Starting phenix.real_space_refine on Mon Mar 11 11:04:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcd_21149/03_2024/6vcd_21149_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcd_21149/03_2024/6vcd_21149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcd_21149/03_2024/6vcd_21149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcd_21149/03_2024/6vcd_21149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcd_21149/03_2024/6vcd_21149_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcd_21149/03_2024/6vcd_21149_updated.pdb" } resolution = 3.0 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= 0.003 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 Fe 2 7.16 5 S 41 5.16 5 C 5169 2.51 5 N 1356 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 19": "OD1" <-> "OD2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A ASP 388": "OD1" <-> "OD2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A GLU 676": "OE1" <-> "OE2" Residue "A ASP 689": "OD1" <-> "OD2" Residue "A ARG 719": "NH1" <-> "NH2" Residue "A ARG 774": "NH1" <-> "NH2" Residue "A ARG 779": "NH1" <-> "NH2" Residue "A ARG 788": "NH1" <-> "NH2" Residue "A ASP 881": "OD1" <-> "OD2" Residue "A ASP 900": "OD1" <-> "OD2" Residue "A ARG 907": "NH1" <-> "NH2" Residue "A GLU 941": "OE1" <-> "OE2" Residue "A ASP 943": "OD1" <-> "OD2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B ARG 386": "NH1" <-> "NH2" Residue "B ARG 598": "NH1" <-> "NH2" Residue "B TYR 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 671": "OD1" <-> "OD2" Residue "B ARG 688": "NH1" <-> "NH2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C ASP 17": "OD1" <-> "OD2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C ASP 33": "OD1" <-> "OD2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C GLU 150": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8082 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5025 Classifications: {'peptide': 643} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 32, 'TRANS': 608} Chain breaks: 3 Chain: "B" Number of atoms: 1975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1975 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 242} Chain breaks: 2 Chain: "C" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1078 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6792 SG CYS B 662 73.515 60.156 67.240 1.00 26.24 S ATOM 6969 SG CYS B 687 73.996 59.465 63.013 1.00 16.01 S ATOM 6886 SG CYS B 676 69.000 54.956 65.606 1.00 24.32 S ATOM 6963 SG CYS B 686 70.184 55.459 61.928 1.00 16.92 S Time building chain proxies: 7.35, per 1000 atoms: 0.91 Number of scatterers: 8082 At special positions: 0 Unit cell: (108.768, 85.536, 119.328, 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) Fe 2 26.01 S 41 16.00 O 1514 8.00 N 1356 7.00 C 5169 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: 3.07 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES B 800 " pdb="FE1 FES B 800 " - pdb=" SG CYS B 662 " pdb="FE2 FES B 800 " - pdb=" SG CYS B 686 " pdb="FE2 FES B 800 " - pdb=" SG CYS B 676 " pdb="FE1 FES B 800 " - pdb=" SG CYS B 687 " Number of angles added : 6 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 10 sheets defined 33.9% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 28 through 31 Processing helix chain 'A' and resid 42 through 51 Processing helix chain 'A' and resid 63 through 66 No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 93 through 109 removed outlier: 3.650A pdb=" N ASP A 98 " --> pdb=" O PRO A 94 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.754A pdb=" N VAL A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 238 Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 283 through 289 removed outlier: 3.610A pdb=" N VAL A 286 " --> pdb=" O ILE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 332 through 346 removed outlier: 3.700A pdb=" N VAL A 346 " --> pdb=" O HIS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 375 through 378 No H-bonds generated for 'chain 'A' and resid 375 through 378' Processing helix chain 'A' and resid 389 through 398 removed outlier: 3.622A pdb=" N HIS A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 414 removed outlier: 4.017A pdb=" N SER A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 440 No H-bonds generated for 'chain 'A' and resid 438 through 440' Processing helix chain 'A' and resid 669 through 672 No H-bonds generated for 'chain 'A' and resid 669 through 672' Processing helix chain 'A' and resid 674 through 677 No H-bonds generated for 'chain 'A' and resid 674 through 677' Processing helix chain 'A' and resid 679 through 688 Processing helix chain 'A' and resid 752 through 755 No H-bonds generated for 'chain 'A' and resid 752 through 755' Processing helix chain 'A' and resid 766 through 773 Processing helix chain 'A' and resid 791 through 795 Processing helix chain 'A' and resid 827 through 836 Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 877 through 886 removed outlier: 3.828A pdb=" N ASP A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS A 882 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 886 " --> pdb=" O HIS A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 901 No H-bonds generated for 'chain 'A' and resid 899 through 901' Processing helix chain 'A' and resid 943 through 950 Processing helix chain 'A' and resid 954 through 961 removed outlier: 3.502A pdb=" N LYS A 961 " --> pdb=" O PHE A 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.568A pdb=" N SER B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 removed outlier: 3.595A pdb=" N SER B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN B 230 " --> pdb=" O CYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 removed outlier: 3.711A pdb=" N GLN B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.776A pdb=" N ALA B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 250 through 255' Processing helix chain 'B' and resid 312 through 319 Processing helix chain 'B' and resid 346 through 349 No H-bonds generated for 'chain 'B' and resid 346 through 349' Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 613 through 617 Processing helix chain 'B' and resid 641 through 650 removed outlier: 3.709A pdb=" N ASP B 646 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 647 " --> pdb=" O GLY B 643 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B 650 " --> pdb=" O ASP B 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 removed outlier: 3.922A pdb=" N GLN C 23 " --> pdb=" O GLU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 52 through 64 removed outlier: 4.461A pdb=" N LYS C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN C 60 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS C 64 " --> pdb=" O GLN C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 92 Processing helix chain 'C' and resid 97 through 110 removed outlier: 3.810A pdb=" N GLU C 102 " --> pdb=" O GLY C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 132 through 139 removed outlier: 4.291A pdb=" N ARG C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.921A pdb=" N GLN C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 14 through 16 Processing sheet with id= B, first strand: chain 'A' and resid 77 through 80 Processing sheet with id= C, first strand: chain 'A' and resid 84 through 87 removed outlier: 7.757A pdb=" N LEU A 87 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASP A 123 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA A 243 " --> pdb=" O LEU A 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 264 through 266 removed outlier: 3.675A pdb=" N PHE A 272 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 320 through 323 removed outlier: 5.847A pdb=" N ILE A 434 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR A 323 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A 436 " --> pdb=" O THR A 323 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 815 through 817 Processing sheet with id= G, first strand: chain 'A' and resid 869 through 872 removed outlier: 6.741A pdb=" N ALA A 889 " --> pdb=" O VAL A 870 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ALA A 872 " --> pdb=" O ALA A 889 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU A 891 " --> pdb=" O ALA A 872 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 922 " --> pdb=" O ALA A 938 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 741 through 745 removed outlier: 3.622A pdb=" N ILE A 842 " --> pdb=" O HIS A 741 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU A 844 " --> pdb=" O LEU A 743 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR A 745 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 334 through 336 removed outlier: 6.353A pdb=" N HIS B 360 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N HIS B 387 " --> pdb=" O LEU B 361 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 13 through 16 168 hydrogen bonds defined for protein. 483 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: 1.99 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.42: 3356 1.42 - 1.61: 4837 1.61 - 1.80: 50 1.80 - 2.00: 6 2.00 - 2.19: 4 Bond restraints: 8253 Sorted by residual: bond pdb=" N TRP C 159 " pdb=" CA TRP C 159 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.90e-02 2.77e+03 1.60e+00 bond pdb=" CG1 ILE A 283 " pdb=" CD1 ILE A 283 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.26e+00 bond pdb=" CA ILE A 14 " pdb=" CB ILE A 14 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.22e+00 bond pdb=" CA MET A 64 " pdb=" C MET A 64 " ideal model delta sigma weight residual 1.524 1.499 0.025 2.25e-02 1.98e+03 1.19e+00 bond pdb=" CB ILE A 291 " pdb=" CG2 ILE A 291 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.08e+00 ... (remaining 8248 not shown) Histogram of bond angle deviations from ideal: 88.77 - 97.82: 4 97.82 - 106.88: 251 106.88 - 115.93: 5225 115.93 - 124.98: 5560 124.98 - 134.03: 140 Bond angle restraints: 11180 Sorted by residual: angle pdb=" S1 FES B 800 " pdb="FE2 FES B 800 " pdb=" S2 FES B 800 " ideal model delta sigma weight residual 104.33 90.38 13.95 1.14e+00 7.69e-01 1.50e+02 angle pdb=" S1 FES B 800 " pdb="FE1 FES B 800 " pdb=" S2 FES B 800 " ideal model delta sigma weight residual 104.33 90.30 14.03 1.20e+00 6.94e-01 1.37e+02 angle pdb="FE1 FES B 800 " pdb=" S2 FES B 800 " pdb="FE2 FES B 800 " ideal model delta sigma weight residual 75.66 88.87 -13.21 1.14e+00 7.69e-01 1.34e+02 angle pdb="FE1 FES B 800 " pdb=" S1 FES B 800 " pdb="FE2 FES B 800 " ideal model delta sigma weight residual 75.66 88.77 -13.11 1.20e+00 6.94e-01 1.19e+02 angle pdb=" C GLN C 158 " pdb=" N TRP C 159 " pdb=" CA TRP C 159 " ideal model delta sigma weight residual 121.70 131.70 -10.00 1.80e+00 3.09e-01 3.09e+01 ... (remaining 11175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 4346 16.02 - 32.05: 462 32.05 - 48.07: 96 48.07 - 64.10: 23 64.10 - 80.12: 8 Dihedral angle restraints: 4935 sinusoidal: 1969 harmonic: 2966 Sorted by residual: dihedral pdb=" CA SER B 377 " pdb=" C SER B 377 " pdb=" N TRP B 378 " pdb=" CA TRP B 378 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA HIS A 22 " pdb=" C HIS A 22 " pdb=" N LYS A 23 " pdb=" CA LYS A 23 " ideal model delta harmonic sigma weight residual 180.00 -152.31 -27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA GLN C 158 " pdb=" C GLN C 158 " pdb=" N TRP C 159 " pdb=" CA TRP C 159 " ideal model delta harmonic sigma weight residual 0.00 -26.63 26.63 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 4932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1042 0.055 - 0.110: 209 0.110 - 0.165: 22 0.165 - 0.220: 1 0.220 - 0.275: 1 Chirality restraints: 1275 Sorted by residual: chirality pdb=" CA TRP C 159 " pdb=" N TRP C 159 " pdb=" C TRP C 159 " pdb=" CB TRP C 159 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CB VAL A 277 " pdb=" CA VAL A 277 " pdb=" CG1 VAL A 277 " pdb=" CG2 VAL A 277 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CB VAL A 415 " pdb=" CA VAL A 415 " pdb=" CG1 VAL A 415 " pdb=" CG2 VAL A 415 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 1272 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 45 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO C 46 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 46 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 46 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 325 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO B 326 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 326 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 326 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 861 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO A 862 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 862 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 862 " 0.023 5.00e-02 4.00e+02 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 388 2.72 - 3.26: 8176 3.26 - 3.81: 12756 3.81 - 4.35: 17434 4.35 - 4.90: 28336 Nonbonded interactions: 67090 Sorted by model distance: nonbonded pdb=" NH1 ARG A 103 " pdb=" O PRO A 113 " model vdw 2.170 2.520 nonbonded pdb=" OE1 GLU A 227 " pdb=" OG SER A 715 " model vdw 2.186 2.440 nonbonded pdb=" O SER B 634 " pdb=" ND2 ASN B 678 " model vdw 2.224 2.520 nonbonded pdb=" NH2 ARG A 779 " pdb=" O CYS B 662 " model vdw 2.225 2.520 nonbonded pdb=" OG SER A 783 " pdb=" O GLY B 690 " model vdw 2.238 2.440 ... (remaining 67085 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 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 7.270 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 29.420 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.005 0.044 8253 Z= 0.302 Angle : 0.701 14.029 11180 Z= 0.419 Chirality : 0.044 0.275 1275 Planarity : 0.005 0.057 1424 Dihedral : 14.129 80.122 3019 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.07 % Favored : 89.73 % Rotamer: Outliers : 0.11 % Allowed : 7.36 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % 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: -4.83 (0.21), residues: 1013 helix: -3.31 (0.17), residues: 396 sheet: -3.37 (0.44), residues: 115 loop : -3.04 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 378 HIS 0.005 0.001 HIS B 387 PHE 0.014 0.001 PHE B 602 TYR 0.021 0.002 TYR B 661 ARG 0.004 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8047 (m-80) cc_final: 0.7773 (m-80) REVERT: A 337 LEU cc_start: 0.8529 (mt) cc_final: 0.8274 (mp) REVERT: A 406 GLU cc_start: 0.7280 (mm-30) cc_final: 0.7050 (mp0) REVERT: B 215 SER cc_start: 0.9050 (t) cc_final: 0.8830 (t) REVERT: B 314 LYS cc_start: 0.8256 (ttpp) cc_final: 0.7921 (ttmm) REVERT: C 154 ARG cc_start: 0.7830 (mtm110) cc_final: 0.7508 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 1.0965 time to fit residues: 159.2752 Evaluate side-chains 100 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 0.0870 chunk 48 optimal weight: 0.3980 chunk 59 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 217 ASN A 241 ASN A 397 HIS A 678 HIS A 754 HIS A 773 ASN A 879 HIS ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN B 247 HIS B 318 HIS ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN C 108 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8253 Z= 0.258 Angle : 0.613 12.606 11180 Z= 0.311 Chirality : 0.043 0.277 1275 Planarity : 0.005 0.056 1424 Dihedral : 5.137 28.892 1093 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.48 % Favored : 90.33 % Rotamer: Outliers : 3.34 % Allowed : 13.38 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % 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: -3.83 (0.23), residues: 1013 helix: -2.36 (0.21), residues: 399 sheet: -3.27 (0.43), residues: 118 loop : -2.43 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 378 HIS 0.006 0.001 HIS B 318 PHE 0.012 0.001 PHE A 272 TYR 0.019 0.002 TYR B 661 ARG 0.006 0.001 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 1.003 Fit side-chains REVERT: A 40 TYR cc_start: 0.8032 (m-80) cc_final: 0.7780 (m-80) REVERT: A 114 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7409 (mt-10) REVERT: A 302 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7300 (tt0) REVERT: A 337 LEU cc_start: 0.8474 (mt) cc_final: 0.8232 (mp) REVERT: A 341 LYS cc_start: 0.7726 (ttpt) cc_final: 0.7319 (tttm) REVERT: A 855 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7833 (mmt90) REVERT: A 936 VAL cc_start: 0.7935 (OUTLIER) cc_final: 0.7722 (p) REVERT: B 248 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8657 (pp) REVERT: B 314 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7873 (ttmm) REVERT: C 154 ARG cc_start: 0.7904 (mtm110) cc_final: 0.7662 (ttm-80) outliers start: 30 outliers final: 10 residues processed: 130 average time/residue: 0.8817 time to fit residues: 124.4630 Evaluate side-chains 113 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain C residue 27 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 92 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN B 322 HIS ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8253 Z= 0.279 Angle : 0.600 12.439 11180 Z= 0.305 Chirality : 0.043 0.277 1275 Planarity : 0.004 0.051 1424 Dihedral : 5.041 28.917 1093 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.38 % Favored : 90.42 % Rotamer: Outliers : 3.68 % Allowed : 15.94 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % 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: -3.24 (0.24), residues: 1013 helix: -1.74 (0.23), residues: 401 sheet: -3.13 (0.44), residues: 118 loop : -2.18 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 378 HIS 0.005 0.001 HIS B 387 PHE 0.027 0.002 PHE A 25 TYR 0.019 0.002 TYR B 661 ARG 0.003 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 98 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8047 (m-80) cc_final: 0.7810 (m-80) REVERT: A 114 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7416 (mt-10) REVERT: A 302 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: A 337 LEU cc_start: 0.8467 (mt) cc_final: 0.8227 (mp) REVERT: A 855 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8112 (mmt90) REVERT: B 248 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8624 (pp) REVERT: B 314 LYS cc_start: 0.8187 (ttpp) cc_final: 0.7846 (ttmm) REVERT: C 154 ARG cc_start: 0.7855 (mtm110) cc_final: 0.7593 (ttm-80) outliers start: 33 outliers final: 16 residues processed: 122 average time/residue: 0.8816 time to fit residues: 116.6898 Evaluate side-chains 120 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain C residue 27 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.0770 chunk 48 optimal weight: 0.9980 chunk 10 optimal weight: 0.0060 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 overall best weight: 0.4554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8253 Z= 0.209 Angle : 0.565 12.165 11180 Z= 0.286 Chirality : 0.042 0.267 1275 Planarity : 0.004 0.050 1424 Dihedral : 4.789 28.888 1093 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.28 % Favored : 90.62 % Rotamer: Outliers : 3.23 % Allowed : 17.17 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % 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: -2.75 (0.25), residues: 1013 helix: -1.29 (0.24), residues: 400 sheet: -2.95 (0.45), residues: 120 loop : -1.92 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 378 HIS 0.004 0.001 HIS B 387 PHE 0.011 0.001 PHE A 272 TYR 0.016 0.001 TYR B 661 ARG 0.004 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8017 (m-80) cc_final: 0.7766 (m-80) REVERT: A 65 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.7909 (t0) REVERT: A 114 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7356 (mt-10) REVERT: A 232 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.8238 (m-10) REVERT: A 302 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: A 337 LEU cc_start: 0.8442 (mt) cc_final: 0.8197 (mp) REVERT: A 374 MET cc_start: 0.7978 (mtp) cc_final: 0.7746 (mtt) REVERT: A 406 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7096 (mp0) REVERT: B 248 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8730 (pp) REVERT: B 314 LYS cc_start: 0.8254 (ttpp) cc_final: 0.7879 (ttmm) REVERT: B 398 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7349 (p0) REVERT: C 154 ARG cc_start: 0.7789 (mtm110) cc_final: 0.7479 (ttm-80) outliers start: 29 outliers final: 13 residues processed: 131 average time/residue: 0.8499 time to fit residues: 121.1318 Evaluate side-chains 121 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain C residue 27 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.8980 chunk 73 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 0.0980 chunk 19 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8253 Z= 0.207 Angle : 0.555 12.033 11180 Z= 0.280 Chirality : 0.042 0.263 1275 Planarity : 0.004 0.048 1424 Dihedral : 4.665 27.938 1093 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.79 % Favored : 91.12 % Rotamer: Outliers : 3.57 % Allowed : 18.17 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % 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: -2.49 (0.26), residues: 1013 helix: -1.08 (0.25), residues: 402 sheet: -2.84 (0.44), residues: 125 loop : -1.72 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 378 HIS 0.004 0.001 HIS B 387 PHE 0.026 0.001 PHE A 25 TYR 0.020 0.002 TYR A 259 ARG 0.004 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 104 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8015 (m-80) cc_final: 0.7792 (m-80) REVERT: A 65 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.7903 (t0) REVERT: A 114 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7378 (mt-10) REVERT: A 302 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: A 337 LEU cc_start: 0.8435 (mt) cc_final: 0.8202 (mp) REVERT: A 406 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7042 (mp0) REVERT: B 248 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8742 (pp) REVERT: B 314 LYS cc_start: 0.8234 (ttpp) cc_final: 0.7846 (ttmm) REVERT: B 398 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7301 (p0) REVERT: C 154 ARG cc_start: 0.7778 (mtm110) cc_final: 0.7444 (ttm-80) outliers start: 32 outliers final: 15 residues processed: 127 average time/residue: 0.8564 time to fit residues: 118.2884 Evaluate side-chains 124 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain C residue 27 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.0980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8253 Z= 0.221 Angle : 0.570 12.060 11180 Z= 0.284 Chirality : 0.042 0.266 1275 Planarity : 0.004 0.048 1424 Dihedral : 4.635 28.165 1093 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.67 % Favored : 90.23 % Rotamer: Outliers : 4.24 % Allowed : 17.84 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % 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: -2.33 (0.26), residues: 1013 helix: -0.95 (0.25), residues: 402 sheet: -2.76 (0.45), residues: 130 loop : -1.61 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 378 HIS 0.004 0.001 HIS B 387 PHE 0.011 0.001 PHE A 272 TYR 0.017 0.001 TYR B 661 ARG 0.004 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 109 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8022 (m-80) cc_final: 0.7819 (m-80) REVERT: A 50 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8344 (t) REVERT: A 65 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7911 (t0) REVERT: A 102 MET cc_start: 0.8925 (ttp) cc_final: 0.8444 (ttm) REVERT: A 302 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7257 (tt0) REVERT: A 337 LEU cc_start: 0.8445 (mt) cc_final: 0.8194 (mp) REVERT: A 406 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7078 (mp0) REVERT: A 417 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8107 (mm) REVERT: B 248 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8715 (pp) REVERT: B 314 LYS cc_start: 0.8203 (ttpp) cc_final: 0.7827 (ttmm) REVERT: B 398 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7323 (p0) REVERT: C 154 ARG cc_start: 0.7738 (mtm110) cc_final: 0.7405 (ttm-80) outliers start: 38 outliers final: 19 residues processed: 136 average time/residue: 0.7751 time to fit residues: 115.3780 Evaluate side-chains 128 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 93 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.0980 chunk 98 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN B 323 ASN B 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8253 Z= 0.304 Angle : 0.621 12.360 11180 Z= 0.308 Chirality : 0.044 0.277 1275 Planarity : 0.004 0.048 1424 Dihedral : 4.806 28.167 1093 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.67 % Favored : 90.13 % Rotamer: Outliers : 4.24 % Allowed : 17.73 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % 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: -2.31 (0.26), residues: 1013 helix: -0.94 (0.25), residues: 401 sheet: -2.71 (0.44), residues: 136 loop : -1.58 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 378 HIS 0.004 0.001 HIS B 387 PHE 0.028 0.002 PHE A 25 TYR 0.020 0.002 TYR B 661 ARG 0.003 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 103 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8058 (m-80) cc_final: 0.7832 (m-80) REVERT: A 50 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8390 (t) REVERT: A 65 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.7951 (t0) REVERT: A 102 MET cc_start: 0.8935 (ttp) cc_final: 0.8234 (ttm) REVERT: A 302 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: A 337 LEU cc_start: 0.8458 (mt) cc_final: 0.8227 (mp) REVERT: A 406 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7087 (mp0) REVERT: A 417 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8099 (mm) REVERT: B 248 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8645 (pp) REVERT: B 314 LYS cc_start: 0.8201 (ttpp) cc_final: 0.7810 (ttmm) REVERT: C 154 ARG cc_start: 0.7683 (mtm110) cc_final: 0.7370 (ttm-80) outliers start: 38 outliers final: 21 residues processed: 131 average time/residue: 0.7969 time to fit residues: 114.2275 Evaluate side-chains 124 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain C residue 27 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN B 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8253 Z= 0.275 Angle : 0.616 12.260 11180 Z= 0.303 Chirality : 0.044 0.273 1275 Planarity : 0.004 0.047 1424 Dihedral : 4.782 28.420 1093 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.58 % Favored : 90.23 % Rotamer: Outliers : 3.34 % Allowed : 18.62 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % 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: -2.21 (0.26), residues: 1013 helix: -0.85 (0.25), residues: 402 sheet: -2.70 (0.45), residues: 131 loop : -1.54 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 378 HIS 0.005 0.001 HIS B 360 PHE 0.013 0.001 PHE B 602 TYR 0.018 0.002 TYR B 661 ARG 0.002 0.000 ARG A 719 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 101 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8041 (m-80) cc_final: 0.7815 (m-80) REVERT: A 50 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8483 (t) REVERT: A 65 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7990 (t0) REVERT: A 102 MET cc_start: 0.8922 (ttp) cc_final: 0.8390 (ttm) REVERT: A 302 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: A 337 LEU cc_start: 0.8461 (mt) cc_final: 0.8228 (mp) REVERT: A 406 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7098 (mp0) REVERT: A 417 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8123 (mm) REVERT: B 248 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8608 (pp) REVERT: B 314 LYS cc_start: 0.8200 (ttpp) cc_final: 0.7812 (ttmm) REVERT: C 154 ARG cc_start: 0.7617 (mtm110) cc_final: 0.7323 (ttm-80) outliers start: 30 outliers final: 21 residues processed: 123 average time/residue: 0.7708 time to fit residues: 104.0774 Evaluate side-chains 125 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain C residue 27 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 0.0870 chunk 96 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.0030 chunk 67 optimal weight: 2.9990 overall best weight: 0.5768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8253 Z= 0.240 Angle : 0.603 12.089 11180 Z= 0.298 Chirality : 0.043 0.267 1275 Planarity : 0.004 0.046 1424 Dihedral : 4.708 28.187 1093 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.28 % Favored : 90.52 % Rotamer: Outliers : 3.34 % Allowed : 18.95 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % 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: -2.11 (0.26), residues: 1013 helix: -0.73 (0.25), residues: 404 sheet: -2.66 (0.44), residues: 136 loop : -1.49 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 378 HIS 0.004 0.001 HIS B 387 PHE 0.027 0.001 PHE A 25 TYR 0.017 0.002 TYR B 661 ARG 0.002 0.000 ARG A 719 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 104 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8035 (m-80) cc_final: 0.7815 (m-80) REVERT: A 65 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7979 (t0) REVERT: A 102 MET cc_start: 0.8907 (ttp) cc_final: 0.8377 (ttm) REVERT: A 302 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: A 337 LEU cc_start: 0.8457 (mt) cc_final: 0.8235 (mp) REVERT: A 406 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7071 (mp0) REVERT: A 417 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8118 (mm) REVERT: A 809 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7798 (mp) REVERT: A 829 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6426 (mp0) REVERT: B 248 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8612 (pp) REVERT: B 314 LYS cc_start: 0.8192 (ttpp) cc_final: 0.7804 (ttmm) REVERT: B 398 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7276 (p0) outliers start: 30 outliers final: 21 residues processed: 126 average time/residue: 0.8299 time to fit residues: 114.5102 Evaluate side-chains 127 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 829 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain C residue 27 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8253 Z= 0.300 Angle : 0.638 12.325 11180 Z= 0.315 Chirality : 0.044 0.276 1275 Planarity : 0.004 0.047 1424 Dihedral : 4.824 28.510 1093 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.67 % Favored : 90.13 % Rotamer: Outliers : 3.46 % Allowed : 19.18 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % 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: -2.12 (0.26), residues: 1013 helix: -0.72 (0.25), residues: 404 sheet: -2.66 (0.45), residues: 131 loop : -1.55 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 378 HIS 0.004 0.001 HIS B 360 PHE 0.014 0.002 PHE B 602 TYR 0.026 0.002 TYR A 259 ARG 0.006 0.001 ARG C 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 103 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8062 (m-80) cc_final: 0.7826 (m-80) REVERT: A 65 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.8007 (t0) REVERT: A 102 MET cc_start: 0.8934 (ttp) cc_final: 0.8412 (ttm) REVERT: A 302 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7286 (tt0) REVERT: A 337 LEU cc_start: 0.8478 (mt) cc_final: 0.8250 (mp) REVERT: A 406 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7082 (mp0) REVERT: A 417 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8119 (mm) REVERT: B 248 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8616 (pp) REVERT: B 314 LYS cc_start: 0.8202 (ttpp) cc_final: 0.7811 (ttmm) REVERT: C 154 ARG cc_start: 0.7543 (ttp80) cc_final: 0.7222 (ttm-80) outliers start: 31 outliers final: 24 residues processed: 126 average time/residue: 0.7631 time to fit residues: 105.6521 Evaluate side-chains 130 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain C residue 27 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 0.0060 chunk 33 optimal weight: 0.1980 chunk 83 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 0.0170 chunk 4 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 0.0470 overall best weight: 0.1332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 HIS B 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.161104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.124349 restraints weight = 8990.828| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.16 r_work: 0.3274 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8253 Z= 0.138 Angle : 0.563 12.045 11180 Z= 0.278 Chirality : 0.041 0.249 1275 Planarity : 0.004 0.044 1424 Dihedral : 4.364 27.991 1093 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.90 % Favored : 92.00 % Rotamer: Outliers : 2.56 % Allowed : 20.40 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % 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: -1.57 (0.27), residues: 1013 helix: -0.20 (0.26), residues: 397 sheet: -2.24 (0.44), residues: 137 loop : -1.31 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 378 HIS 0.007 0.001 HIS B 318 PHE 0.025 0.001 PHE A 25 TYR 0.013 0.001 TYR A 378 ARG 0.006 0.000 ARG C 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2912.09 seconds wall clock time: 52 minutes 31.29 seconds (3151.29 seconds total)