Starting phenix.real_space_refine on Mon Nov 13 21:11:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e50_27899/11_2023/8e50_27899_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e50_27899/11_2023/8e50_27899.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e50_27899/11_2023/8e50_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_27899/11_2023/8e50_27899_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e50_27899/11_2023/8e50_27899_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e50_27899/11_2023/8e50_27899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e50_27899/11_2023/8e50_27899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e50_27899/11_2023/8e50_27899_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e50_27899/11_2023/8e50_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 3.54, per 1000 atoms: 0.67 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: 2.14 Conformation dependent library (CDL) restraints added in 971.1 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: 1.29 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: 1.43 Time building geometry restraints manager: 2.16 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: 0.000 Normalize map: mean=0, sd=1: 2.060 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: 11.630 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.790 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.450 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.623 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2165 time to fit residues: 34.0791 Evaluate side-chains 52 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9254 ------------------------------------------------------------------------------- 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: 0.9990 chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 0.1980 chunk 26 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 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 198 ASN A 363 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN A 715 GLN A 816 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5379 Z= 0.211 Angle : 0.614 7.342 7282 Z= 0.312 Chirality : 0.040 0.152 848 Planarity : 0.004 0.044 904 Dihedral : 14.900 177.257 745 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.94 % Allowed : 9.84 % Favored : 87.22 % 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: -1.17 (0.30), residues: 639 helix: -0.07 (0.25), residues: 384 sheet: -1.19 (0.70), residues: 46 loop : -1.86 (0.37), residues: 209 *********************** 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 76 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.563 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 73 average time/residue: 0.1601 time to fit residues: 15.8846 Evaluate side-chains 53 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.596 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0523 time to fit residues: 1.5161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 308 GLN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN A 741 ASN A 756 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5379 Z= 0.270 Angle : 0.571 7.125 7282 Z= 0.289 Chirality : 0.041 0.145 848 Planarity : 0.004 0.039 904 Dihedral : 14.470 175.528 745 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.94 % Allowed : 12.26 % Favored : 84.80 % 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: 0.04 (0.33), residues: 639 helix: 1.02 (0.27), residues: 376 sheet: -0.63 (0.70), residues: 51 loop : -1.57 (0.39), residues: 212 *********************** 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 70 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 53 time to evaluate : 0.555 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 67 average time/residue: 0.1773 time to fit residues: 15.7630 Evaluate side-chains 50 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.647 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0549 time to fit residues: 1.9553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 39 optimal weight: 0.0030 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN A 816 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5379 Z= 0.182 Angle : 0.508 7.468 7282 Z= 0.253 Chirality : 0.038 0.139 848 Planarity : 0.004 0.040 904 Dihedral : 13.541 172.004 745 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.73 % Allowed : 13.13 % Favored : 85.15 % 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: 0.43 (0.33), residues: 639 helix: 1.36 (0.27), residues: 377 sheet: -0.39 (0.73), residues: 46 loop : -1.49 (0.39), residues: 216 *********************** 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 56 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.647 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 0.1906 time to fit residues: 13.7108 Evaluate side-chains 45 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.604 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0611 time to fit residues: 1.5065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 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 198 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN A 612 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.4615 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= 0.212 Angle : 0.520 8.535 7282 Z= 0.257 Chirality : 0.039 0.132 848 Planarity : 0.004 0.039 904 Dihedral : 12.135 160.502 745 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.21 % Allowed : 13.47 % Favored : 85.32 % 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: 0.60 (0.33), residues: 639 helix: 1.43 (0.27), residues: 377 sheet: -0.06 (0.77), residues: 46 loop : -1.34 (0.40), residues: 216 *********************** 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 52 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.640 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 51 average time/residue: 0.1801 time to fit residues: 12.6103 Evaluate side-chains 42 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.633 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0594 time to fit residues: 1.2882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 52 optimal weight: 0.0030 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.4778 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= 0.160 Angle : 0.481 8.794 7282 Z= 0.237 Chirality : 0.038 0.138 848 Planarity : 0.003 0.038 904 Dihedral : 11.062 154.387 745 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.86 % Allowed : 14.68 % Favored : 84.46 % 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 (0.34), residues: 639 helix: 1.57 (0.27), residues: 378 sheet: -0.20 (0.71), residues: 52 loop : -1.30 (0.41), residues: 209 *********************** 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 50 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 1.211 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 47 average time/residue: 0.2034 time to fit residues: 12.7494 Evaluate side-chains 45 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.603 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0593 time to fit residues: 1.2071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5379 Z= 0.222 Angle : 0.513 8.514 7282 Z= 0.253 Chirality : 0.039 0.194 848 Planarity : 0.004 0.037 904 Dihedral : 10.402 151.730 745 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.35 % Allowed : 15.54 % 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: 0.67 (0.34), residues: 639 helix: 1.52 (0.27), residues: 377 sheet: -0.35 (0.68), residues: 58 loop : -1.36 (0.42), residues: 204 *********************** 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 41 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.667 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 41 average time/residue: 0.1976 time to fit residues: 11.1140 Evaluate side-chains 38 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.666 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.0370 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5379 Z= 0.159 Angle : 0.480 8.737 7282 Z= 0.236 Chirality : 0.038 0.194 848 Planarity : 0.003 0.038 904 Dihedral : 9.866 143.032 745 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.35 % Allowed : 16.23 % Favored : 83.42 % 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: 0.82 (0.34), residues: 639 helix: 1.65 (0.27), residues: 377 sheet: -0.28 (0.68), residues: 58 loop : -1.33 (0.42), residues: 204 *********************** 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 46 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.547 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 46 average time/residue: 0.1895 time to fit residues: 11.7825 Evaluate side-chains 41 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.645 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 52 optimal weight: 0.1980 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 0.0670 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5379 Z= 0.151 Angle : 0.477 8.352 7282 Z= 0.234 Chirality : 0.038 0.198 848 Planarity : 0.003 0.038 904 Dihedral : 9.305 136.669 745 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.17 % Allowed : 16.41 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.34), residues: 639 helix: 1.73 (0.27), residues: 377 sheet: -0.30 (0.68), residues: 58 loop : -1.27 (0.42), residues: 204 *********************** 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 48 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.562 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.2106 time to fit residues: 13.0278 Evaluate side-chains 44 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.647 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0556 time to fit residues: 1.0117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 0.0570 chunk 54 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5379 Z= 0.202 Angle : 0.508 7.904 7282 Z= 0.250 Chirality : 0.039 0.194 848 Planarity : 0.004 0.038 904 Dihedral : 9.361 137.655 745 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 17.27 % 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: 0.84 (0.34), residues: 639 helix: 1.68 (0.27), residues: 376 sheet: -0.44 (0.67), residues: 57 loop : -1.26 (0.42), residues: 206 ********************** 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 44 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.752 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.2391 time to fit residues: 13.9456 Evaluate side-chains 40 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.782 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 0.0020 chunk 9 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 37 optimal weight: 0.0970 chunk 59 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 overall best weight: 0.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 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 = 0.3457 r_free = 0.3457 target = 0.119825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104451 restraints weight = 8475.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.107196 restraints weight = 4852.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.109092 restraints weight = 3297.414| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5379 Z= 0.126 Angle : 0.470 7.745 7282 Z= 0.233 Chirality : 0.038 0.178 848 Planarity : 0.003 0.039 904 Dihedral : 8.879 131.974 745 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.17 % Allowed : 17.44 % Favored : 82.38 % 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 (0.34), residues: 639 helix: 1.83 (0.27), residues: 376 sheet: -0.19 (0.73), residues: 51 loop : -1.18 (0.41), residues: 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1418.62 seconds wall clock time: 26 minutes 35.67 seconds (1595.67 seconds total)