Starting phenix.real_space_refine on Sun Aug 4 06:35:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iz9_35836/08_2024/8iz9_35836_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iz9_35836/08_2024/8iz9_35836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iz9_35836/08_2024/8iz9_35836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iz9_35836/08_2024/8iz9_35836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iz9_35836/08_2024/8iz9_35836_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iz9_35836/08_2024/8iz9_35836_trim.cif" } resolution = 2.95 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= 0.004 sd= 0.075 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 6351 2.51 5 N 1638 2.21 5 O 1747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 7": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A GLU 568": "OE1" <-> "OE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 803": "OE1" <-> "OE2" Residue "A GLU 884": "OE1" <-> "OE2" Residue "A GLU 925": "OE1" <-> "OE2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A GLU 1015": "OE1" <-> "OE2" Residue "A GLU 1020": "OE1" <-> "OE2" Residue "A GLU 1069": "OE1" <-> "OE2" Residue "A GLU 1093": "OE1" <-> "OE2" Residue "A GLU 1140": "OE1" <-> "OE2" Residue "A GLU 1145": "OE1" <-> "OE2" Residue "A GLU 1152": "OE1" <-> "OE2" Residue "A GLU 1160": "OE1" <-> "OE2" Residue "A GLU 1172": "OE1" <-> "OE2" Residue "A GLU 1202": "OE1" <-> "OE2" Residue "A GLU 1221": "OE1" <-> "OE2" Residue "A GLU 1254": "OE1" <-> "OE2" Residue "A GLU 1266": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9779 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 9754 Classifications: {'peptide': 1224} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 1185} Chain breaks: 2 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'XPG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.90, per 1000 atoms: 0.60 Number of scatterers: 9779 At special positions: 0 Unit cell: (74.385, 103.455, 153.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1747 8.00 N 1638 7.00 C 6351 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 1.7 seconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2312 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 3 sheets defined 70.0% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 17 through 24 Processing helix chain 'A' and resid 27 through 37 removed outlier: 3.575A pdb=" N LYS A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 44 removed outlier: 3.516A pdb=" N ASP A 43 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET A 44 " --> pdb=" O GLU A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 44' Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 74 removed outlier: 3.622A pdb=" N LEU A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 122 removed outlier: 5.801A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.602A pdb=" N TYR A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN A 122 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 179 removed outlier: 3.817A pdb=" N LEU A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 Processing helix chain 'A' and resid 190 through 213 removed outlier: 3.501A pdb=" N ILE A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASN A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP A 206 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN A 207 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N HIS A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 234 Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 236 through 282 removed outlier: 4.420A pdb=" N GLY A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.769A pdb=" N PHE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.546A pdb=" N ILE A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 343 removed outlier: 4.067A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 391 removed outlier: 4.092A pdb=" N PHE A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Proline residue: A 370 - end of helix Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.683A pdb=" N LEU A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 522 through 526 removed outlier: 3.983A pdb=" N THR A 526 " --> pdb=" O GLY A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 550 Processing helix chain 'A' and resid 566 through 578 Processing helix chain 'A' and resid 581 through 585 removed outlier: 4.316A pdb=" N GLU A 584 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 597 removed outlier: 3.524A pdb=" N LEU A 597 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 622 Processing helix chain 'A' and resid 697 through 709 removed outlier: 4.018A pdb=" N TYR A 701 " --> pdb=" O GLY A 697 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 751 removed outlier: 3.922A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 807 removed outlier: 3.602A pdb=" N TYR A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 807 " --> pdb=" O GLU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 removed outlier: 4.092A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 861 removed outlier: 3.914A pdb=" N ASP A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE A 829 " --> pdb=" O PHE A 825 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Proline residue: A 837 - end of helix Processing helix chain 'A' and resid 862 through 866 removed outlier: 3.894A pdb=" N ALA A 865 " --> pdb=" O PRO A 862 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 866 " --> pdb=" O TRP A 863 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 862 through 866' Processing helix chain 'A' and resid 867 through 910 removed outlier: 3.940A pdb=" N THR A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER A 898 " --> pdb=" O SER A 894 " (cutoff:3.500A) Proline residue: A 899 - end of helix removed outlier: 3.547A pdb=" N GLY A 910 " --> pdb=" O SER A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 918 Processing helix chain 'A' and resid 919 through 970 removed outlier: 4.057A pdb=" N CYS A 923 " --> pdb=" O ALA A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 974 removed outlier: 3.797A pdb=" N LEU A 974 " --> pdb=" O ALA A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 975 through 987 Processing helix chain 'A' and resid 991 through 1018 removed outlier: 4.436A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1090 Processing helix chain 'A' and resid 1130 through 1136 Processing helix chain 'A' and resid 1142 through 1153 removed outlier: 4.294A pdb=" N LEU A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1160 removed outlier: 3.718A pdb=" N ILE A1159 " --> pdb=" O LEU A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1193 Processing helix chain 'A' and resid 1208 through 1223 Processing helix chain 'A' and resid 1258 through 1264 removed outlier: 3.597A pdb=" N ASN A1264 " --> pdb=" O VAL A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1276 removed outlier: 3.893A pdb=" N LYS A1271 " --> pdb=" O SER A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1297 removed outlier: 3.513A pdb=" N TYR A1297 " --> pdb=" O PHE A1293 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 475 through 477 removed outlier: 4.383A pdb=" N ALA A 476 " --> pdb=" O ILE A 555 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU A 557 " --> pdb=" O ALA A 476 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 558 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 590 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU A 441 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 444 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 603 " --> pdb=" O GLY A 615 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLY A 615 " --> pdb=" O ILE A 603 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1041 through 1042 removed outlier: 4.175A pdb=" N TRP A1099 " --> pdb=" O ILE A1042 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1228 through 1232 removed outlier: 6.486A pdb=" N VAL A1071 " --> pdb=" O THR A1230 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA A1232 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A1073 " --> pdb=" O ALA A1232 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N MET A1245 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL A1074 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU A1247 " --> pdb=" O VAL A1074 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP A1256 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL A1246 " --> pdb=" O GLU A1254 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLU A1254 " --> pdb=" O VAL A1246 " (cutoff:3.500A) 608 hydrogen bonds defined for protein. 1806 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: 2.89 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1616 1.32 - 1.45: 2596 1.45 - 1.57: 5705 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 9987 Sorted by residual: bond pdb=" C13 XPG A1401 " pdb=" C14 XPG A1401 " ideal model delta sigma weight residual 1.328 1.292 0.036 2.00e-02 2.50e+03 3.30e+00 bond pdb=" C18 XPG A1401 " pdb=" C19 XPG A1401 " ideal model delta sigma weight residual 1.524 1.497 0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" C2 XPG A1401 " pdb=" C3 XPG A1401 " ideal model delta sigma weight residual 1.520 1.495 0.025 2.00e-02 2.50e+03 1.61e+00 bond pdb=" N ASN A1139 " pdb=" CA ASN A1139 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.32e+00 bond pdb=" C17 XPG A1401 " pdb=" C18 XPG A1401 " ideal model delta sigma weight residual 1.524 1.501 0.023 2.00e-02 2.50e+03 1.28e+00 ... (remaining 9982 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.60: 158 105.60 - 112.71: 5445 112.71 - 119.81: 3057 119.81 - 126.92: 4752 126.92 - 134.03: 121 Bond angle restraints: 13533 Sorted by residual: angle pdb=" CA LEU A 13 " pdb=" CB LEU A 13 " pdb=" CG LEU A 13 " ideal model delta sigma weight residual 116.30 126.47 -10.17 3.50e+00 8.16e-02 8.44e+00 angle pdb=" C12 XPG A1401 " pdb=" C8 XPG A1401 " pdb=" C7 XPG A1401 " ideal model delta sigma weight residual 114.63 123.33 -8.70 3.00e+00 1.11e-01 8.42e+00 angle pdb=" C7 XPG A1401 " pdb=" C8 XPG A1401 " pdb=" C9 XPG A1401 " ideal model delta sigma weight residual 115.09 106.64 8.45 3.00e+00 1.11e-01 7.92e+00 angle pdb=" N LYS A1156 " pdb=" CA LYS A1156 " pdb=" C LYS A1156 " ideal model delta sigma weight residual 111.36 113.96 -2.60 1.09e+00 8.42e-01 5.68e+00 angle pdb=" N GLY A1072 " pdb=" CA GLY A1072 " pdb=" C GLY A1072 " ideal model delta sigma weight residual 111.46 115.55 -4.09 1.75e+00 3.27e-01 5.46e+00 ... (remaining 13528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.80: 5420 18.80 - 37.61: 458 37.61 - 56.41: 70 56.41 - 75.21: 19 75.21 - 94.02: 11 Dihedral angle restraints: 5978 sinusoidal: 2407 harmonic: 3571 Sorted by residual: dihedral pdb=" CA ASP A1212 " pdb=" CB ASP A1212 " pdb=" CG ASP A1212 " pdb=" OD1 ASP A1212 " ideal model delta sinusoidal sigma weight residual -30.00 -89.05 59.05 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" C15 XPG A1401 " pdb=" C16 XPG A1401 " pdb=" C17 XPG A1401 " pdb=" C18 XPG A1401 " ideal model delta sinusoidal sigma weight residual -176.15 -82.13 -94.02 1 3.00e+01 1.11e-03 1.14e+01 dihedral pdb=" CB LYS A1194 " pdb=" CG LYS A1194 " pdb=" CD LYS A1194 " pdb=" CE LYS A1194 " ideal model delta sinusoidal sigma weight residual 60.00 117.92 -57.92 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 5975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1124 0.036 - 0.072: 352 0.072 - 0.108: 79 0.108 - 0.144: 17 0.144 - 0.180: 1 Chirality restraints: 1573 Sorted by residual: chirality pdb=" CB VAL A1153 " pdb=" CA VAL A1153 " pdb=" CG1 VAL A1153 " pdb=" CG2 VAL A1153 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" C15 XPG A1401 " pdb=" C14 XPG A1401 " pdb=" C16 XPG A1401 " pdb=" O15 XPG A1401 " both_signs ideal model delta sigma weight residual False 2.25 2.39 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE A1073 " pdb=" N ILE A1073 " pdb=" C ILE A1073 " pdb=" CB ILE A1073 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 1570 not shown) Planarity restraints: 1682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 XPG A1401 " 0.101 2.00e-02 2.50e+03 2.09e-01 4.36e+02 pdb=" C13 XPG A1401 " -0.285 2.00e-02 2.50e+03 pdb=" C14 XPG A1401 " 0.274 2.00e-02 2.50e+03 pdb=" C15 XPG A1401 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 11 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.51e+00 pdb=" N PRO A 12 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 12 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 12 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 898 " 0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 899 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 899 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 899 " 0.015 5.00e-02 4.00e+02 ... (remaining 1679 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2439 2.80 - 3.32: 9552 3.32 - 3.85: 16149 3.85 - 4.37: 17170 4.37 - 4.90: 30635 Nonbonded interactions: 75945 Sorted by model distance: nonbonded pdb=" OG1 THR A 269 " pdb=" OE2 GLU A 306 " model vdw 2.273 3.040 nonbonded pdb=" NE2 HIS A 153 " pdb=" OD2 ASP A 953 " model vdw 2.285 3.120 nonbonded pdb=" O GLY A 450 " pdb=" OG SER A 453 " model vdw 2.286 3.040 nonbonded pdb=" O VAL A 484 " pdb=" OG SER A 906 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR A 504 " pdb=" OD2 ASP A 524 " model vdw 2.308 3.040 ... (remaining 75940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.490 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:10.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5823 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 : 0.002 0.036 9987 Z= 0.141 Angle : 0.562 10.169 13533 Z= 0.310 Chirality : 0.037 0.180 1573 Planarity : 0.006 0.209 1682 Dihedral : 14.569 94.017 3666 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.94 (0.23), residues: 1218 helix: 0.38 (0.18), residues: 784 sheet: -1.45 (0.81), residues: 37 loop : -2.59 (0.26), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 763 HIS 0.003 0.000 HIS A 592 PHE 0.006 0.001 PHE A1043 TYR 0.017 0.001 TYR A1270 ARG 0.001 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1145 GLU cc_start: 0.6429 (mp0) cc_final: 0.6208 (pm20) outliers start: 0 outliers final: 2 residues processed: 137 average time/residue: 1.2467 time to fit residues: 183.2863 Evaluate side-chains 82 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 380 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 0.0370 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 95 optimal weight: 0.4980 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 297 ASN A 816 ASN A 931 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1275 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9987 Z= 0.201 Angle : 0.607 12.233 13533 Z= 0.303 Chirality : 0.042 0.152 1573 Planarity : 0.004 0.047 1682 Dihedral : 4.991 60.283 1355 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.31 % Allowed : 12.86 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.56 (0.24), residues: 1218 helix: 1.51 (0.19), residues: 789 sheet: -0.76 (0.85), residues: 35 loop : -1.93 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1025 HIS 0.005 0.001 HIS A1111 PHE 0.013 0.001 PHE A 352 TYR 0.024 0.002 TYR A1255 ARG 0.009 0.001 ARG A1012 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7020 (ttp) REVERT: A 186 MET cc_start: 0.5161 (tpt) cc_final: 0.4883 (mmm) REVERT: A 552 ASP cc_start: 0.7060 (m-30) cc_final: 0.6827 (m-30) REVERT: A 1047 ASN cc_start: 0.3346 (m-40) cc_final: 0.3037 (m-40) outliers start: 14 outliers final: 4 residues processed: 101 average time/residue: 1.0713 time to fit residues: 117.7941 Evaluate side-chains 78 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 288 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.0070 chunk 34 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 98 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9987 Z= 0.195 Angle : 0.561 11.051 13533 Z= 0.287 Chirality : 0.041 0.297 1573 Planarity : 0.004 0.054 1682 Dihedral : 4.458 74.777 1351 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.16 % Allowed : 16.90 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.99 (0.24), residues: 1218 helix: 1.80 (0.19), residues: 797 sheet: -0.44 (0.74), residues: 43 loop : -1.78 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 912 HIS 0.008 0.001 HIS A1111 PHE 0.016 0.001 PHE A 352 TYR 0.011 0.002 TYR A 768 ARG 0.007 0.001 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 231 MET cc_start: 0.7186 (tpp) cc_final: 0.6920 (mmt) REVERT: A 270 ASP cc_start: 0.6623 (m-30) cc_final: 0.6320 (m-30) REVERT: A 730 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8335 (mp) REVERT: A 1047 ASN cc_start: 0.3480 (m-40) cc_final: 0.2956 (m-40) REVERT: A 1157 GLU cc_start: 0.6562 (mp0) cc_final: 0.5737 (tm-30) outliers start: 23 outliers final: 8 residues processed: 95 average time/residue: 1.0965 time to fit residues: 113.6523 Evaluate side-chains 78 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1016 TYR Chi-restraints excluded: chain A residue 1245 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 0.0980 chunk 74 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9987 Z= 0.240 Angle : 0.596 12.420 13533 Z= 0.303 Chirality : 0.042 0.180 1573 Planarity : 0.004 0.053 1682 Dihedral : 4.273 61.520 1351 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.00 % Allowed : 17.00 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.04 (0.24), residues: 1218 helix: 1.76 (0.18), residues: 793 sheet: -0.40 (0.75), residues: 44 loop : -1.53 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 912 HIS 0.008 0.001 HIS A 153 PHE 0.022 0.002 PHE A 352 TYR 0.038 0.002 TYR A1016 ARG 0.021 0.001 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 77 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 231 MET cc_start: 0.7485 (tpp) cc_final: 0.7270 (mmt) REVERT: A 557 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6628 (pp) REVERT: A 589 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6740 (pt) REVERT: A 744 MET cc_start: 0.6197 (tmm) cc_final: 0.5521 (ttm) REVERT: A 936 GLU cc_start: 0.6973 (tt0) cc_final: 0.6734 (tt0) REVERT: A 1047 ASN cc_start: 0.3483 (m-40) cc_final: 0.3008 (m-40) REVERT: A 1049 MET cc_start: 0.6860 (mpp) cc_final: 0.6545 (mpt) REVERT: A 1166 MET cc_start: 0.4108 (tpt) cc_final: 0.3861 (tpp) outliers start: 32 outliers final: 10 residues processed: 102 average time/residue: 1.1454 time to fit residues: 126.4111 Evaluate side-chains 77 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.5980 chunk 1 optimal weight: 0.2980 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 chunk 105 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9987 Z= 0.161 Angle : 0.542 12.274 13533 Z= 0.270 Chirality : 0.040 0.272 1573 Planarity : 0.004 0.093 1682 Dihedral : 4.152 57.917 1351 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.54 % Allowed : 18.87 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.36 (0.24), residues: 1218 helix: 2.03 (0.19), residues: 798 sheet: -0.00 (0.79), residues: 43 loop : -1.56 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 947 HIS 0.009 0.001 HIS A 55 PHE 0.012 0.001 PHE A 352 TYR 0.011 0.001 TYR A 155 ARG 0.006 0.000 ARG A1189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 65 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 65 ASP cc_start: 0.6751 (p0) cc_final: 0.6522 (m-30) REVERT: A 126 MET cc_start: 0.6412 (OUTLIER) cc_final: 0.6099 (mtt) REVERT: A 184 MET cc_start: 0.6093 (mpp) cc_final: 0.5724 (mpm) REVERT: A 231 MET cc_start: 0.7404 (tpp) cc_final: 0.7154 (mmt) REVERT: A 556 TYR cc_start: 0.6560 (m-80) cc_final: 0.6344 (m-80) REVERT: A 557 LEU cc_start: 0.6776 (mp) cc_final: 0.6434 (pp) REVERT: A 589 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7295 (pt) REVERT: A 744 MET cc_start: 0.6139 (tmm) cc_final: 0.5560 (ttm) REVERT: A 1047 ASN cc_start: 0.3533 (m-40) cc_final: 0.3076 (m-40) REVERT: A 1166 MET cc_start: 0.4177 (tpt) cc_final: 0.3938 (tpp) outliers start: 27 outliers final: 8 residues processed: 84 average time/residue: 1.2398 time to fit residues: 112.3929 Evaluate side-chains 65 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1245 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 61 optimal weight: 0.0670 chunk 113 optimal weight: 20.0000 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 HIS ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.7069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 9987 Z= 0.393 Angle : 0.748 13.054 13533 Z= 0.382 Chirality : 0.048 0.296 1573 Planarity : 0.005 0.081 1682 Dihedral : 4.870 58.204 1351 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.10 % Allowed : 19.91 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.45 (0.23), residues: 1218 helix: 1.17 (0.18), residues: 790 sheet: -0.17 (0.76), residues: 44 loop : -1.47 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 912 HIS 0.014 0.002 HIS A 153 PHE 0.034 0.003 PHE A 336 TYR 0.026 0.002 TYR A 339 ARG 0.009 0.001 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 75 time to evaluate : 1.112 Fit side-chains REVERT: A 744 MET cc_start: 0.6425 (tmm) cc_final: 0.6139 (ttm) REVERT: A 906 SER cc_start: 0.8003 (t) cc_final: 0.7752 (m) REVERT: A 972 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7438 (mttp) REVERT: A 1131 MET cc_start: 0.4312 (OUTLIER) cc_final: 0.3812 (mmp) REVERT: A 1181 GLN cc_start: 0.3016 (OUTLIER) cc_final: 0.1035 (mm110) outliers start: 33 outliers final: 9 residues processed: 100 average time/residue: 0.8913 time to fit residues: 98.5583 Evaluate side-chains 73 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1181 GLN Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 0.0970 chunk 65 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 73 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.6908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9987 Z= 0.192 Angle : 0.579 11.525 13533 Z= 0.295 Chirality : 0.041 0.244 1573 Planarity : 0.005 0.101 1682 Dihedral : 4.571 57.865 1351 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.25 % Allowed : 20.75 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.10 (0.24), residues: 1218 helix: 1.74 (0.18), residues: 792 sheet: -0.07 (0.77), residues: 49 loop : -1.38 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 947 HIS 0.005 0.001 HIS A 934 PHE 0.026 0.001 PHE A 324 TYR 0.015 0.001 TYR A 289 ARG 0.007 0.000 ARG A1189 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 70 time to evaluate : 1.142 Fit side-chains REVERT: A 126 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.6130 (mtm) REVERT: A 556 TYR cc_start: 0.6947 (m-80) cc_final: 0.6676 (m-80) REVERT: A 744 MET cc_start: 0.6391 (tmm) cc_final: 0.6075 (ttm) REVERT: A 803 GLU cc_start: 0.7005 (mp0) cc_final: 0.6513 (mp0) REVERT: A 1131 MET cc_start: 0.3887 (OUTLIER) cc_final: 0.3552 (mmp) REVERT: A 1181 GLN cc_start: 0.2686 (OUTLIER) cc_final: 0.1054 (mm110) REVERT: A 1197 ILE cc_start: 0.6041 (mp) cc_final: 0.5821 (mp) outliers start: 24 outliers final: 6 residues processed: 85 average time/residue: 1.0279 time to fit residues: 96.0222 Evaluate side-chains 71 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1181 GLN Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.4476 > 50: distance: 10 - 13: 35.343 distance: 13 - 14: 40.327 distance: 14 - 15: 39.918 distance: 14 - 17: 37.193 distance: 15 - 16: 41.083 distance: 15 - 25: 56.233 distance: 17 - 18: 20.966 distance: 18 - 19: 57.418 distance: 18 - 20: 39.279 distance: 19 - 21: 55.575 distance: 20 - 22: 56.947 distance: 21 - 23: 31.015 distance: 22 - 23: 50.919 distance: 23 - 24: 10.298 distance: 26 - 29: 41.341 distance: 27 - 28: 38.526 distance: 27 - 32: 40.334 distance: 29 - 30: 21.813 distance: 32 - 33: 40.308 distance: 33 - 34: 42.801 distance: 33 - 36: 44.686 distance: 34 - 35: 25.048 distance: 34 - 38: 30.212 distance: 36 - 37: 40.496 distance: 38 - 39: 22.959 distance: 39 - 40: 39.169 distance: 39 - 42: 35.838 distance: 40 - 47: 41.259 distance: 42 - 43: 39.765 distance: 43 - 44: 61.946 distance: 44 - 45: 41.004 distance: 44 - 46: 42.095 distance: 47 - 48: 15.332 distance: 48 - 49: 46.078 distance: 48 - 51: 41.620 distance: 49 - 50: 57.101 distance: 49 - 56: 45.225 distance: 51 - 52: 41.053 distance: 52 - 53: 39.326 distance: 53 - 54: 40.563 distance: 53 - 55: 51.031 distance: 56 - 57: 20.122 distance: 56 - 62: 45.286 distance: 57 - 58: 56.442 distance: 57 - 60: 56.860 distance: 58 - 63: 41.026 distance: 61 - 62: 57.510 distance: 64 - 65: 40.774 distance: 64 - 67: 39.631 distance: 65 - 66: 39.559 distance: 65 - 77: 15.579 distance: 68 - 69: 41.244 distance: 69 - 71: 40.403 distance: 70 - 72: 41.299 distance: 71 - 72: 23.052 distance: 72 - 74: 37.043 distance: 73 - 75: 13.048 distance: 74 - 76: 10.578 distance: 75 - 76: 44.952 distance: 77 - 78: 23.105 distance: 78 - 79: 32.459 distance: 79 - 80: 33.712 distance: 79 - 84: 43.526 distance: 81 - 83: 39.961 distance: 84 - 85: 14.040 distance: 85 - 86: 34.552 distance: 85 - 88: 5.308 distance: 86 - 87: 40.203 distance: 86 - 95: 55.078 distance: 89 - 90: 41.403 distance: 89 - 91: 40.581 distance: 90 - 92: 40.737 distance: 91 - 93: 63.034 distance: 92 - 94: 7.372 distance: 93 - 94: 25.898 distance: 95 - 96: 40.518 distance: 96 - 97: 50.284 distance: 96 - 99: 57.209 distance: 97 - 98: 9.553 distance: 97 - 101: 31.309 distance: 99 - 100: 41.217