Starting phenix.real_space_refine on Sun Jun 15 03:35:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cf0_45525/06_2025/9cf0_45525_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cf0_45525/06_2025/9cf0_45525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cf0_45525/06_2025/9cf0_45525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cf0_45525/06_2025/9cf0_45525.map" model { file = "/net/cci-nas-00/data/ceres_data/9cf0_45525/06_2025/9cf0_45525_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cf0_45525/06_2025/9cf0_45525_neut.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 79 5.49 5 S 35 5.16 5 C 5386 2.51 5 N 1558 2.21 5 O 1816 1.98 5 H 8166 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17040 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2426 Classifications: {'peptide': 162} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 151} Chain: "N" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 349 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "P" Number of atoms: 12097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 12097 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 26, 'TRANS': 699} Chain breaks: 1 Chain: "T" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 446 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "W" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1722 Classifications: {'DNA': 13, 'RNA': 41} Modifications used: {'3*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 16, 'rna3p_pyr': 14} Link IDs: {'rna2p': 11, 'rna3p': 42} Time building chain proxies: 8.25, per 1000 atoms: 0.48 Number of scatterers: 17040 At special positions: 0 Unit cell: (78.375, 119.625, 120.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 79 15.00 O 1816 8.00 N 1558 7.00 C 5386 6.00 H 8166 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.32 Conformation dependent library (CDL) restraints added in 1.1 seconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 8 sheets defined 51.7% alpha, 12.0% beta 22 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 8.03 Creating SS restraints... Processing helix chain 'B' and resid 27 through 40 Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 133 through 142 Processing helix chain 'P' and resid 114 through 118 Processing helix chain 'P' and resid 119 through 121 No H-bonds generated for 'chain 'P' and resid 119 through 121' Processing helix chain 'P' and resid 122 through 153 removed outlier: 3.549A pdb=" N LEU P 126 " --> pdb=" O TYR P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 164 removed outlier: 3.668A pdb=" N ILE P 164 " --> pdb=" O ASN P 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 176 removed outlier: 3.521A pdb=" N PHE P 169 " --> pdb=" O THR P 165 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU P 171 " --> pdb=" O ASP P 167 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU P 176 " --> pdb=" O VAL P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 188 through 210 removed outlier: 3.869A pdb=" N HIS P 201 " --> pdb=" O LEU P 197 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASP P 203 " --> pdb=" O GLY P 199 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ALA P 204 " --> pdb=" O LYS P 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 254 removed outlier: 4.330A pdb=" N LYS P 229 " --> pdb=" O TYR P 225 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLY P 243 " --> pdb=" O LYS P 239 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN P 244 " --> pdb=" O ALA P 240 " (cutoff:3.500A) Processing helix chain 'P' and resid 255 through 270 Processing helix chain 'P' and resid 273 through 285 removed outlier: 3.876A pdb=" N LYS P 283 " --> pdb=" O GLN P 279 " (cutoff:3.500A) Processing helix chain 'P' and resid 285 through 298 removed outlier: 3.671A pdb=" N LYS P 298 " --> pdb=" O LEU P 294 " (cutoff:3.500A) Processing helix chain 'P' and resid 308 through 320 Processing helix chain 'P' and resid 328 through 331 Processing helix chain 'P' and resid 332 through 340 removed outlier: 4.579A pdb=" N VAL P 338 " --> pdb=" O PHE P 334 " (cutoff:3.500A) Processing helix chain 'P' and resid 341 through 343 No H-bonds generated for 'chain 'P' and resid 341 through 343' Processing helix chain 'P' and resid 344 through 358 Processing helix chain 'P' and resid 381 through 388 removed outlier: 3.825A pdb=" N TYR P 386 " --> pdb=" O LYS P 382 " (cutoff:3.500A) Processing helix chain 'P' and resid 396 through 398 No H-bonds generated for 'chain 'P' and resid 396 through 398' Processing helix chain 'P' and resid 399 through 406 removed outlier: 3.750A pdb=" N ARG P 406 " --> pdb=" O ASN P 402 " (cutoff:3.500A) Processing helix chain 'P' and resid 412 through 416 removed outlier: 3.687A pdb=" N PHE P 415 " --> pdb=" O ARG P 412 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS P 416 " --> pdb=" O LYS P 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 412 through 416' Processing helix chain 'P' and resid 419 through 423 Processing helix chain 'P' and resid 466 through 470 Processing helix chain 'P' and resid 471 through 476 Processing helix chain 'P' and resid 511 through 516 Processing helix chain 'P' and resid 516 through 529 Processing helix chain 'P' and resid 531 through 542 Processing helix chain 'P' and resid 550 through 574 removed outlier: 3.572A pdb=" N VAL P 564 " --> pdb=" O ALA P 560 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ASP P 566 " --> pdb=" O ALA P 562 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE P 567 " --> pdb=" O SER P 563 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU P 570 " --> pdb=" O ASP P 566 " (cutoff:3.500A) Processing helix chain 'P' and resid 622 through 639 removed outlier: 3.900A pdb=" N LYS P 626 " --> pdb=" O ASP P 622 " (cutoff:3.500A) Processing helix chain 'P' and resid 640 through 645 Processing helix chain 'P' and resid 648 through 663 removed outlier: 3.823A pdb=" N LEU P 663 " --> pdb=" O ALA P 659 " (cutoff:3.500A) Processing helix chain 'P' and resid 668 through 679 removed outlier: 4.300A pdb=" N LYS P 672 " --> pdb=" O GLU P 668 " (cutoff:3.500A) Processing helix chain 'P' and resid 680 through 684 removed outlier: 3.874A pdb=" N ARG P 683 " --> pdb=" O GLY P 680 " (cutoff:3.500A) Processing helix chain 'P' and resid 686 through 713 removed outlier: 3.855A pdb=" N LYS P 711 " --> pdb=" O LYS P 707 " (cutoff:3.500A) Processing helix chain 'P' and resid 736 through 747 removed outlier: 3.746A pdb=" N LEU P 740 " --> pdb=" O ARG P 736 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ARG P 742 " --> pdb=" O LYS P 738 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET P 743 " --> pdb=" O GLY P 739 " (cutoff:3.500A) Processing helix chain 'P' and resid 780 through 785 removed outlier: 4.662A pdb=" N GLU P 785 " --> pdb=" O PRO P 781 " (cutoff:3.500A) Processing helix chain 'P' and resid 801 through 806 removed outlier: 3.988A pdb=" N GLU P 805 " --> pdb=" O SER P 802 " (cutoff:3.500A) Processing helix chain 'P' and resid 818 through 837 Processing sheet with id=AA1, first strand: chain 'B' and resid 53 through 55 removed outlier: 3.642A pdb=" N ARG B 53 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU B 95 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N MET B 98 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 126 " --> pdb=" O MET B 98 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 19 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA B 10 " --> pdb=" O PRO B 14 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 2 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 158 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU B 9 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N VAL B 156 " --> pdb=" O GLU B 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 107 through 113 removed outlier: 4.119A pdb=" N LEU P 440 " --> pdb=" O THR P 429 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N THR P 429 " --> pdb=" O LEU P 440 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 107 through 113 Processing sheet with id=AA4, first strand: chain 'P' and resid 177 through 178 Processing sheet with id=AA5, first strand: chain 'P' and resid 507 through 510 removed outlier: 6.432A pdb=" N LEU P 719 " --> pdb=" O TYR P 752 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 592 through 593 removed outlier: 3.801A pdb=" N ALA P 607 " --> pdb=" O LEU P 599 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 770 through 772 Processing sheet with id=AA8, first strand: chain 'P' and resid 775 through 777 348 hydrogen bonds defined for protein. 990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 7.27 Time building geometry restraints manager: 5.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 8149 1.12 - 1.30: 1306 1.30 - 1.47: 3741 1.47 - 1.65: 4146 1.65 - 1.82: 53 Bond restraints: 17395 Sorted by residual: bond pdb=" N SER P 693 " pdb=" H SER P 693 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N VAL P 407 " pdb=" H VAL P 407 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASP P 380 " pdb=" H ASP P 380 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NH2 ARG P 193 " pdb="HH21 ARG P 193 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" ND2 ASN P 237 " pdb="HD21 ASN P 237 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 17390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 27228 2.72 - 5.43: 3360 5.43 - 8.15: 818 8.15 - 10.87: 24 10.87 - 13.58: 18 Bond angle restraints: 31448 Sorted by residual: angle pdb=" O3' U W 31 " pdb=" C3' U W 31 " pdb=" C2' U W 31 " ideal model delta sigma weight residual 109.50 122.06 -12.56 1.50e+00 4.44e-01 7.01e+01 angle pdb=" O3' C W 27 " pdb=" P A W 28 " pdb=" O5' A W 28 " ideal model delta sigma weight residual 104.00 115.14 -11.14 1.50e+00 4.44e-01 5.51e+01 angle pdb=" O3' U W 17 " pdb=" C3' U W 17 " pdb=" C2' U W 17 " ideal model delta sigma weight residual 109.50 119.62 -10.12 1.50e+00 4.44e-01 4.55e+01 angle pdb=" O3' U W 30 " pdb=" C3' U W 30 " pdb=" C2' U W 30 " ideal model delta sigma weight residual 109.50 119.56 -10.06 1.50e+00 4.44e-01 4.50e+01 angle pdb=" CA PRO P 103 " pdb=" N PRO P 103 " pdb=" CD PRO P 103 " ideal model delta sigma weight residual 112.00 103.29 8.71 1.40e+00 5.10e-01 3.87e+01 ... (remaining 31443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 7572 35.73 - 71.46: 451 71.46 - 107.19: 27 107.19 - 142.92: 8 142.92 - 178.65: 5 Dihedral angle restraints: 8063 sinusoidal: 4937 harmonic: 3126 Sorted by residual: dihedral pdb=" C5' A W 32 " pdb=" C4' A W 32 " pdb=" C3' A W 32 " pdb=" O3' A W 32 " ideal model delta sinusoidal sigma weight residual 147.00 77.23 69.77 1 8.00e+00 1.56e-02 9.81e+01 dihedral pdb=" O4' A W 32 " pdb=" C4' A W 32 " pdb=" C3' A W 32 " pdb=" C2' A W 32 " ideal model delta sinusoidal sigma weight residual 24.00 -34.44 58.44 1 8.00e+00 1.56e-02 7.15e+01 dihedral pdb=" O4' C W 18 " pdb=" C1' C W 18 " pdb=" N1 C W 18 " pdb=" C2 C W 18 " ideal model delta sinusoidal sigma weight residual 200.00 75.60 124.40 1 1.50e+01 4.44e-03 6.68e+01 ... (remaining 8060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 1147 0.117 - 0.234: 245 0.234 - 0.350: 23 0.350 - 0.467: 6 0.467 - 0.584: 1 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA TYR P 613 " pdb=" N TYR P 613 " pdb=" C TYR P 613 " pdb=" CB TYR P 613 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.53e+00 chirality pdb=" C1' G W 19 " pdb=" O4' G W 19 " pdb=" C2' G W 19 " pdb=" N9 G W 19 " both_signs ideal model delta sigma weight residual False 2.46 2.04 0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" C3' U W 30 " pdb=" C4' U W 30 " pdb=" O3' U W 30 " pdb=" C2' U W 30 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 1419 not shown) Planarity restraints: 2258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G W 19 " 0.735 2.00e-02 2.50e+03 2.58e-01 2.34e+03 pdb=" N9 G W 19 " -0.049 2.00e-02 2.50e+03 pdb=" C8 G W 19 " -0.147 2.00e-02 2.50e+03 pdb=" N7 G W 19 " -0.166 2.00e-02 2.50e+03 pdb=" C5 G W 19 " -0.120 2.00e-02 2.50e+03 pdb=" C6 G W 19 " 0.048 2.00e-02 2.50e+03 pdb=" O6 G W 19 " 0.284 2.00e-02 2.50e+03 pdb=" N1 G W 19 " 0.043 2.00e-02 2.50e+03 pdb=" C2 G W 19 " -0.162 2.00e-02 2.50e+03 pdb=" N2 G W 19 " -0.088 2.00e-02 2.50e+03 pdb=" N3 G W 19 " -0.296 2.00e-02 2.50e+03 pdb=" C4 G W 19 " -0.224 2.00e-02 2.50e+03 pdb=" H8 G W 19 " -0.104 2.00e-02 2.50e+03 pdb=" H1 G W 19 " 0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U W 30 " 0.641 2.00e-02 2.50e+03 2.46e-01 1.82e+03 pdb=" N1 U W 30 " -0.042 2.00e-02 2.50e+03 pdb=" C2 U W 30 " -0.192 2.00e-02 2.50e+03 pdb=" O2 U W 30 " -0.304 2.00e-02 2.50e+03 pdb=" N3 U W 30 " -0.043 2.00e-02 2.50e+03 pdb=" C4 U W 30 " 0.092 2.00e-02 2.50e+03 pdb=" O4 U W 30 " 0.322 2.00e-02 2.50e+03 pdb=" C5 U W 30 " -0.077 2.00e-02 2.50e+03 pdb=" C6 U W 30 " -0.148 2.00e-02 2.50e+03 pdb=" H5 U W 30 " -0.075 2.00e-02 2.50e+03 pdb=" H3 U W 30 " 0.020 2.00e-02 2.50e+03 pdb=" H6 U W 30 " -0.192 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U W 17 " 0.416 2.00e-02 2.50e+03 1.74e-01 9.13e+02 pdb=" N1 U W 17 " 0.011 2.00e-02 2.50e+03 pdb=" C2 U W 17 " -0.065 2.00e-02 2.50e+03 pdb=" O2 U W 17 " -0.290 2.00e-02 2.50e+03 pdb=" N3 U W 17 " 0.026 2.00e-02 2.50e+03 pdb=" C4 U W 17 " 0.078 2.00e-02 2.50e+03 pdb=" O4 U W 17 " 0.228 2.00e-02 2.50e+03 pdb=" C5 U W 17 " -0.053 2.00e-02 2.50e+03 pdb=" C6 U W 17 " -0.081 2.00e-02 2.50e+03 pdb=" H5 U W 17 " -0.116 2.00e-02 2.50e+03 pdb=" H3 U W 17 " -0.005 2.00e-02 2.50e+03 pdb=" H6 U W 17 " -0.149 2.00e-02 2.50e+03 ... (remaining 2255 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 830 2.16 - 2.77: 27522 2.77 - 3.38: 46340 3.38 - 3.99: 61268 3.99 - 4.60: 90602 Nonbonded interactions: 226562 Sorted by model distance: nonbonded pdb="HO2' U W 31 " pdb=" OP1 A W 32 " model vdw 1.552 2.450 nonbonded pdb="HO2' U W 17 " pdb=" OP2 C W 18 " model vdw 1.565 2.450 nonbonded pdb="HO2' A W 33 " pdb=" OP1 U W 34 " model vdw 1.584 2.450 nonbonded pdb=" HG1 THR P 499 " pdb=" OE1 GLU P 506 " model vdw 1.586 2.450 nonbonded pdb=" OE2 GLU P 538 " pdb=" HH TYR P 572 " model vdw 1.598 2.450 ... (remaining 226557 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic 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: 1.870 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: 0.270 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 44.380 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 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 : 0.013 0.051 9229 Z= 0.749 Angle : 1.833 12.561 12780 Z= 1.228 Chirality : 0.095 0.584 1422 Planarity : 0.022 0.263 1349 Dihedral : 20.150 178.652 3856 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.31 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.20 (0.26), residues: 882 helix: -0.77 (0.23), residues: 375 sheet: 0.01 (0.56), residues: 79 loop : -0.86 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.019 TRP P 118 HIS 0.008 0.003 HIS P 628 PHE 0.059 0.011 PHE B 111 TYR 0.151 0.020 TYR P 146 ARG 0.007 0.001 ARG P 741 Details of bonding type rmsd hydrogen bonds : bond 0.17277 ( 398) hydrogen bonds : angle 7.62491 ( 1102) covalent geometry : bond 0.01267 ( 9229) covalent geometry : angle 1.83325 (12780) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 539 THR cc_start: 0.8452 (m) cc_final: 0.8128 (p) REVERT: P 745 LYS cc_start: 0.8356 (mtpt) cc_final: 0.8010 (mtpt) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.7193 time to fit residues: 150.0070 Evaluate side-chains 91 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 287 GLN P 290 ASN P 291 GLN P 628 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.129097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.099307 restraints weight = 58631.128| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.93 r_work: 0.3429 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9229 Z= 0.176 Angle : 0.733 7.755 12780 Z= 0.407 Chirality : 0.044 0.208 1422 Planarity : 0.005 0.057 1349 Dihedral : 23.503 172.387 1998 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.95 % Favored : 96.83 % Rotamer: Outliers : 0.63 % Allowed : 5.81 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.32 (0.27), residues: 882 helix: 0.66 (0.25), residues: 375 sheet: -0.87 (0.49), residues: 89 loop : -0.80 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 724 HIS 0.005 0.001 HIS P 628 PHE 0.022 0.002 PHE B 111 TYR 0.016 0.002 TYR P 601 ARG 0.004 0.001 ARG P 369 Details of bonding type rmsd hydrogen bonds : bond 0.05763 ( 398) hydrogen bonds : angle 5.07844 ( 1102) covalent geometry : bond 0.00377 ( 9229) covalent geometry : angle 0.73294 (12780) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8686 (mm) REVERT: P 745 LYS cc_start: 0.8685 (mtpt) cc_final: 0.8163 (mtpt) outliers start: 5 outliers final: 4 residues processed: 105 average time/residue: 0.5589 time to fit residues: 79.1143 Evaluate side-chains 81 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain P residue 429 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.124898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.095015 restraints weight = 57233.929| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.78 r_work: 0.3361 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9229 Z= 0.219 Angle : 0.675 7.393 12780 Z= 0.378 Chirality : 0.043 0.198 1422 Planarity : 0.005 0.040 1349 Dihedral : 23.269 178.922 1998 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.35 % Rotamer: Outliers : 0.76 % Allowed : 8.84 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.27), residues: 882 helix: 1.09 (0.25), residues: 374 sheet: -1.02 (0.50), residues: 90 loop : -0.97 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 816 HIS 0.004 0.001 HIS P 139 PHE 0.024 0.002 PHE P 773 TYR 0.018 0.002 TYR P 572 ARG 0.013 0.001 ARG P 524 Details of bonding type rmsd hydrogen bonds : bond 0.05250 ( 398) hydrogen bonds : angle 4.94869 ( 1102) covalent geometry : bond 0.00482 ( 9229) covalent geometry : angle 0.67516 (12780) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8699 (mm) REVERT: P 745 LYS cc_start: 0.8721 (mtpt) cc_final: 0.8206 (mtpt) outliers start: 6 outliers final: 3 residues processed: 84 average time/residue: 0.4698 time to fit residues: 55.0597 Evaluate side-chains 73 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 507 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 4 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 60 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 615 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.124363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.094598 restraints weight = 56977.517| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.75 r_work: 0.3361 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9229 Z= 0.193 Angle : 0.632 8.622 12780 Z= 0.351 Chirality : 0.042 0.176 1422 Planarity : 0.004 0.034 1349 Dihedral : 23.120 176.055 1998 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.08 % Favored : 95.80 % Rotamer: Outliers : 1.01 % Allowed : 9.60 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.28), residues: 882 helix: 1.36 (0.26), residues: 374 sheet: -1.01 (0.57), residues: 75 loop : -1.00 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 816 HIS 0.004 0.001 HIS P 387 PHE 0.020 0.002 PHE P 773 TYR 0.016 0.001 TYR P 572 ARG 0.003 0.000 ARG P 524 Details of bonding type rmsd hydrogen bonds : bond 0.04699 ( 398) hydrogen bonds : angle 4.78098 ( 1102) covalent geometry : bond 0.00422 ( 9229) covalent geometry : angle 0.63178 (12780) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8735 (mm) outliers start: 8 outliers final: 4 residues processed: 77 average time/residue: 0.4089 time to fit residues: 46.1020 Evaluate side-chains 71 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 546 THR Chi-restraints excluded: chain P residue 613 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 58 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 84 optimal weight: 0.4980 chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.127443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.098088 restraints weight = 57421.427| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.78 r_work: 0.3423 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9229 Z= 0.115 Angle : 0.557 6.810 12780 Z= 0.311 Chirality : 0.038 0.189 1422 Planarity : 0.004 0.036 1349 Dihedral : 22.827 175.902 1998 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.40 % Favored : 96.49 % Rotamer: Outliers : 0.76 % Allowed : 9.60 % Favored : 89.65 % 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: 0.52 (0.28), residues: 882 helix: 1.87 (0.26), residues: 378 sheet: -1.03 (0.56), residues: 75 loop : -0.79 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 119 HIS 0.006 0.001 HIS P 642 PHE 0.024 0.001 PHE P 773 TYR 0.011 0.001 TYR P 205 ARG 0.003 0.000 ARG P 524 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 398) hydrogen bonds : angle 4.40956 ( 1102) covalent geometry : bond 0.00245 ( 9229) covalent geometry : angle 0.55728 (12780) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8732 (mm) REVERT: B 110 PHE cc_start: 0.8422 (p90) cc_final: 0.8204 (p90) REVERT: P 328 PHE cc_start: 0.7517 (m-80) cc_final: 0.7135 (m-10) outliers start: 6 outliers final: 5 residues processed: 81 average time/residue: 0.4196 time to fit residues: 49.1875 Evaluate side-chains 69 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain P residue 177 VAL Chi-restraints excluded: chain P residue 296 ILE Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 613 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 287 GLN P 291 GLN P 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.124112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.094641 restraints weight = 57474.449| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.75 r_work: 0.3359 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9229 Z= 0.200 Angle : 0.600 8.365 12780 Z= 0.333 Chirality : 0.041 0.181 1422 Planarity : 0.004 0.030 1349 Dihedral : 22.763 176.244 1998 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.76 % Favored : 95.12 % Rotamer: Outliers : 1.52 % Allowed : 9.34 % Favored : 89.14 % 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: 0.27 (0.28), residues: 882 helix: 1.76 (0.26), residues: 379 sheet: -0.99 (0.51), residues: 90 loop : -1.06 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 816 HIS 0.004 0.001 HIS B 124 PHE 0.028 0.001 PHE P 773 TYR 0.012 0.001 TYR P 572 ARG 0.002 0.000 ARG P 741 Details of bonding type rmsd hydrogen bonds : bond 0.04440 ( 398) hydrogen bonds : angle 4.56709 ( 1102) covalent geometry : bond 0.00443 ( 9229) covalent geometry : angle 0.59969 (12780) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8786 (mm) REVERT: P 254 PHE cc_start: 0.8326 (t80) cc_final: 0.8103 (t80) outliers start: 12 outliers final: 9 residues processed: 70 average time/residue: 0.3630 time to fit residues: 38.5839 Evaluate side-chains 76 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain P residue 177 VAL Chi-restraints excluded: chain P residue 296 ILE Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 470 LEU Chi-restraints excluded: chain P residue 546 THR Chi-restraints excluded: chain P residue 613 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 70 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 287 GLN P 291 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.124512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.095130 restraints weight = 57017.969| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.72 r_work: 0.3370 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9229 Z= 0.166 Angle : 0.570 7.886 12780 Z= 0.317 Chirality : 0.040 0.184 1422 Planarity : 0.004 0.036 1349 Dihedral : 22.694 174.588 1998 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.35 % Rotamer: Outliers : 0.88 % Allowed : 10.61 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.29), residues: 882 helix: 1.91 (0.27), residues: 378 sheet: -0.99 (0.50), residues: 93 loop : -1.01 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 119 HIS 0.004 0.001 HIS P 642 PHE 0.030 0.001 PHE P 773 TYR 0.011 0.001 TYR P 572 ARG 0.002 0.000 ARG P 524 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 398) hydrogen bonds : angle 4.48475 ( 1102) covalent geometry : bond 0.00364 ( 9229) covalent geometry : angle 0.56977 (12780) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8795 (mm) REVERT: P 254 PHE cc_start: 0.8338 (t80) cc_final: 0.8115 (t80) REVERT: P 328 PHE cc_start: 0.7557 (m-80) cc_final: 0.7171 (m-10) outliers start: 7 outliers final: 4 residues processed: 68 average time/residue: 0.4787 time to fit residues: 49.2489 Evaluate side-chains 67 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain P residue 296 ILE Chi-restraints excluded: chain P residue 546 THR Chi-restraints excluded: chain P residue 613 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 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 = 0.4021 r_free = 0.4021 target = 0.125448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.096432 restraints weight = 56747.919| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.70 r_work: 0.3396 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9229 Z= 0.138 Angle : 0.553 7.309 12780 Z= 0.307 Chirality : 0.039 0.186 1422 Planarity : 0.004 0.033 1349 Dihedral : 22.603 174.257 1998 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.20 % Favored : 95.69 % Rotamer: Outliers : 1.14 % Allowed : 10.73 % Favored : 88.13 % 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: 0.59 (0.29), residues: 882 helix: 2.12 (0.27), residues: 378 sheet: -0.91 (0.52), residues: 88 loop : -0.97 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 119 HIS 0.004 0.001 HIS P 642 PHE 0.030 0.001 PHE P 773 TYR 0.009 0.001 TYR P 572 ARG 0.002 0.000 ARG P 524 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 398) hydrogen bonds : angle 4.37829 ( 1102) covalent geometry : bond 0.00303 ( 9229) covalent geometry : angle 0.55341 (12780) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8764 (mm) REVERT: P 254 PHE cc_start: 0.8317 (t80) cc_final: 0.8074 (t80) REVERT: P 328 PHE cc_start: 0.7503 (m-80) cc_final: 0.7257 (m-10) outliers start: 9 outliers final: 6 residues processed: 69 average time/residue: 0.3878 time to fit residues: 40.0058 Evaluate side-chains 70 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain P residue 296 ILE Chi-restraints excluded: chain P residue 470 LEU Chi-restraints excluded: chain P residue 546 THR Chi-restraints excluded: chain P residue 613 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 82 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 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 = 0.4023 r_free = 0.4023 target = 0.125613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.096600 restraints weight = 56900.968| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.71 r_work: 0.3393 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9229 Z= 0.137 Angle : 0.551 7.226 12780 Z= 0.305 Chirality : 0.039 0.188 1422 Planarity : 0.004 0.036 1349 Dihedral : 22.502 173.836 1998 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.42 % Favored : 95.46 % Rotamer: Outliers : 1.01 % Allowed : 10.86 % Favored : 88.13 % 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: 0.66 (0.29), residues: 882 helix: 2.19 (0.27), residues: 378 sheet: -0.76 (0.54), residues: 83 loop : -0.97 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 816 HIS 0.004 0.001 HIS P 642 PHE 0.034 0.001 PHE P 773 TYR 0.009 0.001 TYR P 572 ARG 0.002 0.000 ARG P 683 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 398) hydrogen bonds : angle 4.32390 ( 1102) covalent geometry : bond 0.00302 ( 9229) covalent geometry : angle 0.55127 (12780) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8701 (mm) REVERT: P 254 PHE cc_start: 0.8328 (t80) cc_final: 0.8080 (t80) outliers start: 8 outliers final: 6 residues processed: 67 average time/residue: 0.3721 time to fit residues: 38.5778 Evaluate side-chains 69 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain P residue 296 ILE Chi-restraints excluded: chain P residue 546 THR Chi-restraints excluded: chain P residue 613 TYR Chi-restraints excluded: chain P residue 721 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 5 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 52 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 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 = 0.4027 r_free = 0.4027 target = 0.125921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.096896 restraints weight = 56971.211| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.72 r_work: 0.3399 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9229 Z= 0.135 Angle : 0.549 7.118 12780 Z= 0.303 Chirality : 0.038 0.190 1422 Planarity : 0.003 0.034 1349 Dihedral : 22.441 173.561 1998 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.31 % Favored : 95.58 % Rotamer: Outliers : 1.14 % Allowed : 11.36 % Favored : 87.50 % 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: 0.74 (0.29), residues: 882 helix: 2.21 (0.27), residues: 382 sheet: -0.71 (0.52), residues: 88 loop : -0.92 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 816 HIS 0.004 0.001 HIS P 642 PHE 0.038 0.001 PHE P 773 TYR 0.009 0.001 TYR P 572 ARG 0.002 0.000 ARG P 683 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 398) hydrogen bonds : angle 4.30849 ( 1102) covalent geometry : bond 0.00298 ( 9229) covalent geometry : angle 0.54857 (12780) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8714 (mm) REVERT: P 254 PHE cc_start: 0.8325 (t80) cc_final: 0.8077 (t80) REVERT: P 398 ASP cc_start: 0.8696 (p0) cc_final: 0.8480 (p0) outliers start: 9 outliers final: 8 residues processed: 68 average time/residue: 0.3461 time to fit residues: 36.3248 Evaluate side-chains 75 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain P residue 296 ILE Chi-restraints excluded: chain P residue 384 LEU Chi-restraints excluded: chain P residue 470 LEU Chi-restraints excluded: chain P residue 546 THR Chi-restraints excluded: chain P residue 613 TYR Chi-restraints excluded: chain P residue 721 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 25 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 HIS ** 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 = 0.3997 r_free = 0.3997 target = 0.123877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.095012 restraints weight = 57248.789| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.67 r_work: 0.3369 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.5858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9229 Z= 0.194 Angle : 0.597 12.713 12780 Z= 0.326 Chirality : 0.040 0.190 1422 Planarity : 0.004 0.034 1349 Dihedral : 22.436 174.196 1998 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.33 % Favored : 94.56 % Rotamer: Outliers : 1.14 % Allowed : 11.36 % Favored : 87.50 % 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: 0.57 (0.29), residues: 882 helix: 2.03 (0.27), residues: 377 sheet: -0.69 (0.56), residues: 78 loop : -0.95 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 816 HIS 0.004 0.001 HIS B 124 PHE 0.043 0.002 PHE P 773 TYR 0.012 0.001 TYR P 141 ARG 0.002 0.000 ARG P 741 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 398) hydrogen bonds : angle 4.48335 ( 1102) covalent geometry : bond 0.00429 ( 9229) covalent geometry : angle 0.59709 (12780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8555.61 seconds wall clock time: 149 minutes 26.73 seconds (8966.73 seconds total)