Starting phenix.real_space_refine on Fri Feb 16 09:25:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lth_0968/02_2024/6lth_0968.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lth_0968/02_2024/6lth_0968.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/6lth_0968/02_2024/6lth_0968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lth_0968/02_2024/6lth_0968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lth_0968/02_2024/6lth_0968.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lth_0968/02_2024/6lth_0968.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= 0.001 sd= 0.046 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 Zn 1 6.06 5 S 78 5.16 5 C 9485 2.51 5 N 2636 2.21 5 O 2770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I ARG 370": "NH1" <-> "NH2" Residue "I ARG 408": "NH1" <-> "NH2" Residue "I GLU 449": "OE1" <-> "OE2" Residue "L GLU 1718": "OE1" <-> "OE2" Residue "L ARG 1721": "NH1" <-> "NH2" Residue "L GLU 1956": "OE1" <-> "OE2" Residue "L GLU 2120": "OE1" <-> "OE2" Residue "L ARG 2232": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M ARG 190": "NH1" <-> "NH2" Residue "M ARG 201": "NH1" <-> "NH2" Residue "M PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 246": "OE1" <-> "OE2" Residue "M ARG 261": "NH1" <-> "NH2" Residue "N ARG 443": "NH1" <-> "NH2" Residue "N ARG 487": "NH1" <-> "NH2" Residue "N ARG 630": "NH1" <-> "NH2" Residue "N GLU 893": "OE1" <-> "OE2" Residue "N ARG 917": "NH1" <-> "NH2" Residue "N GLU 937": "OE1" <-> "OE2" Residue "O ARG 466": "NH1" <-> "NH2" Residue "O ARG 599": "NH1" <-> "NH2" Residue "O GLU 600": "OE1" <-> "OE2" Residue "O GLU 611": "OE1" <-> "OE2" Residue "O ARG 630": "NH1" <-> "NH2" Residue "O ARG 882": "NH1" <-> "NH2" Residue "P GLU 429": "OE1" <-> "OE2" Residue "P ARG 446": "NH1" <-> "NH2" Residue "P GLU 480": "OE1" <-> "OE2" Residue "P GLU 489": "OE1" <-> "OE2" Residue "P ARG 503": "NH1" <-> "NH2" Residue "Q ARG 201": "NH1" <-> "NH2" Residue "Q GLU 209": "OE1" <-> "OE2" Residue "Q ARG 223": "NH1" <-> "NH2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "R ARG 62": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14970 Number of models: 1 Model: "" Number of chains: 9 Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1022 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain breaks: 1 Chain: "L" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3670 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 25, 'TRANS': 440} Chain breaks: 4 Chain: "M" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2070 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 13, 'TRANS': 245} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "N" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2120 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 6, 'TRANS': 254} Chain breaks: 3 Chain: "O" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2632 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 19, 'TRANS': 305} Chain breaks: 3 Chain: "P" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 2015 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 14, 'TRANS': 224} Chain breaks: 2 Chain: "Q" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 860 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "R" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 580 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3342 SG CYS L2094 67.010 67.650 63.954 1.00 48.48 S Time building chain proxies: 7.73, per 1000 atoms: 0.52 Number of scatterers: 14970 At special positions: 0 Unit cell: (148.72, 160.16, 134.16, 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) Zn 1 29.99 S 78 16.00 O 2770 8.00 N 2636 7.00 C 9485 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: 5.67 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L2301 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2019 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2021 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2090 " pdb="ZN ZN L2301 " - pdb=" SG CYS L2094 " Number of angles added : 3 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3572 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 8 sheets defined 67.2% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'I' and resid 362 through 387 removed outlier: 3.565A pdb=" N ASN I 387 " --> pdb=" O GLN I 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 409 Processing helix chain 'I' and resid 409 through 428 removed outlier: 3.553A pdb=" N GLN I 415 " --> pdb=" O ASN I 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 430 through 434 Processing helix chain 'I' and resid 446 through 475 removed outlier: 3.883A pdb=" N ALA I 450 " --> pdb=" O SER I 446 " (cutoff:3.500A) Processing helix chain 'L' and resid 1645 through 1649 Processing helix chain 'L' and resid 1668 through 1679 removed outlier: 4.055A pdb=" N GLY L1679 " --> pdb=" O SER L1675 " (cutoff:3.500A) Processing helix chain 'L' and resid 1680 through 1697 Processing helix chain 'L' and resid 1698 through 1701 removed outlier: 3.727A pdb=" N ILE L1701 " --> pdb=" O ASP L1698 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1698 through 1701' Processing helix chain 'L' and resid 1705 through 1709 Processing helix chain 'L' and resid 1711 through 1729 Processing helix chain 'L' and resid 1740 through 1745 Processing helix chain 'L' and resid 1840 through 1846 removed outlier: 3.578A pdb=" N TRP L1844 " --> pdb=" O GLY L1840 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE L1846 " --> pdb=" O LEU L1842 " (cutoff:3.500A) Processing helix chain 'L' and resid 1971 through 1992 Processing helix chain 'L' and resid 1996 through 2002 removed outlier: 4.200A pdb=" N GLU L2000 " --> pdb=" O GLY L1996 " (cutoff:3.500A) Processing helix chain 'L' and resid 2004 through 2016 removed outlier: 4.405A pdb=" N LEU L2016 " --> pdb=" O GLY L2012 " (cutoff:3.500A) Processing helix chain 'L' and resid 2049 through 2068 removed outlier: 3.643A pdb=" N MET L2055 " --> pdb=" O ASP L2051 " (cutoff:3.500A) Processing helix chain 'L' and resid 2069 through 2071 No H-bonds generated for 'chain 'L' and resid 2069 through 2071' Processing helix chain 'L' and resid 2077 through 2094 Proline residue: L2083 - end of helix Processing helix chain 'L' and resid 2113 through 2127 Processing helix chain 'L' and resid 2128 through 2137 Processing helix chain 'L' and resid 2140 through 2158 removed outlier: 3.722A pdb=" N LEU L2144 " --> pdb=" O PRO L2140 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG L2158 " --> pdb=" O PHE L2154 " (cutoff:3.500A) Processing helix chain 'L' and resid 2160 through 2178 Processing helix chain 'L' and resid 2178 through 2187 removed outlier: 3.655A pdb=" N ALA L2182 " --> pdb=" O ASP L2178 " (cutoff:3.500A) Processing helix chain 'L' and resid 2190 through 2209 removed outlier: 3.704A pdb=" N GLN L2209 " --> pdb=" O ALA L2205 " (cutoff:3.500A) Processing helix chain 'L' and resid 2228 through 2243 Processing helix chain 'L' and resid 2247 through 2252 removed outlier: 3.552A pdb=" N PHE L2251 " --> pdb=" O ASN L2247 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR L2252 " --> pdb=" O HIS L2248 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2247 through 2252' Processing helix chain 'L' and resid 2254 through 2264 Processing helix chain 'L' and resid 2268 through 2284 Processing helix chain 'M' and resid 29 through 36 Processing helix chain 'M' and resid 41 through 47 Processing helix chain 'M' and resid 56 through 66 Processing helix chain 'M' and resid 80 through 84 Processing helix chain 'M' and resid 93 through 98 Processing helix chain 'M' and resid 173 through 181 Processing helix chain 'M' and resid 214 through 226 Processing helix chain 'M' and resid 229 through 248 Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 289 through 302 Processing helix chain 'M' and resid 305 through 324 removed outlier: 4.135A pdb=" N THR M 309 " --> pdb=" O GLY M 305 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA M 312 " --> pdb=" O VAL M 308 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS M 324 " --> pdb=" O SER M 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 342 through 348 Processing helix chain 'N' and resid 427 through 431 Processing helix chain 'N' and resid 440 through 446 Processing helix chain 'N' and resid 447 through 452 removed outlier: 4.693A pdb=" N GLY N 452 " --> pdb=" O GLU N 448 " (cutoff:3.500A) Processing helix chain 'N' and resid 458 through 475 removed outlier: 3.533A pdb=" N LEU N 475 " --> pdb=" O ASP N 471 " (cutoff:3.500A) Processing helix chain 'N' and resid 482 through 490 removed outlier: 3.676A pdb=" N ASN N 489 " --> pdb=" O ALA N 485 " (cutoff:3.500A) Processing helix chain 'N' and resid 493 through 507 Processing helix chain 'N' and resid 603 through 616 Processing helix chain 'N' and resid 620 through 628 removed outlier: 3.554A pdb=" N SER N 624 " --> pdb=" O TRP N 620 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY N 628 " --> pdb=" O SER N 624 " (cutoff:3.500A) Processing helix chain 'N' and resid 631 through 641 Processing helix chain 'N' and resid 672 through 682 Processing helix chain 'N' and resid 685 through 702 Processing helix chain 'N' and resid 859 through 949 Processing helix chain 'O' and resid 439 through 446 removed outlier: 3.599A pdb=" N ARG O 443 " --> pdb=" O HIS O 439 " (cutoff:3.500A) Processing helix chain 'O' and resid 447 through 450 Processing helix chain 'O' and resid 458 through 475 Processing helix chain 'O' and resid 482 through 490 removed outlier: 3.825A pdb=" N CYS O 486 " --> pdb=" O THR O 482 " (cutoff:3.500A) Processing helix chain 'O' and resid 493 through 507 Processing helix chain 'O' and resid 602 through 616 Processing helix chain 'O' and resid 619 through 628 Processing helix chain 'O' and resid 631 through 641 Processing helix chain 'O' and resid 645 through 650 Processing helix chain 'O' and resid 657 through 661 removed outlier: 4.133A pdb=" N TYR O 661 " --> pdb=" O PRO O 658 " (cutoff:3.500A) Processing helix chain 'O' and resid 671 through 684 removed outlier: 3.740A pdb=" N THR O 676 " --> pdb=" O PRO O 672 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE O 679 " --> pdb=" O SER O 675 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL O 684 " --> pdb=" O LEU O 680 " (cutoff:3.500A) Processing helix chain 'O' and resid 685 through 705 removed outlier: 3.535A pdb=" N GLU O 705 " --> pdb=" O SER O 701 " (cutoff:3.500A) Processing helix chain 'O' and resid 711 through 716 Processing helix chain 'O' and resid 868 through 952 removed outlier: 4.277A pdb=" N LYS O 872 " --> pdb=" O ALA O 868 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 132 removed outlier: 3.687A pdb=" N LYS P 131 " --> pdb=" O MET P 128 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE P 132 " --> pdb=" O ALA P 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 128 through 132' Processing helix chain 'P' and resid 134 through 141 Processing helix chain 'P' and resid 143 through 173 removed outlier: 3.604A pdb=" N TYR P 147 " --> pdb=" O GLU P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 306 Processing helix chain 'P' and resid 312 through 327 Processing helix chain 'P' and resid 353 through 355 No H-bonds generated for 'chain 'P' and resid 353 through 355' Processing helix chain 'P' and resid 356 through 361 Processing helix chain 'P' and resid 400 through 411 Processing helix chain 'P' and resid 414 through 447 removed outlier: 3.830A pdb=" N ASP P 447 " --> pdb=" O SER P 443 " (cutoff:3.500A) Processing helix chain 'P' and resid 447 through 468 Processing helix chain 'P' and resid 478 through 484 removed outlier: 3.701A pdb=" N PHE P 483 " --> pdb=" O GLU P 480 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN P 484 " --> pdb=" O PHE P 481 " (cutoff:3.500A) Processing helix chain 'P' and resid 486 through 505 Processing helix chain 'Q' and resid 186 through 207 Processing helix chain 'Q' and resid 220 through 276 Processing helix chain 'R' and resid 14 through 38 Processing helix chain 'R' and resid 58 through 62 Processing sheet with id=AA1, first strand: chain 'L' and resid 1814 through 1816 removed outlier: 6.197A pdb=" N LYS L1815 " --> pdb=" O ILE O 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'M' and resid 26 through 28 Processing sheet with id=AA3, first strand: chain 'M' and resid 186 through 195 Processing sheet with id=AA4, first strand: chain 'M' and resid 261 through 270 Processing sheet with id=AA5, first strand: chain 'N' and resid 424 through 426 removed outlier: 7.440A pdb=" N ILE N 424 " --> pdb=" O LEU O 534 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'N' and resid 437 through 439 removed outlier: 6.781A pdb=" N VAL N 438 " --> pdb=" O LEU R 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 523 through 524 Processing sheet with id=AA8, first strand: chain 'P' and resid 309 through 311 removed outlier: 3.550A pdb=" N MET P 366 " --> pdb=" O LYS P 296 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2691 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: 4.14 Time building geometry restraints manager: 6.07 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: 4993 1.34 - 1.46: 3097 1.46 - 1.58: 7030 1.58 - 1.70: 0 1.70 - 1.81: 129 Bond restraints: 15249 Sorted by residual: bond pdb=" CA SER N 456 " pdb=" CB SER N 456 " ideal model delta sigma weight residual 1.532 1.489 0.043 1.65e-02 3.67e+03 6.65e+00 bond pdb=" N SER Q 208 " pdb=" CA SER Q 208 " ideal model delta sigma weight residual 1.454 1.482 -0.028 1.21e-02 6.83e+03 5.34e+00 bond pdb=" N ASN L1692 " pdb=" CA ASN L1692 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.28e-02 6.10e+03 5.14e+00 bond pdb=" N ARG I 408 " pdb=" CA ARG I 408 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.23e-02 6.61e+03 5.00e+00 bond pdb=" CA SER Q 210 " pdb=" CB SER Q 210 " ideal model delta sigma weight residual 1.530 1.492 0.038 1.69e-02 3.50e+03 4.98e+00 ... (remaining 15244 not shown) Histogram of bond angle deviations from ideal: 97.40 - 104.75: 301 104.75 - 112.09: 7602 112.09 - 119.44: 5155 119.44 - 126.78: 7319 126.78 - 134.13: 204 Bond angle restraints: 20581 Sorted by residual: angle pdb=" C GLY M 304 " pdb=" N GLY M 305 " pdb=" CA GLY M 305 " ideal model delta sigma weight residual 121.32 112.36 8.96 1.79e+00 3.12e-01 2.51e+01 angle pdb=" N ASP M 345 " pdb=" CA ASP M 345 " pdb=" C ASP M 345 " ideal model delta sigma weight residual 111.11 105.49 5.62 1.20e+00 6.94e-01 2.20e+01 angle pdb=" N VAL O 707 " pdb=" CA VAL O 707 " pdb=" C VAL O 707 " ideal model delta sigma weight residual 109.02 104.88 4.14 9.30e-01 1.16e+00 1.98e+01 angle pdb=" C ASN N 511 " pdb=" CA ASN N 511 " pdb=" CB ASN N 511 " ideal model delta sigma weight residual 111.73 117.49 -5.76 1.42e+00 4.96e-01 1.64e+01 angle pdb=" C LYS L1662 " pdb=" N ASP L1663 " pdb=" CA ASP L1663 " ideal model delta sigma weight residual 125.66 132.45 -6.79 1.85e+00 2.92e-01 1.35e+01 ... (remaining 20576 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 8300 17.85 - 35.70: 916 35.70 - 53.54: 153 53.54 - 71.39: 32 71.39 - 89.24: 11 Dihedral angle restraints: 9412 sinusoidal: 3968 harmonic: 5444 Sorted by residual: dihedral pdb=" CA MET M 38 " pdb=" C MET M 38 " pdb=" N PHE M 39 " pdb=" CA PHE M 39 " ideal model delta harmonic sigma weight residual -180.00 -150.94 -29.06 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ASN M 342 " pdb=" C ASN M 342 " pdb=" N THR M 343 " pdb=" CA THR M 343 " ideal model delta harmonic sigma weight residual -180.00 -152.93 -27.07 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ARG R 38 " pdb=" C ARG R 38 " pdb=" N LEU R 39 " pdb=" CA LEU R 39 " ideal model delta harmonic sigma weight residual -180.00 -155.21 -24.79 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 9409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1928 0.061 - 0.121: 351 0.121 - 0.182: 18 0.182 - 0.242: 0 0.242 - 0.303: 3 Chirality restraints: 2300 Sorted by residual: chirality pdb=" CA ASN N 511 " pdb=" N ASN N 511 " pdb=" C ASN N 511 " pdb=" CB ASN N 511 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA GLU N 505 " pdb=" N GLU N 505 " pdb=" C GLU N 505 " pdb=" CB GLU N 505 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA GLU Q 209 " pdb=" N GLU Q 209 " pdb=" C GLU Q 209 " pdb=" CB GLU Q 209 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2297 not shown) Planarity restraints: 2650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR O 458 " -0.045 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO O 459 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO O 459 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO O 459 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS M 350 " 0.043 5.00e-02 4.00e+02 6.49e-02 6.75e+00 pdb=" N PRO M 351 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO M 351 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO M 351 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR O 537 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO O 538 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO O 538 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO O 538 " 0.034 5.00e-02 4.00e+02 ... (remaining 2647 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 876 2.72 - 3.26: 16043 3.26 - 3.81: 25396 3.81 - 4.35: 31645 4.35 - 4.90: 52289 Nonbonded interactions: 126249 Sorted by model distance: nonbonded pdb=" OD1 ASP L2157 " pdb=" N ARG L2158 " model vdw 2.174 2.520 nonbonded pdb=" OG SER L1645 " pdb=" OG SER O 669 " model vdw 2.203 2.440 nonbonded pdb=" O SER P 410 " pdb=" OG SER P 413 " model vdw 2.212 2.440 nonbonded pdb=" O LEU L2017 " pdb=" NH2 ARG L2057 " model vdw 2.213 2.520 nonbonded pdb=" OD1 ASP N 471 " pdb=" OG1 THR O 528 " model vdw 2.215 2.440 ... (remaining 126244 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=0.21 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: 18.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 23.780 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 40.840 Find NCS groups from input model: 0.410 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:10.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 0.072 15249 Z= 0.350 Angle : 0.720 8.963 20581 Z= 0.422 Chirality : 0.045 0.303 2300 Planarity : 0.005 0.067 2650 Dihedral : 15.071 89.242 5840 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.12 % Allowed : 5.79 % Favored : 94.09 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.16), residues: 1795 helix: -1.79 (0.12), residues: 1156 sheet: -3.03 (0.62), residues: 46 loop : -2.97 (0.22), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 507 HIS 0.007 0.001 HIS Q 252 PHE 0.019 0.002 PHE N 906 TYR 0.018 0.002 TYR M 26 ARG 0.006 0.000 ARG I 441 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 365 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 399 LYS cc_start: 0.8694 (mttt) cc_final: 0.8262 (tmmt) REVERT: I 449 GLU cc_start: 0.6571 (pt0) cc_final: 0.6181 (pt0) REVERT: I 453 THR cc_start: 0.7723 (m) cc_final: 0.6962 (m) REVERT: I 457 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8195 (mt-10) REVERT: M 178 GLU cc_start: 0.7996 (tp30) cc_final: 0.7622 (tp30) REVERT: O 616 TYR cc_start: 0.8152 (m-80) cc_final: 0.7933 (m-80) REVERT: P 154 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7175 (tm-30) REVERT: P 158 ASP cc_start: 0.8056 (p0) cc_final: 0.7474 (p0) REVERT: P 162 MET cc_start: 0.7669 (tpt) cc_final: 0.7357 (tpp) REVERT: P 339 CYS cc_start: 0.6624 (m) cc_final: 0.4851 (m) REVERT: P 359 GLN cc_start: 0.7436 (pt0) cc_final: 0.6725 (tp40) REVERT: Q 223 ARG cc_start: 0.6949 (ttt-90) cc_final: 0.6743 (mmm-85) outliers start: 2 outliers final: 1 residues processed: 366 average time/residue: 1.5214 time to fit residues: 604.0231 Evaluate side-chains 248 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 247 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 167 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 46 optimal weight: 0.4980 chunk 92 optimal weight: 0.4980 chunk 73 optimal weight: 0.1980 chunk 141 optimal weight: 0.0870 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 356 GLN L1997 ASN L2268 ASN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 229 ASN M 322 HIS N 451 ASN ** N 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 511 ASN N 513 GLN N 604 GLN ** N 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 638 HIS N 938 GLN N 948 GLN O 439 HIS O 501 HIS ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 632 GLN O 925 GLN P 321 GLN P 432 ASN P 457 GLN P 484 GLN Q 190 HIS Q 253 GLN Q 267 ASN ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 HIS R 70 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15249 Z= 0.234 Angle : 0.620 7.626 20581 Z= 0.322 Chirality : 0.041 0.161 2300 Planarity : 0.005 0.048 2650 Dihedral : 5.018 32.874 2005 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.29 % Allowed : 15.16 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.19), residues: 1795 helix: 0.23 (0.14), residues: 1167 sheet: -1.96 (0.73), residues: 46 loop : -2.16 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 507 HIS 0.008 0.001 HIS Q 252 PHE 0.020 0.002 PHE N 906 TYR 0.024 0.002 TYR M 47 ARG 0.007 0.000 ARG P 478 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 280 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 399 LYS cc_start: 0.8678 (mttt) cc_final: 0.8253 (tmmt) REVERT: I 449 GLU cc_start: 0.6347 (pt0) cc_final: 0.6082 (pt0) REVERT: I 457 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8037 (mt-10) REVERT: M 46 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7737 (tpt-90) REVERT: M 178 GLU cc_start: 0.7994 (tp30) cc_final: 0.7642 (tp30) REVERT: N 913 MET cc_start: 0.7962 (tmm) cc_final: 0.7379 (tmm) REVERT: O 930 ASP cc_start: 0.6921 (m-30) cc_final: 0.6629 (OUTLIER) REVERT: P 154 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7031 (tm-30) REVERT: P 158 ASP cc_start: 0.8029 (p0) cc_final: 0.7712 (p0) REVERT: P 166 LEU cc_start: 0.8939 (mp) cc_final: 0.8711 (mp) REVERT: Q 223 ARG cc_start: 0.6927 (ttt-90) cc_final: 0.6610 (mmm-85) REVERT: Q 250 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7819 (tm-30) outliers start: 54 outliers final: 18 residues processed: 303 average time/residue: 1.4253 time to fit residues: 470.5809 Evaluate side-chains 268 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 250 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 356 GLN Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain L residue 1833 ARG Chi-restraints excluded: chain M residue 46 ARG Chi-restraints excluded: chain M residue 51 TRP Chi-restraints excluded: chain M residue 81 TYR Chi-restraints excluded: chain N residue 515 ASP Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain O residue 510 ILE Chi-restraints excluded: chain O residue 631 THR Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 892 VAL Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain P residue 439 GLU Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 253 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 0.3980 chunk 51 optimal weight: 0.4980 chunk 136 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 164 optimal weight: 0.0030 chunk 177 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 163 optimal weight: 0.5980 chunk 56 optimal weight: 0.0970 chunk 132 optimal weight: 2.9990 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 356 GLN L1708 GLN L1843 HIS ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 489 ASN N 511 ASN ** N 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 925 GLN P 310 GLN Q 267 ASN ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15249 Z= 0.210 Angle : 0.587 7.427 20581 Z= 0.302 Chirality : 0.040 0.154 2300 Planarity : 0.004 0.046 2650 Dihedral : 4.625 26.528 2005 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.47 % Allowed : 16.69 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.20), residues: 1795 helix: 1.10 (0.15), residues: 1174 sheet: -1.33 (0.77), residues: 46 loop : -1.78 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 507 HIS 0.005 0.001 HIS Q 252 PHE 0.020 0.001 PHE N 906 TYR 0.023 0.002 TYR O 941 ARG 0.011 0.000 ARG I 469 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 269 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 399 LYS cc_start: 0.8693 (mttt) cc_final: 0.8249 (tmmt) REVERT: I 449 GLU cc_start: 0.6223 (pt0) cc_final: 0.5983 (pt0) REVERT: I 457 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8052 (mt-10) REVERT: M 178 GLU cc_start: 0.7964 (tp30) cc_final: 0.7620 (tp30) REVERT: M 185 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8909 (m) REVERT: N 913 MET cc_start: 0.7958 (tmm) cc_final: 0.7124 (tmm) REVERT: O 930 ASP cc_start: 0.6962 (m-30) cc_final: 0.6708 (t0) REVERT: P 154 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7213 (tm-30) REVERT: P 158 ASP cc_start: 0.8019 (p0) cc_final: 0.7734 (p0) REVERT: P 162 MET cc_start: 0.7623 (tpp) cc_final: 0.7309 (tpp) REVERT: P 366 MET cc_start: 0.6643 (OUTLIER) cc_final: 0.6324 (mpt) REVERT: Q 249 GLU cc_start: 0.7929 (tp30) cc_final: 0.7686 (tm-30) REVERT: Q 250 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7754 (tm-30) outliers start: 57 outliers final: 24 residues processed: 302 average time/residue: 1.3994 time to fit residues: 462.8716 Evaluate side-chains 271 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 245 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 458 LYS Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1833 ARG Chi-restraints excluded: chain L residue 1850 ASP Chi-restraints excluded: chain L residue 1853 GLU Chi-restraints excluded: chain M residue 51 TRP Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain N residue 461 ILE Chi-restraints excluded: chain N residue 515 ASP Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 918 GLU Chi-restraints excluded: chain N residue 939 LEU Chi-restraints excluded: chain O residue 615 MET Chi-restraints excluded: chain O residue 631 THR Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 712 VAL Chi-restraints excluded: chain O residue 884 ILE Chi-restraints excluded: chain O residue 892 VAL Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 439 GLU Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 220 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 0.7980 chunk 123 optimal weight: 0.3980 chunk 85 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 165 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1708 GLN ** L1843 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 489 ASN N 511 ASN ** N 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 925 GLN P 308 HIS P 310 GLN P 500 GLN ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 15249 Z= 0.311 Angle : 0.619 7.418 20581 Z= 0.317 Chirality : 0.042 0.172 2300 Planarity : 0.005 0.046 2650 Dihedral : 4.993 85.335 2005 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.84 % Allowed : 18.70 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.20), residues: 1795 helix: 1.30 (0.15), residues: 1173 sheet: -0.83 (0.96), residues: 34 loop : -1.54 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 507 HIS 0.008 0.001 HIS P 362 PHE 0.020 0.002 PHE M 17 TYR 0.026 0.002 TYR O 941 ARG 0.007 0.000 ARG I 469 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 248 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 399 LYS cc_start: 0.8735 (mttt) cc_final: 0.8270 (tmmt) REVERT: I 449 GLU cc_start: 0.6313 (pt0) cc_final: 0.6041 (pt0) REVERT: I 457 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8191 (mt-10) REVERT: I 472 HIS cc_start: 0.7441 (OUTLIER) cc_final: 0.7166 (m170) REVERT: M 185 VAL cc_start: 0.9080 (OUTLIER) cc_final: 0.8871 (m) REVERT: N 674 MET cc_start: 0.6163 (mmt) cc_final: 0.4876 (mtp) REVERT: N 913 MET cc_start: 0.7846 (tmm) cc_final: 0.7130 (tmm) REVERT: N 914 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7604 (t0) REVERT: O 913 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8198 (tpt) REVERT: O 921 GLU cc_start: 0.8040 (tp30) cc_final: 0.7839 (tp30) REVERT: O 930 ASP cc_start: 0.7140 (m-30) cc_final: 0.6863 (t0) REVERT: P 154 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7061 (tm-30) REVERT: P 158 ASP cc_start: 0.8028 (p0) cc_final: 0.7718 (p0) REVERT: P 162 MET cc_start: 0.7584 (tpp) cc_final: 0.7346 (tpp) REVERT: P 167 ASP cc_start: 0.8232 (t70) cc_final: 0.7994 (OUTLIER) REVERT: Q 249 GLU cc_start: 0.7988 (tp30) cc_final: 0.7743 (tm-30) REVERT: Q 250 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7647 (tm-30) REVERT: Q 253 GLN cc_start: 0.8498 (tp40) cc_final: 0.8149 (tp40) REVERT: Q 269 GLU cc_start: 0.7903 (tp30) cc_final: 0.7681 (tp30) outliers start: 63 outliers final: 31 residues processed: 286 average time/residue: 1.3898 time to fit residues: 435.7450 Evaluate side-chains 267 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 233 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 472 HIS Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1833 ARG Chi-restraints excluded: chain L residue 1850 ASP Chi-restraints excluded: chain L residue 1853 GLU Chi-restraints excluded: chain L residue 1972 ASP Chi-restraints excluded: chain L residue 2138 THR Chi-restraints excluded: chain L residue 2187 VAL Chi-restraints excluded: chain M residue 51 TRP Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain N residue 461 ILE Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 685 ASP Chi-restraints excluded: chain N residue 914 ASP Chi-restraints excluded: chain N residue 918 GLU Chi-restraints excluded: chain N residue 939 LEU Chi-restraints excluded: chain O residue 510 ILE Chi-restraints excluded: chain O residue 631 THR Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 712 VAL Chi-restraints excluded: chain O residue 884 ILE Chi-restraints excluded: chain O residue 892 VAL Chi-restraints excluded: chain O residue 913 MET Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain P residue 339 CYS Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 439 GLU Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 231 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 72 optimal weight: 0.0970 chunk 149 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 chunk 157 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 356 GLN L1708 GLN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 511 ASN ** N 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 632 GLN O 925 GLN O 935 HIS ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15249 Z= 0.259 Angle : 0.595 7.257 20581 Z= 0.303 Chirality : 0.041 0.177 2300 Planarity : 0.004 0.049 2650 Dihedral : 4.494 27.867 2003 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.51 % Allowed : 19.06 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 1795 helix: 1.52 (0.15), residues: 1174 sheet: -0.57 (0.97), residues: 34 loop : -1.38 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 507 HIS 0.007 0.001 HIS P 362 PHE 0.022 0.002 PHE M 17 TYR 0.027 0.002 TYR O 941 ARG 0.007 0.000 ARG Q 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 255 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 399 LYS cc_start: 0.8732 (mttt) cc_final: 0.8265 (tmmt) REVERT: I 449 GLU cc_start: 0.6253 (pt0) cc_final: 0.5980 (pt0) REVERT: I 457 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8188 (mt-10) REVERT: I 471 LYS cc_start: 0.8650 (tppt) cc_final: 0.8188 (tmmm) REVERT: I 472 HIS cc_start: 0.7391 (OUTLIER) cc_final: 0.7119 (m170) REVERT: M 185 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8873 (m) REVERT: N 674 MET cc_start: 0.6149 (mmt) cc_final: 0.4876 (mtp) REVERT: N 913 MET cc_start: 0.7804 (tmm) cc_final: 0.7126 (tmm) REVERT: O 913 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8111 (tpt) REVERT: O 930 ASP cc_start: 0.7005 (m-30) cc_final: 0.6759 (t0) REVERT: P 154 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7122 (tm-30) REVERT: P 158 ASP cc_start: 0.8004 (p0) cc_final: 0.7463 (p0) REVERT: P 162 MET cc_start: 0.7565 (tpp) cc_final: 0.7310 (tpp) REVERT: P 366 MET cc_start: 0.6676 (OUTLIER) cc_final: 0.6358 (mpt) outliers start: 74 outliers final: 37 residues processed: 303 average time/residue: 1.3351 time to fit residues: 443.2876 Evaluate side-chains 276 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 235 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 356 GLN Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 472 HIS Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1833 ARG Chi-restraints excluded: chain L residue 1850 ASP Chi-restraints excluded: chain L residue 1853 GLU Chi-restraints excluded: chain L residue 2138 THR Chi-restraints excluded: chain L residue 2187 VAL Chi-restraints excluded: chain L residue 2239 LEU Chi-restraints excluded: chain M residue 51 TRP Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 342 ASN Chi-restraints excluded: chain M residue 348 GLN Chi-restraints excluded: chain N residue 448 GLU Chi-restraints excluded: chain N residue 461 ILE Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 685 ASP Chi-restraints excluded: chain N residue 939 LEU Chi-restraints excluded: chain N residue 944 MET Chi-restraints excluded: chain O residue 510 ILE Chi-restraints excluded: chain O residue 631 THR Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 712 VAL Chi-restraints excluded: chain O residue 884 ILE Chi-restraints excluded: chain O residue 892 VAL Chi-restraints excluded: chain O residue 913 MET Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain P residue 339 CYS Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 439 GLU Chi-restraints excluded: chain Q residue 211 VAL Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 231 VAL Chi-restraints excluded: chain Q residue 241 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 175 optimal weight: 0.5980 chunk 145 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 91 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1708 GLN L2176 GLN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 925 GLN P 310 GLN ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15249 Z= 0.281 Angle : 0.620 7.737 20581 Z= 0.314 Chirality : 0.042 0.173 2300 Planarity : 0.005 0.047 2650 Dihedral : 4.465 27.439 2003 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.20 % Allowed : 20.52 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.20), residues: 1795 helix: 1.58 (0.15), residues: 1175 sheet: -0.48 (0.97), residues: 34 loop : -1.32 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 507 HIS 0.006 0.001 HIS Q 252 PHE 0.021 0.002 PHE M 17 TYR 0.026 0.002 TYR O 941 ARG 0.009 0.000 ARG Q 229 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 247 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 399 LYS cc_start: 0.8739 (mttt) cc_final: 0.8269 (tmmt) REVERT: I 449 GLU cc_start: 0.6190 (pt0) cc_final: 0.5953 (pt0) REVERT: I 457 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8187 (mt-10) REVERT: I 471 LYS cc_start: 0.8669 (tppt) cc_final: 0.8171 (tmmm) REVERT: L 1745 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7452 (tm) REVERT: L 1962 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8062 (ptmt) REVERT: N 674 MET cc_start: 0.6161 (mmt) cc_final: 0.4843 (mtm) REVERT: N 913 MET cc_start: 0.7810 (tmm) cc_final: 0.7124 (tmm) REVERT: O 904 ARG cc_start: 0.7498 (ptt180) cc_final: 0.7186 (ptt180) REVERT: O 913 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8150 (tpt) REVERT: O 930 ASP cc_start: 0.7003 (m-30) cc_final: 0.6762 (t0) REVERT: P 154 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7123 (tm-30) REVERT: P 158 ASP cc_start: 0.8025 (p0) cc_final: 0.7472 (p0) REVERT: P 167 ASP cc_start: 0.8169 (t70) cc_final: 0.7941 (OUTLIER) outliers start: 69 outliers final: 40 residues processed: 295 average time/residue: 1.3413 time to fit residues: 433.7843 Evaluate side-chains 277 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 235 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1745 LEU Chi-restraints excluded: chain L residue 1833 ARG Chi-restraints excluded: chain L residue 1850 ASP Chi-restraints excluded: chain L residue 1962 LYS Chi-restraints excluded: chain L residue 2138 THR Chi-restraints excluded: chain L residue 2171 LEU Chi-restraints excluded: chain L residue 2187 VAL Chi-restraints excluded: chain L residue 2239 LEU Chi-restraints excluded: chain M residue 51 TRP Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 342 ASN Chi-restraints excluded: chain N residue 448 GLU Chi-restraints excluded: chain N residue 461 ILE Chi-restraints excluded: chain N residue 636 ILE Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 685 ASP Chi-restraints excluded: chain N residue 939 LEU Chi-restraints excluded: chain N residue 944 MET Chi-restraints excluded: chain O residue 510 ILE Chi-restraints excluded: chain O residue 603 GLU Chi-restraints excluded: chain O residue 631 THR Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 688 VAL Chi-restraints excluded: chain O residue 712 VAL Chi-restraints excluded: chain O residue 884 ILE Chi-restraints excluded: chain O residue 892 VAL Chi-restraints excluded: chain O residue 913 MET Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 311 THR Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain P residue 339 CYS Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 439 GLU Chi-restraints excluded: chain Q residue 211 VAL Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 231 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 127 optimal weight: 0.0010 chunk 147 optimal weight: 0.5980 chunk 97 optimal weight: 0.0970 chunk 174 optimal weight: 0.5980 chunk 109 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1708 GLN L2100 GLN L2176 GLN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 925 GLN ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 15 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15249 Z= 0.218 Angle : 0.599 8.695 20581 Z= 0.304 Chirality : 0.040 0.178 2300 Planarity : 0.004 0.048 2650 Dihedral : 4.328 27.223 2003 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.90 % Allowed : 21.01 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.20), residues: 1795 helix: 1.71 (0.15), residues: 1178 sheet: -0.37 (0.97), residues: 34 loop : -1.19 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 507 HIS 0.006 0.001 HIS Q 252 PHE 0.015 0.001 PHE N 906 TYR 0.022 0.002 TYR O 941 ARG 0.010 0.000 ARG Q 229 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 254 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 399 LYS cc_start: 0.8725 (mttt) cc_final: 0.8235 (tmmt) REVERT: I 457 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8129 (mt-10) REVERT: L 1745 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7340 (tm) REVERT: L 1962 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8058 (ptmt) REVERT: L 2230 MET cc_start: 0.8559 (tpp) cc_final: 0.7983 (mmp) REVERT: L 2250 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8061 (mt-10) REVERT: N 674 MET cc_start: 0.6207 (mmt) cc_final: 0.4958 (mtm) REVERT: N 913 MET cc_start: 0.7762 (tmm) cc_final: 0.7203 (tmm) REVERT: N 944 MET cc_start: 0.5379 (OUTLIER) cc_final: 0.4677 (tpp) REVERT: O 687 ARG cc_start: 0.7642 (mtm110) cc_final: 0.7392 (mtm110) REVERT: O 913 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8080 (tpt) REVERT: O 917 ARG cc_start: 0.8689 (ttm-80) cc_final: 0.8486 (ptp-110) REVERT: O 930 ASP cc_start: 0.6995 (m-30) cc_final: 0.6757 (t0) REVERT: P 154 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7070 (tm-30) REVERT: P 158 ASP cc_start: 0.8014 (p0) cc_final: 0.7414 (p0) REVERT: P 366 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.6235 (mpt) REVERT: Q 249 GLU cc_start: 0.7950 (tp30) cc_final: 0.7623 (tm-30) outliers start: 64 outliers final: 36 residues processed: 298 average time/residue: 1.3569 time to fit residues: 444.5748 Evaluate side-chains 276 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 234 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1745 LEU Chi-restraints excluded: chain L residue 1833 ARG Chi-restraints excluded: chain L residue 1853 GLU Chi-restraints excluded: chain L residue 1962 LYS Chi-restraints excluded: chain L residue 2138 THR Chi-restraints excluded: chain L residue 2171 LEU Chi-restraints excluded: chain L residue 2187 VAL Chi-restraints excluded: chain L residue 2239 LEU Chi-restraints excluded: chain L residue 2250 GLU Chi-restraints excluded: chain M residue 51 TRP Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain M residue 342 ASN Chi-restraints excluded: chain N residue 448 GLU Chi-restraints excluded: chain N residue 461 ILE Chi-restraints excluded: chain N residue 685 ASP Chi-restraints excluded: chain N residue 918 GLU Chi-restraints excluded: chain N residue 939 LEU Chi-restraints excluded: chain N residue 944 MET Chi-restraints excluded: chain O residue 510 ILE Chi-restraints excluded: chain O residue 515 ASP Chi-restraints excluded: chain O residue 631 THR Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 688 VAL Chi-restraints excluded: chain O residue 709 THR Chi-restraints excluded: chain O residue 712 VAL Chi-restraints excluded: chain O residue 884 ILE Chi-restraints excluded: chain O residue 892 VAL Chi-restraints excluded: chain O residue 913 MET Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain P residue 339 CYS Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 439 GLU Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 231 VAL Chi-restraints excluded: chain Q residue 241 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 33 optimal weight: 0.0980 chunk 110 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 158 optimal weight: 0.4980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 356 GLN ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1708 GLN L2100 GLN L2176 GLN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 925 GLN ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15249 Z= 0.238 Angle : 0.629 10.726 20581 Z= 0.316 Chirality : 0.041 0.193 2300 Planarity : 0.004 0.052 2650 Dihedral : 4.295 29.049 2003 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.96 % Allowed : 21.32 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.20), residues: 1795 helix: 1.71 (0.15), residues: 1179 sheet: -0.21 (1.00), residues: 34 loop : -1.14 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 507 HIS 0.006 0.001 HIS Q 252 PHE 0.015 0.001 PHE P 153 TYR 0.020 0.002 TYR L2076 ARG 0.013 0.000 ARG O 882 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 245 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 399 LYS cc_start: 0.8735 (mttt) cc_final: 0.8240 (tmmt) REVERT: I 457 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8168 (mt-10) REVERT: L 2250 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8051 (mt-10) REVERT: N 674 MET cc_start: 0.6259 (mmt) cc_final: 0.5059 (mtm) REVERT: N 913 MET cc_start: 0.7764 (tmm) cc_final: 0.7238 (tmm) REVERT: O 687 ARG cc_start: 0.7596 (mtm110) cc_final: 0.7372 (mtm110) REVERT: O 913 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8156 (tpt) REVERT: O 930 ASP cc_start: 0.6952 (m-30) cc_final: 0.6750 (t0) REVERT: P 154 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7107 (tm-30) REVERT: P 158 ASP cc_start: 0.8031 (p0) cc_final: 0.7431 (p0) REVERT: P 366 MET cc_start: 0.6613 (OUTLIER) cc_final: 0.6278 (mpt) REVERT: Q 253 GLN cc_start: 0.8412 (tp40) cc_final: 0.7869 (mm110) outliers start: 65 outliers final: 43 residues processed: 289 average time/residue: 1.3230 time to fit residues: 419.5004 Evaluate side-chains 281 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 235 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1708 GLN Chi-restraints excluded: chain L residue 1850 ASP Chi-restraints excluded: chain L residue 1853 GLU Chi-restraints excluded: chain L residue 2138 THR Chi-restraints excluded: chain L residue 2171 LEU Chi-restraints excluded: chain L residue 2187 VAL Chi-restraints excluded: chain L residue 2239 LEU Chi-restraints excluded: chain L residue 2250 GLU Chi-restraints excluded: chain L residue 2263 VAL Chi-restraints excluded: chain M residue 51 TRP Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain M residue 342 ASN Chi-restraints excluded: chain M residue 348 GLN Chi-restraints excluded: chain N residue 448 GLU Chi-restraints excluded: chain N residue 461 ILE Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 685 ASP Chi-restraints excluded: chain N residue 939 LEU Chi-restraints excluded: chain O residue 510 ILE Chi-restraints excluded: chain O residue 515 ASP Chi-restraints excluded: chain O residue 603 GLU Chi-restraints excluded: chain O residue 615 MET Chi-restraints excluded: chain O residue 631 THR Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 688 VAL Chi-restraints excluded: chain O residue 709 THR Chi-restraints excluded: chain O residue 712 VAL Chi-restraints excluded: chain O residue 884 ILE Chi-restraints excluded: chain O residue 892 VAL Chi-restraints excluded: chain O residue 913 MET Chi-restraints excluded: chain P residue 301 LEU Chi-restraints excluded: chain P residue 311 THR Chi-restraints excluded: chain P residue 339 CYS Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 439 GLU Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 231 VAL Chi-restraints excluded: chain Q residue 241 LEU Chi-restraints excluded: chain R residue 37 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 0.6980 chunk 152 optimal weight: 0.9990 chunk 162 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 0.0170 chunk 127 optimal weight: 0.0980 chunk 49 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 chunk 153 optimal weight: 0.2980 chunk 106 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2176 GLN ** N 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 925 GLN P 310 GLN Q 267 ASN ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15249 Z= 0.217 Angle : 0.639 11.325 20581 Z= 0.320 Chirality : 0.041 0.201 2300 Planarity : 0.005 0.060 2650 Dihedral : 4.241 30.274 2003 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.11 % Allowed : 22.96 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.21 (0.20), residues: 1795 helix: 1.75 (0.15), residues: 1176 sheet: -0.16 (1.00), residues: 34 loop : -1.12 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 507 HIS 0.006 0.001 HIS P 362 PHE 0.014 0.001 PHE N 906 TYR 0.019 0.002 TYR L2076 ARG 0.021 0.000 ARG O 882 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 243 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 399 LYS cc_start: 0.8730 (mttt) cc_final: 0.8231 (tmmt) REVERT: I 457 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8169 (mt-10) REVERT: L 1745 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7295 (tm) REVERT: L 2250 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: N 674 MET cc_start: 0.6219 (mmt) cc_final: 0.5027 (mtm) REVERT: N 913 MET cc_start: 0.7779 (tmm) cc_final: 0.7331 (tmm) REVERT: O 913 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8260 (tpt) REVERT: P 154 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7097 (tm-30) REVERT: P 158 ASP cc_start: 0.8031 (p0) cc_final: 0.7428 (p0) REVERT: P 366 MET cc_start: 0.6674 (OUTLIER) cc_final: 0.6251 (mpt) REVERT: Q 267 ASN cc_start: 0.7960 (m-40) cc_final: 0.7458 (t0) outliers start: 51 outliers final: 40 residues processed: 278 average time/residue: 1.3061 time to fit residues: 398.7473 Evaluate side-chains 273 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 229 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1745 LEU Chi-restraints excluded: chain L residue 1850 ASP Chi-restraints excluded: chain L residue 1853 GLU Chi-restraints excluded: chain L residue 2138 THR Chi-restraints excluded: chain L residue 2187 VAL Chi-restraints excluded: chain L residue 2239 LEU Chi-restraints excluded: chain L residue 2250 GLU Chi-restraints excluded: chain L residue 2263 VAL Chi-restraints excluded: chain M residue 51 TRP Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain M residue 342 ASN Chi-restraints excluded: chain M residue 348 GLN Chi-restraints excluded: chain N residue 448 GLU Chi-restraints excluded: chain N residue 461 ILE Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 685 ASP Chi-restraints excluded: chain N residue 918 GLU Chi-restraints excluded: chain N residue 939 LEU Chi-restraints excluded: chain O residue 510 ILE Chi-restraints excluded: chain O residue 515 ASP Chi-restraints excluded: chain O residue 603 GLU Chi-restraints excluded: chain O residue 631 THR Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 688 VAL Chi-restraints excluded: chain O residue 709 THR Chi-restraints excluded: chain O residue 712 VAL Chi-restraints excluded: chain O residue 884 ILE Chi-restraints excluded: chain O residue 892 VAL Chi-restraints excluded: chain O residue 913 MET Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 301 LEU Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 439 GLU Chi-restraints excluded: chain P residue 457 GLN Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 231 VAL Chi-restraints excluded: chain Q residue 241 LEU Chi-restraints excluded: chain R residue 26 ASN Chi-restraints excluded: chain R residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 180 optimal weight: 0.6980 chunk 165 optimal weight: 0.9980 chunk 143 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 chunk 88 optimal weight: 0.3980 chunk 114 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1708 GLN L1858 HIS L2176 GLN ** N 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 925 GLN P 310 GLN ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 15249 Z= 0.286 Angle : 0.683 11.796 20581 Z= 0.341 Chirality : 0.042 0.202 2300 Planarity : 0.005 0.063 2650 Dihedral : 4.338 29.883 2003 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.23 % Allowed : 23.20 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.20), residues: 1795 helix: 1.62 (0.14), residues: 1186 sheet: -0.20 (0.99), residues: 34 loop : -1.15 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 507 HIS 0.006 0.001 HIS Q 252 PHE 0.014 0.002 PHE P 153 TYR 0.026 0.002 TYR M 47 ARG 0.014 0.000 ARG Q 229 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 235 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 399 LYS cc_start: 0.8749 (mttt) cc_final: 0.8248 (tmmt) REVERT: I 457 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8155 (mt-10) REVERT: L 2250 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7892 (mt-10) REVERT: N 674 MET cc_start: 0.6268 (mmt) cc_final: 0.5067 (mtm) REVERT: N 913 MET cc_start: 0.7760 (tmm) cc_final: 0.7298 (tmm) REVERT: O 913 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8257 (tpt) REVERT: P 154 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7123 (tm-30) REVERT: P 158 ASP cc_start: 0.8017 (p0) cc_final: 0.7433 (p0) REVERT: Q 267 ASN cc_start: 0.7952 (m-40) cc_final: 0.7410 (t0) outliers start: 53 outliers final: 42 residues processed: 273 average time/residue: 1.4221 time to fit residues: 432.6456 Evaluate side-chains 272 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 228 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1850 ASP Chi-restraints excluded: chain L residue 1853 GLU Chi-restraints excluded: chain L residue 2138 THR Chi-restraints excluded: chain L residue 2187 VAL Chi-restraints excluded: chain L residue 2239 LEU Chi-restraints excluded: chain L residue 2250 GLU Chi-restraints excluded: chain M residue 51 TRP Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain M residue 342 ASN Chi-restraints excluded: chain N residue 448 GLU Chi-restraints excluded: chain N residue 461 ILE Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 685 ASP Chi-restraints excluded: chain N residue 918 GLU Chi-restraints excluded: chain N residue 939 LEU Chi-restraints excluded: chain O residue 438 VAL Chi-restraints excluded: chain O residue 510 ILE Chi-restraints excluded: chain O residue 515 ASP Chi-restraints excluded: chain O residue 603 GLU Chi-restraints excluded: chain O residue 615 MET Chi-restraints excluded: chain O residue 631 THR Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 688 VAL Chi-restraints excluded: chain O residue 709 THR Chi-restraints excluded: chain O residue 712 VAL Chi-restraints excluded: chain O residue 884 ILE Chi-restraints excluded: chain O residue 892 VAL Chi-restraints excluded: chain O residue 913 MET Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 301 LEU Chi-restraints excluded: chain P residue 339 CYS Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 439 GLU Chi-restraints excluded: chain P residue 457 GLN Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 241 LEU Chi-restraints excluded: chain R residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 0.6980 chunk 132 optimal weight: 0.0050 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 0.2980 chunk 143 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 147 optimal weight: 0.0870 chunk 18 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.2972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 356 GLN ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1708 GLN ** N 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 925 GLN ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** 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 = 0.3624 r_free = 0.3624 target = 0.114432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.093771 restraints weight = 29223.818| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.99 r_work: 0.3193 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15249 Z= 0.210 Angle : 0.651 11.883 20581 Z= 0.327 Chirality : 0.041 0.302 2300 Planarity : 0.005 0.064 2650 Dihedral : 4.270 30.462 2003 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.23 % Allowed : 23.39 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.23 (0.20), residues: 1795 helix: 1.73 (0.15), residues: 1188 sheet: -0.16 (0.99), residues: 34 loop : -1.08 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 507 HIS 0.006 0.001 HIS P 362 PHE 0.014 0.001 PHE Q 196 TYR 0.032 0.002 TYR M 47 ARG 0.021 0.000 ARG O 882 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7198.20 seconds wall clock time: 128 minutes 23.17 seconds (7703.17 seconds total)