Starting phenix.real_space_refine on Fri Mar 15 01:49:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x24_32957/03_2024/7x24_32957_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x24_32957/03_2024/7x24_32957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x24_32957/03_2024/7x24_32957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x24_32957/03_2024/7x24_32957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x24_32957/03_2024/7x24_32957_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x24_32957/03_2024/7x24_32957_updated.pdb" } resolution = 3.4 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= 0.004 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: 9 Type Number sf(0) Gaussians K 3 8.98 5 Al 1 5.89 5 P 5 5.49 5 Mg 1 5.21 5 S 50 5.16 5 C 6673 2.51 5 N 1651 2.21 5 O 1898 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 83": "OE1" <-> "OE2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A ASP 275": "OD1" <-> "OD2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 688": "OE1" <-> "OE2" Residue "A PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 765": "OD1" <-> "OD2" Residue "A ASP 782": "OD1" <-> "OD2" Residue "A TYR 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 983": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1031": "OD1" <-> "OD2" Residue "B ASP 114": "OD1" <-> "OD2" Residue "B ASP 125": "OD1" <-> "OD2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10286 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7666 Classifications: {'peptide': 986} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 36, 'TRANS': 949} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2255 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 257} Chain: "A" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 323 Unusual residues: {' K': 3, ' MG': 1, 'ALF': 1, 'CLR': 2, 'PCW': 5} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.02, per 1000 atoms: 0.59 Number of scatterers: 10286 At special positions: 0 Unit cell: (122.01, 103.75, 171.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) K 3 19.00 S 50 16.00 P 5 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1898 8.00 N 1651 7.00 C 6673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 277 " distance=2.03 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=3, symmetry=0 Links applied NAG-ASN " NAG B 401 " - " ASN B 158 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.01 Conformation dependent library (CDL) restraints added in 1.7 seconds 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2350 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 10 sheets defined 43.7% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 78 through 87 Processing helix chain 'A' and resid 101 through 110 removed outlier: 3.906A pdb=" N GLN A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET A 109 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 133 Processing helix chain 'A' and resid 142 through 162 Processing helix chain 'A' and resid 170 through 175 removed outlier: 3.698A pdb=" N SER A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LYS A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 170 through 175' Processing helix chain 'A' and resid 228 through 231 No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 278 through 288 Processing helix chain 'A' and resid 295 through 325 Processing helix chain 'A' and resid 329 through 342 Processing helix chain 'A' and resid 346 through 366 removed outlier: 4.615A pdb=" N ALA A 350 " --> pdb=" O GLU A 346 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS A 366 " --> pdb=" O ARG A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 removed outlier: 3.631A pdb=" N VAL A 376 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 377 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A 378 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A 379 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY A 380 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 439 Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 463 through 476 Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 523 through 528 Processing helix chain 'A' and resid 544 through 559 Processing helix chain 'A' and resid 611 through 620 Processing helix chain 'A' and resid 633 through 643 Processing helix chain 'A' and resid 653 through 660 Processing helix chain 'A' and resid 679 through 683 Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 707 through 720 removed outlier: 3.932A pdb=" N GLN A 720 " --> pdb=" O GLY A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 739 Proline residue: A 735 - end of helix Processing helix chain 'A' and resid 752 through 757 Processing helix chain 'A' and resid 767 through 808 removed outlier: 3.867A pdb=" N THR A 793 " --> pdb=" O TYR A 790 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 794 " --> pdb=" O THR A 791 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE A 796 " --> pdb=" O THR A 793 " (cutoff:3.500A) Proline residue: A 797 - end of helix removed outlier: 4.509A pdb=" N CYS A 800 " --> pdb=" O PRO A 797 " (cutoff:3.500A) Proline residue: A 801 - end of helix removed outlier: 4.421A pdb=" N ALA A 808 " --> pdb=" O TYR A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 827 through 836 removed outlier: 3.935A pdb=" N ALA A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR A 836 " --> pdb=" O ILE A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 845 No H-bonds generated for 'chain 'A' and resid 843 through 845' Processing helix chain 'A' and resid 859 through 866 Processing helix chain 'A' and resid 871 through 888 removed outlier: 3.817A pdb=" N GLN A 888 " --> pdb=" O VAL A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 895 Processing helix chain 'A' and resid 899 through 902 No H-bonds generated for 'chain 'A' and resid 899 through 902' Processing helix chain 'A' and resid 920 through 949 Processing helix chain 'A' and resid 956 through 959 No H-bonds generated for 'chain 'A' and resid 956 through 959' Processing helix chain 'A' and resid 965 through 983 Processing helix chain 'A' and resid 998 through 1001 Processing helix chain 'A' and resid 1005 through 1024 Processing helix chain 'A' and resid 1031 through 1034 No H-bonds generated for 'chain 'A' and resid 1031 through 1034' Processing helix chain 'B' and resid 29 through 60 removed outlier: 3.880A pdb=" N THR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 109 removed outlier: 4.659A pdb=" N ALA B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N TYR B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 117 Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 165 through 168 removed outlier: 3.649A pdb=" N GLY B 168 " --> pdb=" O GLU B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 219 through 225 removed outlier: 4.020A pdb=" N ASP B 223 " --> pdb=" O ASP B 219 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing sheet with id= A, first strand: chain 'A' and resid 180 through 185 Processing sheet with id= B, first strand: chain 'A' and resid 202 through 205 Processing sheet with id= C, first strand: chain 'A' and resid 368 through 370 removed outlier: 3.537A pdb=" N ILE A 742 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET A 746 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 384 " --> pdb=" O ALA A 725 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N THR A 727 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N CYS A 386 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS A 624 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N SER A 387 " --> pdb=" O LYS A 624 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A 626 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE A 700 " --> pdb=" O MET A 627 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 408 through 411 removed outlier: 6.810A pdb=" N SER A 602 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 403 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU A 600 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 515 " --> pdb=" O LEU A 572 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 539 through 541 removed outlier: 7.053A pdb=" N PHE A 595 " --> pdb=" O SER A 531 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE A 533 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE A 597 " --> pdb=" O ILE A 533 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 214 through 217 removed outlier: 5.970A pdb=" N ARG A 216 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL A 270 " --> pdb=" O ARG A 216 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 224 through 226 removed outlier: 3.793A pdb=" N GLU A 263 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASP A 226 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N CYS A 261 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 77 through 79 Processing sheet with id= I, first strand: chain 'B' and resid 87 through 91 removed outlier: 6.458A pdb=" N LYS B 299 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N PHE B 90 " --> pdb=" O LYS B 299 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLU B 301 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 209 through 211 398 hydrogen bonds defined for protein. 1056 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: 3.21 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3192 1.34 - 1.46: 1544 1.46 - 1.58: 5660 1.58 - 1.69: 10 1.69 - 1.81: 83 Bond restraints: 10489 Sorted by residual: bond pdb=" C11 PCW A1104 " pdb=" O3 PCW A1104 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C11 PCW A1106 " pdb=" O3 PCW A1106 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C11 PCW A1109 " pdb=" O3 PCW A1109 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C11 PCW A1108 " pdb=" O3 PCW A1108 " ideal model delta sigma weight residual 1.326 1.452 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C31 PCW A1104 " pdb=" O2 PCW A1104 " ideal model delta sigma weight residual 1.333 1.458 -0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 10484 not shown) Histogram of bond angle deviations from ideal: 89.72 - 107.70: 388 107.70 - 125.68: 13663 125.68 - 143.65: 138 143.65 - 161.63: 0 161.63 - 179.61: 2 Bond angle restraints: 14191 Sorted by residual: angle pdb=" F1 ALF A1111 " pdb="AL ALF A1111 " pdb=" F2 ALF A1111 " ideal model delta sigma weight residual 108.68 179.31 -70.63 3.00e+00 1.11e-01 5.54e+02 angle pdb=" F3 ALF A1111 " pdb="AL ALF A1111 " pdb=" F4 ALF A1111 " ideal model delta sigma weight residual 109.63 179.61 -69.98 3.00e+00 1.11e-01 5.44e+02 angle pdb=" F2 ALF A1111 " pdb="AL ALF A1111 " pdb=" F4 ALF A1111 " ideal model delta sigma weight residual 110.21 89.78 20.43 3.00e+00 1.11e-01 4.64e+01 angle pdb=" F1 ALF A1111 " pdb="AL ALF A1111 " pdb=" F3 ALF A1111 " ideal model delta sigma weight residual 109.69 89.72 19.97 3.00e+00 1.11e-01 4.43e+01 angle pdb=" F2 ALF A1111 " pdb="AL ALF A1111 " pdb=" F3 ALF A1111 " ideal model delta sigma weight residual 109.59 90.14 19.45 3.00e+00 1.11e-01 4.20e+01 ... (remaining 14186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.79: 6325 32.79 - 65.57: 183 65.57 - 98.36: 17 98.36 - 131.15: 3 131.15 - 163.93: 4 Dihedral angle restraints: 6532 sinusoidal: 2874 harmonic: 3658 Sorted by residual: dihedral pdb=" CB CYS B 159 " pdb=" SG CYS B 159 " pdb=" SG CYS B 175 " pdb=" CB CYS B 175 " ideal model delta sinusoidal sigma weight residual -86.00 -137.28 51.28 1 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" N PCW A1106 " pdb=" C4 PCW A1106 " pdb=" C5 PCW A1106 " pdb=" O4P PCW A1106 " ideal model delta sinusoidal sigma weight residual -66.66 97.27 -163.93 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" N PCW A1108 " pdb=" C4 PCW A1108 " pdb=" C5 PCW A1108 " pdb=" O4P PCW A1108 " ideal model delta sinusoidal sigma weight residual 293.34 143.48 149.86 1 3.00e+01 1.11e-03 1.99e+01 ... (remaining 6529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1405 0.067 - 0.134: 187 0.134 - 0.201: 9 0.201 - 0.269: 3 0.269 - 0.336: 2 Chirality restraints: 1606 Sorted by residual: chirality pdb=" C2 PCW A1104 " pdb=" C1 PCW A1104 " pdb=" C3 PCW A1104 " pdb=" O2 PCW A1104 " both_signs ideal model delta sigma weight residual False -2.32 -2.66 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C13 CLR A1107 " pdb=" C12 CLR A1107 " pdb=" C14 CLR A1107 " pdb=" C17 CLR A1107 " both_signs ideal model delta sigma weight residual False -2.93 -2.66 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C13 CLR B 402 " pdb=" C12 CLR B 402 " pdb=" C14 CLR B 402 " pdb=" C17 CLR B 402 " both_signs ideal model delta sigma weight residual False -2.93 -2.70 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1603 not shown) Planarity restraints: 1770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 401 " -0.301 2.00e-02 2.50e+03 2.53e-01 8.01e+02 pdb=" C7 NAG B 401 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B 401 " -0.189 2.00e-02 2.50e+03 pdb=" N2 NAG B 401 " 0.433 2.00e-02 2.50e+03 pdb=" O7 NAG B 401 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 686 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A 687 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 687 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 687 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 128 " 0.007 2.00e-02 2.50e+03 1.13e-02 2.23e+00 pdb=" CG PHE A 128 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 128 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 128 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 128 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 128 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 128 " 0.000 2.00e-02 2.50e+03 ... (remaining 1767 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.69: 188 2.69 - 3.30: 11702 3.30 - 3.92: 19757 3.92 - 4.53: 27129 4.53 - 5.14: 42534 Nonbonded interactions: 101310 Sorted by model distance: nonbonded pdb=" F1 ALF A1111 " pdb="MG MG A1112 " model vdw 2.080 2.120 nonbonded pdb=" OD2 ASP A 388 " pdb="MG MG A1112 " model vdw 2.090 2.170 nonbonded pdb=" O THR A 390 " pdb="MG MG A1112 " model vdw 2.105 2.170 nonbonded pdb=" O ILE A 907 " pdb=" NH2 ARG A 923 " model vdw 2.252 2.520 nonbonded pdb=" OD2 ASP A 388 " pdb=" F1 ALF A1111 " model vdw 2.272 2.390 ... (remaining 101305 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.870 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 31.180 Find NCS groups from input model: 0.240 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 : 0.006 0.128 10489 Z= 0.406 Angle : 1.212 70.627 14191 Z= 0.466 Chirality : 0.047 0.336 1606 Planarity : 0.007 0.253 1769 Dihedral : 15.936 163.933 4173 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.37 (0.24), residues: 1259 helix: 1.45 (0.23), residues: 525 sheet: -0.33 (0.39), residues: 164 loop : -0.67 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 968 HIS 0.003 0.001 HIS A 868 PHE 0.025 0.002 PHE A 128 TYR 0.015 0.001 TYR A 805 ARG 0.007 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 LYS cc_start: 0.7743 (tttp) cc_final: 0.7481 (mtpp) REVERT: A 421 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6735 (mm-40) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2522 time to fit residues: 52.9622 Evaluate side-chains 125 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10489 Z= 0.260 Angle : 0.571 7.623 14191 Z= 0.291 Chirality : 0.044 0.163 1606 Planarity : 0.004 0.048 1769 Dihedral : 12.636 147.902 1790 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.55 % Allowed : 9.09 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.26 (0.24), residues: 1259 helix: 1.31 (0.23), residues: 524 sheet: -0.41 (0.38), residues: 162 loop : -0.67 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1001 HIS 0.003 0.001 HIS A 868 PHE 0.011 0.002 PHE A 935 TYR 0.019 0.001 TYR A 881 ARG 0.003 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 139 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 365 LYS cc_start: 0.7755 (tttp) cc_final: 0.7455 (mtpp) REVERT: A 421 GLN cc_start: 0.7308 (mm-40) cc_final: 0.6844 (mm110) outliers start: 6 outliers final: 4 residues processed: 140 average time/residue: 0.2604 time to fit residues: 49.4610 Evaluate side-chains 133 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 219 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10489 Z= 0.182 Angle : 0.509 7.465 14191 Z= 0.262 Chirality : 0.042 0.158 1606 Planarity : 0.004 0.046 1769 Dihedral : 12.148 149.738 1790 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.19 % Allowed : 10.74 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.24), residues: 1259 helix: 1.34 (0.23), residues: 525 sheet: -0.14 (0.39), residues: 151 loop : -0.61 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1001 HIS 0.002 0.001 HIS A 569 PHE 0.011 0.001 PHE A 318 TYR 0.016 0.001 TYR A 881 ARG 0.003 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6584 (mt) REVERT: A 87 ARG cc_start: 0.5964 (ttt-90) cc_final: 0.5364 (ptm160) REVERT: A 125 TRP cc_start: 0.6920 (t60) cc_final: 0.6700 (t60) REVERT: A 365 LYS cc_start: 0.7741 (tttp) cc_final: 0.7432 (mtpp) REVERT: A 421 GLN cc_start: 0.7261 (mm-40) cc_final: 0.6709 (mm110) REVERT: B 103 LEU cc_start: 0.8066 (mt) cc_final: 0.7776 (mm) outliers start: 13 outliers final: 8 residues processed: 143 average time/residue: 0.2517 time to fit residues: 49.1250 Evaluate side-chains 130 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 10489 Z= 0.301 Angle : 0.582 8.295 14191 Z= 0.298 Chirality : 0.045 0.194 1606 Planarity : 0.004 0.046 1769 Dihedral : 12.646 153.481 1790 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.02 % Allowed : 12.03 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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 (0.24), residues: 1259 helix: 1.01 (0.23), residues: 523 sheet: -0.57 (0.39), residues: 155 loop : -0.68 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1001 HIS 0.003 0.001 HIS A 868 PHE 0.015 0.002 PHE A 500 TYR 0.019 0.002 TYR A 881 ARG 0.003 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6680 (mm) REVERT: A 87 ARG cc_start: 0.6088 (ttt-90) cc_final: 0.5453 (ptm160) REVERT: A 365 LYS cc_start: 0.7788 (tttp) cc_final: 0.7417 (mtpp) REVERT: A 421 GLN cc_start: 0.7264 (mm-40) cc_final: 0.6918 (mm-40) REVERT: B 229 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6769 (mm-30) outliers start: 22 outliers final: 15 residues processed: 141 average time/residue: 0.2594 time to fit residues: 50.1075 Evaluate side-chains 137 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 103 optimal weight: 0.0670 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10489 Z= 0.304 Angle : 0.582 8.367 14191 Z= 0.297 Chirality : 0.045 0.215 1606 Planarity : 0.004 0.049 1769 Dihedral : 12.837 155.132 1790 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.20 % Allowed : 13.59 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.12 (0.23), residues: 1259 helix: 0.83 (0.23), residues: 526 sheet: -0.48 (0.39), residues: 150 loop : -0.75 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1001 HIS 0.004 0.001 HIS A 868 PHE 0.013 0.002 PHE A 935 TYR 0.019 0.002 TYR A 881 ARG 0.004 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6473 (mt) REVERT: A 87 ARG cc_start: 0.6057 (ttt-90) cc_final: 0.5426 (ptm160) REVERT: A 365 LYS cc_start: 0.7772 (tttp) cc_final: 0.7405 (mtpp) REVERT: A 421 GLN cc_start: 0.7310 (mm-40) cc_final: 0.6861 (mm110) REVERT: B 220 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7349 (pm20) REVERT: B 229 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6740 (mm-30) outliers start: 24 outliers final: 17 residues processed: 137 average time/residue: 0.2539 time to fit residues: 47.5200 Evaluate side-chains 138 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 0.3980 chunk 116 optimal weight: 3.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS A 689 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 10489 Z= 0.341 Angle : 0.610 9.487 14191 Z= 0.309 Chirality : 0.046 0.322 1606 Planarity : 0.005 0.049 1769 Dihedral : 13.130 157.908 1790 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.39 % Allowed : 14.60 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.29 (0.23), residues: 1259 helix: 0.63 (0.23), residues: 532 sheet: -0.67 (0.38), residues: 154 loop : -0.75 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1001 HIS 0.004 0.001 HIS A 868 PHE 0.013 0.002 PHE A 935 TYR 0.019 0.002 TYR A 881 ARG 0.004 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 1.194 Fit side-chains REVERT: A 84 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6584 (mt) REVERT: A 87 ARG cc_start: 0.6162 (ttt-90) cc_final: 0.5571 (ptm160) REVERT: A 365 LYS cc_start: 0.7740 (tttp) cc_final: 0.7362 (mtpp) REVERT: A 421 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6847 (mm-40) REVERT: A 473 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6435 (mm-30) REVERT: A 501 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7178 (pp30) REVERT: B 220 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7350 (pm20) outliers start: 26 outliers final: 21 residues processed: 139 average time/residue: 0.2547 time to fit residues: 48.7092 Evaluate side-chains 145 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10489 Z= 0.156 Angle : 0.495 7.322 14191 Z= 0.255 Chirality : 0.041 0.161 1606 Planarity : 0.004 0.047 1769 Dihedral : 12.253 155.119 1790 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.93 % Allowed : 16.07 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.19 (0.24), residues: 1259 helix: 1.14 (0.23), residues: 525 sheet: -0.32 (0.39), residues: 150 loop : -0.64 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1001 HIS 0.003 0.001 HIS A 569 PHE 0.012 0.001 PHE A 318 TYR 0.015 0.001 TYR A 881 ARG 0.004 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6831 (mt) REVERT: A 87 ARG cc_start: 0.5994 (ttt-90) cc_final: 0.5436 (ptm160) REVERT: A 365 LYS cc_start: 0.7780 (tttp) cc_final: 0.7404 (mtpp) REVERT: A 421 GLN cc_start: 0.7126 (mm-40) cc_final: 0.6808 (mm-40) REVERT: A 501 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7255 (pp30) REVERT: B 229 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6761 (mm-30) outliers start: 21 outliers final: 17 residues processed: 143 average time/residue: 0.2732 time to fit residues: 53.1423 Evaluate side-chains 142 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10489 Z= 0.159 Angle : 0.491 6.994 14191 Z= 0.252 Chirality : 0.041 0.171 1606 Planarity : 0.004 0.048 1769 Dihedral : 11.917 155.759 1790 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.11 % Allowed : 16.25 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.26 (0.24), residues: 1259 helix: 1.20 (0.23), residues: 533 sheet: -0.26 (0.39), residues: 150 loop : -0.64 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1001 HIS 0.002 0.001 HIS A 569 PHE 0.012 0.001 PHE A 318 TYR 0.015 0.001 TYR A 881 ARG 0.007 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6738 (mt) REVERT: A 87 ARG cc_start: 0.6046 (ttt-90) cc_final: 0.5489 (ptm160) REVERT: A 365 LYS cc_start: 0.7799 (tttp) cc_final: 0.7408 (mtpp) REVERT: A 421 GLN cc_start: 0.7299 (mm-40) cc_final: 0.6775 (mm-40) REVERT: A 501 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7284 (pp30) REVERT: B 229 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6707 (mm-30) outliers start: 23 outliers final: 18 residues processed: 146 average time/residue: 0.2641 time to fit residues: 52.3466 Evaluate side-chains 142 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 219 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10489 Z= 0.195 Angle : 0.583 17.350 14191 Z= 0.285 Chirality : 0.044 0.359 1606 Planarity : 0.004 0.048 1769 Dihedral : 12.088 156.192 1790 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.30 % Allowed : 15.98 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.25 (0.24), residues: 1259 helix: 1.19 (0.23), residues: 533 sheet: -0.23 (0.39), residues: 151 loop : -0.65 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1001 HIS 0.002 0.001 HIS A 569 PHE 0.019 0.001 PHE B 264 TYR 0.016 0.001 TYR A 881 ARG 0.008 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6734 (mm) REVERT: A 87 ARG cc_start: 0.6155 (ttt-90) cc_final: 0.5604 (ptm160) REVERT: A 365 LYS cc_start: 0.7783 (tttp) cc_final: 0.7366 (mtpp) REVERT: A 421 GLN cc_start: 0.7169 (mm-40) cc_final: 0.6744 (mm-40) REVERT: A 501 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7314 (pp30) REVERT: B 220 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7327 (pm20) REVERT: B 229 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6703 (mm-30) REVERT: B 266 ASN cc_start: 0.6803 (m-40) cc_final: 0.6509 (m-40) outliers start: 25 outliers final: 19 residues processed: 149 average time/residue: 0.2516 time to fit residues: 52.1089 Evaluate side-chains 150 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 128 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 220 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 114 optimal weight: 0.0980 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10489 Z= 0.155 Angle : 0.531 13.148 14191 Z= 0.266 Chirality : 0.042 0.248 1606 Planarity : 0.004 0.048 1769 Dihedral : 11.724 155.812 1790 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.93 % Allowed : 16.62 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.44 (0.24), residues: 1259 helix: 1.43 (0.23), residues: 526 sheet: -0.21 (0.39), residues: 154 loop : -0.59 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 430 HIS 0.002 0.001 HIS A 569 PHE 0.012 0.001 PHE A 318 TYR 0.015 0.001 TYR A 881 ARG 0.010 0.000 ARG A 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6901 (mm) REVERT: A 87 ARG cc_start: 0.6198 (ttt-90) cc_final: 0.5682 (ptm160) REVERT: A 190 LYS cc_start: 0.7558 (ptpt) cc_final: 0.7196 (ptpt) REVERT: A 365 LYS cc_start: 0.7708 (tttp) cc_final: 0.7321 (mtpp) REVERT: A 421 GLN cc_start: 0.7084 (mm-40) cc_final: 0.6768 (mm-40) REVERT: A 501 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7343 (pp30) REVERT: A 988 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7972 (p) REVERT: B 220 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7386 (pm20) REVERT: B 229 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6638 (mm-30) REVERT: B 266 ASN cc_start: 0.6765 (m-40) cc_final: 0.6373 (m-40) outliers start: 21 outliers final: 17 residues processed: 150 average time/residue: 0.2462 time to fit residues: 50.3950 Evaluate side-chains 150 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 220 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 101 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS A 569 HIS A 860 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.152833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.116562 restraints weight = 12610.145| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.73 r_work: 0.2949 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10489 Z= 0.334 Angle : 0.632 10.666 14191 Z= 0.315 Chirality : 0.046 0.275 1606 Planarity : 0.005 0.047 1769 Dihedral : 12.706 159.344 1790 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.20 % Allowed : 16.80 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.06 (0.24), residues: 1259 helix: 1.05 (0.23), residues: 516 sheet: -0.46 (0.39), residues: 158 loop : -0.68 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 430 HIS 0.003 0.001 HIS A 868 PHE 0.014 0.002 PHE A 935 TYR 0.019 0.002 TYR A 881 ARG 0.007 0.000 ARG A 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2156.10 seconds wall clock time: 39 minutes 34.20 seconds (2374.20 seconds total)