Starting phenix.real_space_refine on Sun Jul 21 11:22:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7e_41091/07_2024/8t7e_41091_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7e_41091/07_2024/8t7e_41091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7e_41091/07_2024/8t7e_41091.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7e_41091/07_2024/8t7e_41091.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7e_41091/07_2024/8t7e_41091_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7e_41091/07_2024/8t7e_41091_neut.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 P 37 5.49 5 S 79 5.16 5 C 8981 2.51 5 N 2512 2.21 5 O 2664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 236": "OE1" <-> "OE2" Residue "B TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14273 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7158 Classifications: {'peptide': 908} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 60, 'TRANS': 847} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3188 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 18, 'TRANS': 379} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3166 Classifications: {'peptide': 400} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 14} Link IDs: {'PTRANS': 18, 'TRANS': 381} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "P" Number of atoms: 394 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 18, 373 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Conformer: "B" Number of residues, atoms: 18, 373 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} bond proxies already assigned to first conformer: 395 Chain: "T" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 367 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A DA P 27 " occ=0.50 ... (40 atoms not shown) pdb=" C4 B DA P 27 " occ=0.50 Time building chain proxies: 8.24, per 1000 atoms: 0.58 Number of scatterers: 14273 At special positions: 0 Unit cell: (105.728, 102.424, 142.072, 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) S 79 16.00 P 37 15.00 O 2664 8.00 N 2512 7.00 C 8981 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: 5.57 Conformation dependent library (CDL) restraints added in 2.2 seconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3178 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 10 sheets defined 34.9% alpha, 11.1% beta 17 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 4.43 Creating SS restraints... Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 134 through 140 Processing helix chain 'A' and resid 141 through 146 removed outlier: 4.317A pdb=" N GLN A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.820A pdb=" N ALA A 154 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 306 through 316 removed outlier: 3.568A pdb=" N SER A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 351 removed outlier: 4.079A pdb=" N ASP A 349 " --> pdb=" O TRP A 345 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 351 " --> pdb=" O TRP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.154A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 448 removed outlier: 3.526A pdb=" N ALA A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 469 removed outlier: 3.880A pdb=" N MET A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 550 Processing helix chain 'A' and resid 570 through 575 Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 793 through 809 removed outlier: 5.254A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 903 removed outlier: 3.766A pdb=" N TRP A 897 " --> pdb=" O SER A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 919 Processing helix chain 'A' and resid 932 through 940 removed outlier: 4.367A pdb=" N THR A 938 " --> pdb=" O LYS A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 955 removed outlier: 4.308A pdb=" N ILE A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 969 removed outlier: 3.505A pdb=" N ALA A 962 " --> pdb=" O GLY A 958 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 980 Processing helix chain 'A' and resid 982 through 989 removed outlier: 3.747A pdb=" N TYR A 986 " --> pdb=" O ALA A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1066 Processing helix chain 'A' and resid 1095 through 1115 Processing helix chain 'A' and resid 1145 through 1168 removed outlier: 3.650A pdb=" N ASN A1157 " --> pdb=" O LEU A1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 77 removed outlier: 3.819A pdb=" N GLN B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 173 through 177 removed outlier: 3.603A pdb=" N LYS B 176 " --> pdb=" O ASN B 173 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR B 177 " --> pdb=" O VAL B 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 173 through 177' Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 192 through 200 Processing helix chain 'B' and resid 247 through 265 removed outlier: 3.888A pdb=" N ASP B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 394 through 409 removed outlier: 3.894A pdb=" N VAL B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 424 through 435 removed outlier: 3.883A pdb=" N LEU B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.603A pdb=" N THR B 447 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU B 448 " --> pdb=" O GLU B 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 444 through 448' Processing helix chain 'B' and resid 470 through 485 Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 87 through 93 removed outlier: 3.724A pdb=" N LEU C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 185 through 192 removed outlier: 3.692A pdb=" N ALA C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 200 Processing helix chain 'C' and resid 247 through 264 removed outlier: 3.655A pdb=" N LEU C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 391 through 409 removed outlier: 3.542A pdb=" N LEU C 395 " --> pdb=" O PRO C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 450 removed outlier: 3.897A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 478 Processing helix chain 'C' and resid 479 through 484 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 186 removed outlier: 3.536A pdb=" N VAL A 185 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 212 " --> pdb=" O TRP A 223 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A 213 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP A 198 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 436 removed outlier: 3.703A pdb=" N LEU A 435 " --> pdb=" O ILE A 840 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 884 through 890 Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.209A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA7, first strand: chain 'B' and resid 413 through 415 removed outlier: 6.844A pdb=" N TRP B 414 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYS B 382 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL B 441 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.138A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB1, first strand: chain 'C' and resid 413 through 415 removed outlier: 6.997A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1350 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 4.77 Time building geometry restraints manager: 6.10 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: 4252 1.34 - 1.46: 3109 1.46 - 1.58: 7144 1.58 - 1.70: 72 1.70 - 1.82: 125 Bond restraints: 14702 Sorted by residual: bond pdb=" C ILE A1069 " pdb=" N PRO A1070 " ideal model delta sigma weight residual 1.335 1.381 -0.046 8.70e-03 1.32e+04 2.75e+01 bond pdb=" N GLU B 394 " pdb=" CA GLU B 394 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.30e-02 5.92e+03 6.63e+00 bond pdb=" C3' DT P 16 " pdb=" O3' DT P 16 " ideal model delta sigma weight residual 1.422 1.499 -0.077 3.00e-02 1.11e+03 6.53e+00 bond pdb=" N GLY B 390 " pdb=" CA GLY B 390 " ideal model delta sigma weight residual 1.443 1.477 -0.035 1.37e-02 5.33e+03 6.48e+00 bond pdb=" N GLY B 388 " pdb=" CA GLY B 388 " ideal model delta sigma weight residual 1.446 1.479 -0.033 1.30e-02 5.92e+03 6.38e+00 ... (remaining 14697 not shown) Histogram of bond angle deviations from ideal: 76.95 - 90.64: 4 90.64 - 104.33: 390 104.33 - 118.01: 10869 118.01 - 131.70: 8762 131.70 - 145.39: 65 Bond angle restraints: 20090 Sorted by residual: angle pdb=" O3' DC P 25 " pdb=" P DG P 26 " pdb=" OP2 DG P 26 " ideal model delta sigma weight residual 108.00 76.95 31.05 3.00e+00 1.11e-01 1.07e+02 angle pdb=" OP1 DG P 26 " pdb=" P DG P 26 " pdb=" O5' DG P 26 " ideal model delta sigma weight residual 109.00 78.32 30.68 3.00e+00 1.11e-01 1.05e+02 angle pdb=" O3' DC P 25 " pdb=" P DG P 26 " pdb=" OP1 DG P 26 " ideal model delta sigma weight residual 108.00 80.15 27.85 3.00e+00 1.11e-01 8.62e+01 angle pdb=" OP1 DG P 26 " pdb=" P DG P 26 " pdb=" OP2 DG P 26 " ideal model delta sigma weight residual 120.00 145.39 -25.39 3.00e+00 1.11e-01 7.16e+01 angle pdb=" N PRO A 625 " pdb=" CA PRO A 625 " pdb=" CB PRO A 625 " ideal model delta sigma weight residual 103.25 111.57 -8.32 1.05e+00 9.07e-01 6.28e+01 ... (remaining 20085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 8288 34.84 - 69.67: 344 69.67 - 104.51: 23 104.51 - 139.35: 2 139.35 - 174.19: 4 Dihedral angle restraints: 8661 sinusoidal: 3743 harmonic: 4918 Sorted by residual: dihedral pdb=" CA HIS B 77 " pdb=" C HIS B 77 " pdb=" N PHE B 78 " pdb=" CA PHE B 78 " ideal model delta harmonic sigma weight residual 180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA PRO A 241 " pdb=" C PRO A 241 " pdb=" N ALA A 242 " pdb=" CA ALA A 242 " ideal model delta harmonic sigma weight residual 180.00 -150.81 -29.19 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA PRO A 745 " pdb=" C PRO A 745 " pdb=" N GLY A 746 " pdb=" CA GLY A 746 " ideal model delta harmonic sigma weight residual 180.00 151.92 28.08 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 8658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 2084 0.120 - 0.240: 96 0.240 - 0.360: 3 0.360 - 0.480: 0 0.480 - 0.600: 1 Chirality restraints: 2184 Sorted by residual: chirality pdb=" P DG P 26 " pdb=" OP1 DG P 26 " pdb=" OP2 DG P 26 " pdb=" O5' DG P 26 " both_signs ideal model delta sigma weight residual True 2.35 1.75 0.60 2.00e-01 2.50e+01 8.99e+00 chirality pdb=" CA ILE A 744 " pdb=" N ILE A 744 " pdb=" C ILE A 744 " pdb=" CB ILE A 744 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE A1185 " pdb=" CA ILE A1185 " pdb=" CG1 ILE A1185 " pdb=" CG2 ILE A1185 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2181 not shown) Planarity restraints: 2452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 309 " -0.663 9.50e-02 1.11e+02 2.97e-01 5.38e+01 pdb=" NE ARG A 309 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG A 309 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 309 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 309 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 389 " 0.543 9.50e-02 1.11e+02 2.44e-01 3.62e+01 pdb=" NE ARG B 389 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG B 389 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 389 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 389 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 139 " 0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO B 140 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 140 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 140 " 0.044 5.00e-02 4.00e+02 ... (remaining 2449 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3615 2.81 - 3.33: 12917 3.33 - 3.86: 24734 3.86 - 4.38: 28176 4.38 - 4.90: 45888 Nonbonded interactions: 115330 Sorted by model distance: nonbonded pdb=" OH TYR C 193 " pdb=" O LEU C 322 " model vdw 2.288 2.440 nonbonded pdb=" OG SER B 457 " pdb=" O THR B 460 " model vdw 2.327 2.440 nonbonded pdb=" O PRO B 244 " pdb=" OG SER B 248 " model vdw 2.337 2.440 nonbonded pdb=" O SER A 615 " pdb=" NZ LYS A 751 " model vdw 2.337 2.520 nonbonded pdb=" O GLU A 447 " pdb=" OG1 THR A 451 " model vdw 2.337 2.440 ... (remaining 115325 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 68 through 104 or (resid 105 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD )) or resid 106 through 136 or (r \ esid 137 and (name N or name CA or name C or name O )) or resid 138 through 219 \ or resid 229 through 283 or (resid 284 and (name N or name CA or name C or name \ O or name CB )) or resid 285 through 327 or (resid 328 and (name N or name CA or \ name C or name O or name CB )) or resid 329 through 355 or resid 368 through 48 \ 5)) selection = (chain 'C' and (resid 68 through 161 or (resid 169 through 178 and (name N or na \ me CA or name C or name O or name CB )) or resid 179 through 219 or resid 229 th \ rough 485)) } 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=0.00 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: 1.650 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 41.270 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6145 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 14702 Z= 0.290 Angle : 1.092 31.048 20090 Z= 0.543 Chirality : 0.056 0.600 2184 Planarity : 0.011 0.297 2452 Dihedral : 18.219 174.187 5483 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.62 % Favored : 92.26 % Rotamer: Outliers : 0.69 % Allowed : 8.54 % Favored : 90.77 % 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: -2.94 (0.18), residues: 1680 helix: -1.93 (0.17), residues: 589 sheet: -0.58 (0.34), residues: 220 loop : -2.35 (0.19), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 241 HIS 0.011 0.001 HIS C 454 PHE 0.025 0.002 PHE A 197 TYR 0.033 0.002 TYR A 150 ARG 0.009 0.001 ARG A1187 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 298 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6726 (mm-30) REVERT: A 457 ARG cc_start: 0.6798 (mtm180) cc_final: 0.6571 (ptp-170) REVERT: A 544 MET cc_start: 0.7305 (ppp) cc_final: 0.6993 (ppp) REVERT: A 812 MET cc_start: 0.5800 (ppp) cc_final: 0.5520 (ptm) REVERT: A 907 PHE cc_start: 0.7592 (t80) cc_final: 0.7344 (t80) REVERT: A 970 ASN cc_start: 0.6988 (t0) cc_final: 0.6768 (t0) REVERT: A 1079 ILE cc_start: 0.6772 (tt) cc_final: 0.6343 (tt) REVERT: A 1170 LEU cc_start: 0.6554 (pt) cc_final: 0.6294 (pp) REVERT: B 74 GLN cc_start: 0.7411 (mp10) cc_final: 0.7161 (mp10) REVERT: C 325 ARG cc_start: 0.6100 (tpp-160) cc_final: 0.5768 (tpp-160) REVERT: C 400 GLN cc_start: 0.7551 (tm-30) cc_final: 0.7075 (tm-30) outliers start: 10 outliers final: 2 residues processed: 306 average time/residue: 0.2960 time to fit residues: 129.4961 Evaluate side-chains 198 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 920 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 134 ASN A 264 GLN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN A 409 GLN A 440 ASN A 564 GLN ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 GLN A 894 GLN A 911 HIS A 959 GLN A 968 GLN A 970 ASN A1089 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS B 249 ASN B 272 ASN B 313 HIS B 323 HIS B 400 GLN B 404 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 318 ASN ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 GLN C 454 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 14702 Z= 0.430 Angle : 0.852 25.027 20090 Z= 0.426 Chirality : 0.066 2.193 2184 Planarity : 0.006 0.082 2452 Dihedral : 17.411 173.188 2232 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.57 % Favored : 91.31 % Rotamer: Outliers : 2.91 % Allowed : 15.48 % Favored : 81.61 % 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: -2.11 (0.19), residues: 1680 helix: -0.68 (0.20), residues: 601 sheet: -0.65 (0.34), residues: 225 loop : -2.18 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1118 HIS 0.010 0.002 HIS C 258 PHE 0.035 0.003 PHE B 266 TYR 0.024 0.003 TYR A 434 ARG 0.006 0.001 ARG A 807 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 219 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.6581 (pp30) cc_final: 0.6188 (pp30) REVERT: A 544 MET cc_start: 0.7701 (ppp) cc_final: 0.7462 (ppp) REVERT: A 744 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8192 (mm) REVERT: A 907 PHE cc_start: 0.7760 (t80) cc_final: 0.6940 (t80) REVERT: A 955 TYR cc_start: 0.7495 (m-80) cc_final: 0.7068 (m-80) REVERT: A 964 ARG cc_start: 0.6688 (mpt90) cc_final: 0.6481 (mmt-90) REVERT: A 1093 MET cc_start: 0.5329 (tpt) cc_final: 0.4646 (ptp) REVERT: B 74 GLN cc_start: 0.7889 (mp10) cc_final: 0.7550 (mp10) REVERT: B 256 LEU cc_start: 0.8359 (tt) cc_final: 0.7803 (tt) REVERT: C 256 LEU cc_start: 0.7909 (tt) cc_final: 0.7447 (tp) REVERT: C 325 ARG cc_start: 0.6271 (tpp-160) cc_final: 0.6047 (tpp-160) REVERT: C 400 GLN cc_start: 0.7550 (tm-30) cc_final: 0.7013 (tm-30) outliers start: 42 outliers final: 24 residues processed: 248 average time/residue: 0.2727 time to fit residues: 98.0982 Evaluate side-chains 212 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 187 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 440 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 105 optimal weight: 0.0980 chunk 42 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 168 optimal weight: 0.0270 chunk 138 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 124 optimal weight: 0.5980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 565 HIS A 803 ASN A 959 GLN B 77 HIS ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN C 261 GLN ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14702 Z= 0.177 Angle : 0.713 24.730 20090 Z= 0.344 Chirality : 0.061 2.037 2184 Planarity : 0.004 0.053 2452 Dihedral : 17.324 173.510 2231 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.10 % Favored : 91.79 % Rotamer: Outliers : 2.29 % Allowed : 17.21 % Favored : 80.50 % 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: -1.51 (0.20), residues: 1680 helix: 0.07 (0.22), residues: 599 sheet: -0.40 (0.35), residues: 201 loop : -1.97 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 312 HIS 0.006 0.001 HIS C 258 PHE 0.022 0.001 PHE A 961 TYR 0.021 0.001 TYR A1108 ARG 0.006 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 215 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.6473 (pp30) cc_final: 0.6062 (pp30) REVERT: A 382 MET cc_start: 0.1070 (tpt) cc_final: 0.0860 (tpp) REVERT: A 544 MET cc_start: 0.7523 (ppp) cc_final: 0.7184 (ppp) REVERT: A 559 LEU cc_start: 0.5604 (OUTLIER) cc_final: 0.5320 (mt) REVERT: A 744 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8104 (mm) REVERT: A 812 MET cc_start: 0.6753 (ppp) cc_final: 0.6058 (ptm) REVERT: A 907 PHE cc_start: 0.7723 (t80) cc_final: 0.6925 (t80) REVERT: A 955 TYR cc_start: 0.7404 (m-80) cc_final: 0.7094 (m-80) REVERT: A 1093 MET cc_start: 0.5111 (tpt) cc_final: 0.4584 (ptp) REVERT: B 74 GLN cc_start: 0.7713 (mp10) cc_final: 0.7418 (mp10) REVERT: C 400 GLN cc_start: 0.7459 (tm-30) cc_final: 0.6920 (tm-30) outliers start: 33 outliers final: 20 residues processed: 240 average time/residue: 0.2585 time to fit residues: 92.0629 Evaluate side-chains 219 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 197 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 440 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 0.0170 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 104 optimal weight: 0.0570 chunk 156 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 147 optimal weight: 0.0370 chunk 44 optimal weight: 0.7980 overall best weight: 0.9816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 472 GLN A 959 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS B 368 HIS ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14702 Z= 0.206 Angle : 0.703 24.261 20090 Z= 0.340 Chirality : 0.061 2.044 2184 Planarity : 0.004 0.052 2452 Dihedral : 17.181 173.759 2231 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.45 % Favored : 91.37 % Rotamer: Outliers : 2.64 % Allowed : 18.39 % Favored : 78.97 % 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: -1.36 (0.21), residues: 1680 helix: 0.34 (0.22), residues: 594 sheet: -0.44 (0.36), residues: 201 loop : -1.95 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 312 HIS 0.007 0.001 HIS B 313 PHE 0.015 0.001 PHE A 610 TYR 0.034 0.001 TYR B 432 ARG 0.007 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 205 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6748 (ttm) cc_final: 0.6417 (ttm) REVERT: A 146 GLN cc_start: 0.6549 (pp30) cc_final: 0.6198 (pp30) REVERT: A 345 TRP cc_start: 0.5117 (m-90) cc_final: 0.3369 (t-100) REVERT: A 544 MET cc_start: 0.7549 (ppp) cc_final: 0.7207 (ppp) REVERT: A 559 LEU cc_start: 0.5499 (OUTLIER) cc_final: 0.5160 (mt) REVERT: A 744 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8112 (mm) REVERT: A 812 MET cc_start: 0.6859 (ppp) cc_final: 0.6116 (ptm) REVERT: A 907 PHE cc_start: 0.7786 (t80) cc_final: 0.6951 (t80) REVERT: A 1093 MET cc_start: 0.5056 (tpt) cc_final: 0.4604 (ptp) REVERT: A 1131 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7784 (mm) REVERT: B 74 GLN cc_start: 0.7747 (mp10) cc_final: 0.7488 (mp10) REVERT: C 256 LEU cc_start: 0.7856 (tt) cc_final: 0.7393 (tp) REVERT: C 400 GLN cc_start: 0.7461 (tm-30) cc_final: 0.6901 (tm-30) outliers start: 38 outliers final: 27 residues processed: 231 average time/residue: 0.2696 time to fit residues: 93.7112 Evaluate side-chains 220 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 190 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 440 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 2 optimal weight: 20.0000 chunk 123 optimal weight: 0.7980 chunk 68 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 0 optimal weight: 10.9990 chunk 84 optimal weight: 2.9990 chunk 148 optimal weight: 0.3980 chunk 41 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 HIS ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14702 Z= 0.179 Angle : 0.683 24.242 20090 Z= 0.329 Chirality : 0.060 2.036 2184 Planarity : 0.004 0.050 2452 Dihedral : 17.051 174.302 2231 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.51 % Favored : 91.31 % Rotamer: Outliers : 3.61 % Allowed : 18.04 % Favored : 78.35 % 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 (0.21), residues: 1680 helix: 0.47 (0.22), residues: 601 sheet: -0.28 (0.35), residues: 204 loop : -1.91 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 312 HIS 0.005 0.001 HIS C 258 PHE 0.021 0.001 PHE A 961 TYR 0.018 0.001 TYR B 432 ARG 0.006 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 202 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6803 (ttm) cc_final: 0.6516 (ttm) REVERT: A 146 GLN cc_start: 0.6552 (pp30) cc_final: 0.6230 (pp30) REVERT: A 345 TRP cc_start: 0.5103 (m-90) cc_final: 0.3604 (t-100) REVERT: A 559 LEU cc_start: 0.5393 (OUTLIER) cc_final: 0.5046 (mt) REVERT: A 744 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.8071 (mm) REVERT: A 907 PHE cc_start: 0.7813 (t80) cc_final: 0.6997 (t80) REVERT: A 1057 MET cc_start: 0.6988 (ppp) cc_final: 0.6703 (ppp) REVERT: A 1093 MET cc_start: 0.4877 (tpt) cc_final: 0.4560 (ptp) REVERT: A 1131 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7721 (mm) REVERT: B 74 GLN cc_start: 0.7751 (mp10) cc_final: 0.7545 (mp10) REVERT: C 256 LEU cc_start: 0.7909 (tt) cc_final: 0.7512 (tp) REVERT: C 400 GLN cc_start: 0.7451 (tm-30) cc_final: 0.7224 (tm-30) REVERT: C 479 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6459 (pt) outliers start: 52 outliers final: 28 residues processed: 242 average time/residue: 0.2624 time to fit residues: 94.0385 Evaluate side-chains 221 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 189 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 6.9990 chunk 148 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 0.0040 chunk 40 optimal weight: 0.5980 chunk 165 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14702 Z= 0.181 Angle : 0.690 24.496 20090 Z= 0.331 Chirality : 0.060 2.027 2184 Planarity : 0.004 0.049 2452 Dihedral : 16.990 174.405 2231 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.57 % Favored : 91.25 % Rotamer: Outliers : 3.33 % Allowed : 19.22 % Favored : 77.45 % 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: -1.15 (0.21), residues: 1680 helix: 0.52 (0.22), residues: 601 sheet: -0.25 (0.35), residues: 204 loop : -1.87 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 312 HIS 0.004 0.001 HIS C 258 PHE 0.017 0.001 PHE A 610 TYR 0.018 0.001 TYR B 432 ARG 0.007 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 199 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6801 (ttm) cc_final: 0.6515 (ttm) REVERT: A 146 GLN cc_start: 0.6646 (pp30) cc_final: 0.6312 (pp30) REVERT: A 345 TRP cc_start: 0.5040 (m-90) cc_final: 0.3592 (t-100) REVERT: A 559 LEU cc_start: 0.5346 (OUTLIER) cc_final: 0.4995 (mt) REVERT: A 744 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8094 (mm) REVERT: A 907 PHE cc_start: 0.7820 (t80) cc_final: 0.6987 (t80) REVERT: A 1093 MET cc_start: 0.4778 (tpt) cc_final: 0.4501 (ptp) REVERT: A 1116 MET cc_start: 0.5401 (mtm) cc_final: 0.5184 (mtt) REVERT: A 1131 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7714 (mm) REVERT: C 256 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7597 (tp) REVERT: C 400 GLN cc_start: 0.7512 (tm-30) cc_final: 0.7274 (tm-30) REVERT: C 479 ILE cc_start: 0.6852 (OUTLIER) cc_final: 0.6423 (pt) outliers start: 48 outliers final: 30 residues processed: 232 average time/residue: 0.2375 time to fit residues: 83.3918 Evaluate side-chains 225 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 190 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14702 Z= 0.266 Angle : 0.733 24.964 20090 Z= 0.358 Chirality : 0.061 2.007 2184 Planarity : 0.004 0.048 2452 Dihedral : 17.002 174.663 2231 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.99 % Favored : 90.83 % Rotamer: Outliers : 3.89 % Allowed : 19.29 % Favored : 76.82 % 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: -1.35 (0.21), residues: 1680 helix: 0.35 (0.21), residues: 611 sheet: -0.38 (0.35), residues: 208 loop : -2.02 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 312 HIS 0.013 0.001 HIS C 258 PHE 0.021 0.002 PHE A 961 TYR 0.015 0.002 TYR B 291 ARG 0.009 0.001 ARG A 972 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 194 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 TRP cc_start: 0.5248 (m-90) cc_final: 0.3534 (t-100) REVERT: A 907 PHE cc_start: 0.7900 (t80) cc_final: 0.7058 (t80) REVERT: A 1093 MET cc_start: 0.4636 (tpt) cc_final: 0.4381 (ptp) REVERT: B 427 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6552 (pm20) REVERT: C 256 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7791 (tp) REVERT: C 400 GLN cc_start: 0.7529 (tm-30) cc_final: 0.7306 (tm-30) REVERT: C 479 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6602 (pt) outliers start: 56 outliers final: 36 residues processed: 235 average time/residue: 0.2368 time to fit residues: 85.2081 Evaluate side-chains 221 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 182 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 0.1980 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 GLN ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14702 Z= 0.199 Angle : 0.711 25.107 20090 Z= 0.344 Chirality : 0.060 2.005 2184 Planarity : 0.004 0.048 2452 Dihedral : 16.972 174.889 2231 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.10 % Favored : 91.73 % Rotamer: Outliers : 3.26 % Allowed : 20.19 % Favored : 76.54 % 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: -1.18 (0.21), residues: 1680 helix: 0.60 (0.22), residues: 595 sheet: -0.32 (0.35), residues: 204 loop : -1.95 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 312 HIS 0.011 0.001 HIS C 258 PHE 0.017 0.001 PHE A 750 TYR 0.011 0.001 TYR B 193 ARG 0.008 0.000 ARG A 972 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 197 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 TRP cc_start: 0.5161 (m-90) cc_final: 0.3456 (t-100) REVERT: A 907 PHE cc_start: 0.7904 (t80) cc_final: 0.7084 (t80) REVERT: A 1108 TYR cc_start: 0.6949 (OUTLIER) cc_final: 0.5310 (m-80) REVERT: A 1170 LEU cc_start: 0.6739 (pp) cc_final: 0.6495 (pp) REVERT: C 256 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7780 (tp) REVERT: C 400 GLN cc_start: 0.7499 (tm-30) cc_final: 0.7281 (tm-30) REVERT: C 479 ILE cc_start: 0.6892 (OUTLIER) cc_final: 0.6471 (pt) outliers start: 47 outliers final: 34 residues processed: 230 average time/residue: 0.2388 time to fit residues: 82.9643 Evaluate side-chains 219 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 182 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 420 HIS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1108 TYR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 153 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 HIS B 132 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 14702 Z= 0.458 Angle : 0.856 25.687 20090 Z= 0.425 Chirality : 0.064 1.961 2184 Planarity : 0.006 0.079 2452 Dihedral : 17.082 175.567 2231 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.36 % Favored : 89.46 % Rotamer: Outliers : 3.26 % Allowed : 20.12 % Favored : 76.61 % 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: -1.80 (0.20), residues: 1680 helix: -0.04 (0.21), residues: 606 sheet: -0.65 (0.36), residues: 202 loop : -2.24 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 312 HIS 0.007 0.001 HIS B 454 PHE 0.023 0.002 PHE B 266 TYR 0.020 0.002 TYR B 291 ARG 0.008 0.001 ARG A 972 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 197 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7757 (ppp) cc_final: 0.7447 (ppp) REVERT: A 907 PHE cc_start: 0.8142 (t80) cc_final: 0.7422 (t80) REVERT: A 1108 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.5500 (m-80) REVERT: A 1170 LEU cc_start: 0.6798 (pp) cc_final: 0.6525 (pp) REVERT: C 256 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8072 (tp) REVERT: C 400 GLN cc_start: 0.7549 (tm-30) cc_final: 0.7338 (tm-30) REVERT: C 466 MET cc_start: 0.7514 (ttm) cc_final: 0.7223 (ttm) REVERT: C 479 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.6821 (pt) outliers start: 47 outliers final: 37 residues processed: 229 average time/residue: 0.2622 time to fit residues: 89.2570 Evaluate side-chains 225 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 185 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 420 HIS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1108 TYR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 112 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 HIS A 959 GLN ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14702 Z= 0.202 Angle : 0.758 25.671 20090 Z= 0.368 Chirality : 0.061 1.960 2184 Planarity : 0.004 0.050 2452 Dihedral : 16.942 175.342 2231 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.33 % Favored : 91.49 % Rotamer: Outliers : 2.71 % Allowed : 21.17 % Favored : 76.13 % 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: -1.43 (0.20), residues: 1680 helix: 0.29 (0.22), residues: 603 sheet: -0.47 (0.35), residues: 198 loop : -2.03 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 312 HIS 0.005 0.001 HIS A 906 PHE 0.018 0.002 PHE A 750 TYR 0.012 0.001 TYR B 349 ARG 0.008 0.001 ARG C 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 195 time to evaluate : 1.537 Fit side-chains revert: symmetry clash REVERT: A 275 ARG cc_start: 0.6515 (tmt170) cc_final: 0.6128 (ttt90) REVERT: A 345 TRP cc_start: 0.5219 (m-90) cc_final: 0.3489 (t-100) REVERT: A 907 PHE cc_start: 0.8068 (t80) cc_final: 0.7367 (t80) REVERT: A 1108 TYR cc_start: 0.6860 (OUTLIER) cc_final: 0.5262 (m-80) REVERT: A 1170 LEU cc_start: 0.6725 (pp) cc_final: 0.6480 (pp) REVERT: C 256 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7892 (tp) REVERT: C 400 GLN cc_start: 0.7447 (tm-30) cc_final: 0.7240 (tm-30) REVERT: C 479 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6520 (pt) outliers start: 39 outliers final: 32 residues processed: 221 average time/residue: 0.2520 time to fit residues: 83.6638 Evaluate side-chains 223 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 188 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 420 HIS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 906 HIS Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1108 TYR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 135 optimal weight: 0.0980 chunk 56 optimal weight: 0.5980 chunk 139 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.0170 chunk 119 optimal weight: 0.5980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 GLN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 HIS A 906 HIS B 368 HIS ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.184795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.140014 restraints weight = 36950.664| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 3.67 r_work: 0.3704 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14702 Z= 0.181 Angle : 0.749 25.665 20090 Z= 0.362 Chirality : 0.060 1.946 2184 Planarity : 0.004 0.048 2452 Dihedral : 16.819 174.882 2231 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.51 % Favored : 91.25 % Rotamer: Outliers : 2.50 % Allowed : 21.93 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.21), residues: 1680 helix: 0.49 (0.22), residues: 600 sheet: -0.37 (0.35), residues: 206 loop : -1.89 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP A 312 HIS 0.007 0.001 HIS A 906 PHE 0.022 0.002 PHE A 961 TYR 0.015 0.001 TYR A 986 ARG 0.007 0.000 ARG C 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3406.31 seconds wall clock time: 62 minutes 21.70 seconds (3741.70 seconds total)