7136 (mp) REVERT: A 629 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7035 (tp30) REVERT: A 794 GLU cc_start: 0.7293 (tt0) cc_final: 0.6626 (pm20) outliers start: 20 outliers final: 16 residues processed: 63 average time/residue: 0.1773 time to fit residues: 14.8468 Evaluate side-chains 64 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 45 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 740 HIS Chi-restraints excluded: chain A residue 795 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5379 Z= 0.183 Angle : 0.502 8.551 7282 Z= 0.245 Chirality : 0.038 0.194 848 Planarity : 0.004 0.038 904 Dihedral : 9.589 141.082 745 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.45 % Allowed : 14.51 % Favored : 82.04 % 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: 0.89 (0.33), residues: 639 helix: 1.68 (0.27), residues: 376 sheet: -0.15 (0.70), residues: 58 loop : -1.26 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 191 HIS 0.004 0.001 HIS A 471 PHE 0.018 0.001 PHE A 738 TYR 0.009 0.001 TYR A 236 ARG 0.004 0.000 ARG A 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 67 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 47 time to evaluate : 0.613 Fit side-chains REVERT: A 104 TRP cc_start: 0.7205 (m-90) cc_final: 0.6850 (m-10) REVERT: A 108 ARG cc_start: 0.6725 (mtt90) cc_final: 0.6258 (tpp-160) REVERT: A 138 ARG cc_start: 0.6818 (mmp-170) cc_final: 0.6449 (mmm160) REVERT: A 239 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7185 (tm) REVERT: A 287 ARG cc_start: 0.7743 (mtt180) cc_final: 0.6847 (mtm-85) REVERT: A 326 CYS cc_start: 0.8034 (t) cc_final: 0.7303 (p) REVERT: A 356 TYR cc_start: 0.8005 (m-80) cc_final: 0.7505 (m-80) REVERT: A 357 ASP cc_start: 0.8084 (t0) cc_final: 0.7866 (t0) REVERT: A 426 GLN cc_start: 0.7664 (tp40) cc_final: 0.6653 (mt0) REVERT: A 478 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6744 (mmtt) REVERT: A 546 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7106 (mp) REVERT: A 629 GLU cc_start: 0.7725 (tm-30) cc_final: 0.6916 (tp30) REVERT: A 788 ASP cc_start: 0.8176 (t0) cc_final: 0.7923 (t0) REVERT: A 794 GLU cc_start: 0.7236 (tt0) cc_final: 0.6567 (pm20) outliers start: 20 outliers final: 17 residues processed: 64 average time/residue: 0.1972 time to fit residues: 16.3761 Evaluate side-chains 65 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 45 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 740 HIS Chi-restraints excluded: chain A residue 795 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.0270 chunk 34 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.117954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.102280 restraints weight = 8389.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.105024 restraints weight = 4802.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.106806 restraints weight = 3259.194| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5379 Z= 0.163 Angle : 0.481 8.685 7282 Z= 0.236 Chirality : 0.038 0.187 848 Planarity : 0.003 0.039 904 Dihedral : 9.133 138.721 745 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.28 % Allowed : 14.68 % Favored : 82.04 % 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: 1.00 (0.34), residues: 639 helix: 1.79 (0.27), residues: 376 sheet: -0.16 (0.70), residues: 58 loop : -1.22 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 191 HIS 0.004 0.001 HIS A 471 PHE 0.017 0.001 PHE A 738 TYR 0.009 0.001 TYR A 236 ARG 0.004 0.000 ARG A 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1485.29 seconds wall clock time: 27 minutes 50.48 seconds (1670.48 seconds total)