Starting phenix.real_space_refine on Sat Nov 16 21:59:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5o_29751/11_2024/8g5o_29751.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5o_29751/11_2024/8g5o_29751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5o_29751/11_2024/8g5o_29751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5o_29751/11_2024/8g5o_29751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5o_29751/11_2024/8g5o_29751.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5o_29751/11_2024/8g5o_29751.cif" } resolution = 2.61 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= 0.012 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 38 5.49 5 S 47 5.16 5 C 7308 2.51 5 N 2199 2.21 5 O 2360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11952 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 919, 7219 Classifications: {'peptide': 919} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 61, 'TRANS': 857} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 1962 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 353} Link IDs: {'PTRANS': 18, 'TRANS': 378} Chain breaks: 3 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1324 Unresolved non-hydrogen angles: 1700 Unresolved non-hydrogen dihedrals: 1131 Unresolved non-hydrogen chiralities: 115 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 15, 'TYR:plan': 11, 'ASN:plan1': 18, 'TRP:plan': 10, 'ASP:plan': 18, 'PHE:plan': 17, 'GLU:plan': 25, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 723 Chain: "C" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 1974 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 356} Link IDs: {'PTRANS': 18, 'TRANS': 381} Chain breaks: 2 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1331 Unresolved non-hydrogen angles: 1710 Unresolved non-hydrogen dihedrals: 1136 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 15, 'TYR:plan': 11, 'ASN:plan1': 17, 'TRP:plan': 10, 'ASP:plan': 17, 'PHE:plan': 17, 'GLU:plan': 28, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 728 Chain: "R" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 370 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna2p': 12, 'rna3p': 4} Chain: "T" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 427 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Time building chain proxies: 7.93, per 1000 atoms: 0.66 Number of scatterers: 11952 At special positions: 0 Unit cell: (104.851, 101.549, 140.352, 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 47 16.00 P 38 15.00 O 2360 8.00 N 2199 7.00 C 7308 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 - 3.00 Amino acid : True - 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: 3.43 Conformation dependent library (CDL) restraints added in 1.8 seconds 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3194 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 11 sheets defined 38.2% alpha, 12.1% beta 16 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.854A pdb=" N LYS A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.687A pdb=" N ASP A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 305 through 315 removed outlier: 3.660A pdb=" N SER A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 381 through 388 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: 3.938A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 470 Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 541 through 551 removed outlier: 3.654A pdb=" N LEU A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 removed outlier: 3.543A pdb=" N LEU A 559 " --> pdb=" O THR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 771 through 775 removed outlier: 3.708A pdb=" N GLU A 775 " --> pdb=" O PRO A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 809 removed outlier: 3.772A pdb=" N LEU A 792 " --> pdb=" O GLY A 788 " (cutoff:3.500A) WARNING: missing atoms! removed outlier: 5.187A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 916 through 923 Processing helix chain 'A' and resid 945 through 955 removed outlier: 3.811A pdb=" N ARG A 953 " --> pdb=" O PHE A 949 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR A 955 " --> pdb=" O TYR A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 982 through 988 Processing helix chain 'A' and resid 1058 through 1066 Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.750A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1167 Processing helix chain 'A' and resid 1202 through 1206 Processing helix chain 'A' and resid 1216 through 1221 removed outlier: 3.630A pdb=" N TYR A1221 " --> pdb=" O LEU A1218 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 185 through 200 removed outlier: 4.360A pdb=" N VAL B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 265 Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.559A pdb=" N PHE B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 409 removed outlier: 3.695A pdb=" N VAL B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 removed outlier: 4.027A pdb=" N LEU B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 removed outlier: 4.310A pdb=" N LEU B 448 " --> pdb=" O GLU B 445 " (cutoff:3.500A) 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: 3.932A 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 200 removed outlier: 4.705A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ASN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 266 removed outlier: 4.521A pdb=" N ASN C 249 " --> pdb=" O PRO C 245 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLN C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' 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 Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 444 through 451 Processing helix chain 'C' and resid 468 through 484 removed outlier: 4.014A pdb=" N LYS C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.714A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA A 200 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA A 212 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA A 198 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA A 214 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL A 196 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 6.459A 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: 3.504A pdb=" N VAL A 814 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1127 through 1133 removed outlier: 6.785A pdb=" N GLY A1127 " --> pdb=" O ARG A1142 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ARG A1142 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N PHE A1129 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A1140 " --> pdb=" O PHE A1129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.868A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 289 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR B 302 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN B 287 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TRP B 304 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LYS B 285 " --> pdb=" O TRP B 304 " (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 325 Processing sheet with id=AA7, first strand: chain 'B' and resid 413 through 415 removed outlier: 6.986A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 133 through 134 removed outlier: 3.704A pdb=" N LYS C 134 " --> pdb=" O LYS C 180 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS C 180 " --> pdb=" O LYS C 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 207 through 218 removed outlier: 6.633A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB2, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.981A pdb=" N TRP C 414 " --> pdb=" O ILE C 381 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYS C 382 " --> pdb=" O PHE C 439 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL C 441 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET C 462 " --> pdb=" O SER C 457 " (cutoff:3.500A) 547 hydrogen bonds defined for protein. 1572 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 4.26 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2347 1.33 - 1.45: 3034 1.45 - 1.57: 6698 1.57 - 1.69: 77 1.69 - 1.81: 77 Bond restraints: 12233 Sorted by residual: bond pdb=" CG PRO A1203 " pdb=" CD PRO A1203 " ideal model delta sigma weight residual 1.503 1.267 0.236 3.40e-02 8.65e+02 4.81e+01 bond pdb=" N THR A 586 " pdb=" CA THR A 586 " ideal model delta sigma weight residual 1.458 1.488 -0.030 7.40e-03 1.83e+04 1.66e+01 bond pdb=" N THR A1199 " pdb=" CA THR A1199 " ideal model delta sigma weight residual 1.462 1.491 -0.028 7.70e-03 1.69e+04 1.36e+01 bond pdb=" CG PRO A 867 " pdb=" CD PRO A 867 " ideal model delta sigma weight residual 1.503 1.396 0.107 3.40e-02 8.65e+02 9.87e+00 bond pdb=" N LEU A 771 " pdb=" CA LEU A 771 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.11e+00 ... (remaining 12228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 16763 3.81 - 7.62: 140 7.62 - 11.42: 7 11.42 - 15.23: 1 15.23 - 19.04: 2 Bond angle restraints: 16913 Sorted by residual: angle pdb=" N PRO A1203 " pdb=" CD PRO A1203 " pdb=" CG PRO A1203 " ideal model delta sigma weight residual 103.20 85.11 18.09 1.50e+00 4.44e-01 1.45e+02 angle pdb=" CA PRO A1203 " pdb=" CB PRO A1203 " pdb=" CG PRO A1203 " ideal model delta sigma weight residual 104.50 85.46 19.04 1.90e+00 2.77e-01 1.00e+02 angle pdb=" CA PRO A 867 " pdb=" N PRO A 867 " pdb=" CD PRO A 867 " ideal model delta sigma weight residual 112.00 98.43 13.57 1.40e+00 5.10e-01 9.40e+01 angle pdb=" N PRO A 625 " pdb=" CA PRO A 625 " pdb=" CB PRO A 625 " ideal model delta sigma weight residual 103.33 110.43 -7.10 9.30e-01 1.16e+00 5.83e+01 angle pdb=" N PRO A 340 " pdb=" CA PRO A 340 " pdb=" CB PRO A 340 " ideal model delta sigma weight residual 103.00 110.46 -7.46 1.10e+00 8.26e-01 4.60e+01 ... (remaining 16908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.47: 6924 32.47 - 64.94: 267 64.94 - 97.41: 22 97.41 - 129.87: 0 129.87 - 162.34: 1 Dihedral angle restraints: 7214 sinusoidal: 2288 harmonic: 4926 Sorted by residual: dihedral pdb=" CD ARG A 927 " pdb=" NE ARG A 927 " pdb=" CZ ARG A 927 " pdb=" NH1 ARG A 927 " ideal model delta sinusoidal sigma weight residual 0.00 -82.49 82.49 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CD ARG A 140 " pdb=" NE ARG A 140 " pdb=" CZ ARG A 140 " pdb=" NH1 ARG A 140 " ideal model delta sinusoidal sigma weight residual 0.00 -42.47 42.47 1 1.00e+01 1.00e-02 2.52e+01 dihedral pdb=" CA ASN A 438 " pdb=" C ASN A 438 " pdb=" N GLN A 439 " pdb=" CA GLN A 439 " ideal model delta harmonic sigma weight residual 180.00 155.73 24.27 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 7211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1517 0.043 - 0.086: 310 0.086 - 0.129: 147 0.129 - 0.172: 12 0.172 - 0.215: 5 Chirality restraints: 1991 Sorted by residual: chirality pdb=" CA PRO A 340 " pdb=" N PRO A 340 " pdb=" C PRO A 340 " pdb=" CB PRO A 340 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA PRO A 625 " pdb=" N PRO A 625 " pdb=" C PRO A 625 " pdb=" CB PRO A 625 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE B 156 " pdb=" N ILE B 156 " pdb=" C ILE B 156 " pdb=" CB ILE B 156 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.40e-01 ... (remaining 1988 not shown) Planarity restraints: 2137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 927 " -1.091 9.50e-02 1.11e+02 4.89e-01 1.44e+02 pdb=" NE ARG A 927 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 927 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 927 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 927 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 140 " -0.721 9.50e-02 1.11e+02 3.23e-01 6.36e+01 pdb=" NE ARG A 140 " 0.044 2.00e-02 2.50e+03 pdb=" CZ ARG A 140 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 140 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 140 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 866 " 0.087 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO A 867 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO A 867 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 867 " 0.065 5.00e-02 4.00e+02 ... (remaining 2134 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 117 2.58 - 3.16: 10164 3.16 - 3.74: 18634 3.74 - 4.32: 22907 4.32 - 4.90: 38160 Nonbonded interactions: 89982 Sorted by model distance: nonbonded pdb=" OG1 THR A 989 " pdb=" OE1 GLU A1056 " model vdw 2.003 3.040 nonbonded pdb=" O HIS A 805 " pdb=" OG SER A 809 " model vdw 2.018 3.040 nonbonded pdb=" OD1 ASP A 904 " pdb=" N ALA A 905 " model vdw 2.042 3.120 nonbonded pdb=" OG SER A 237 " pdb=" OG SER A 240 " model vdw 2.063 3.040 nonbonded pdb=" OG1 THR A 885 " pdb=" O ASP A1186 " model vdw 2.067 3.040 ... (remaining 89977 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 68 through 139 or (resid 140 and (name N or name CA or nam \ e C or name O or name CB )) or resid 141 through 219 or resid 229 through 355 or \ resid 368 through 485)) selection = (chain 'C' and (resid 68 through 160 or resid 169 through 219 or resid 229 throu \ gh 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=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: 0.010 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.380 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5137 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 0.236 12233 Z= 0.351 Angle : 0.839 19.038 16913 Z= 0.499 Chirality : 0.044 0.215 1991 Planarity : 0.014 0.489 2137 Dihedral : 16.529 162.343 4020 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.72 % Allowed : 22.06 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1690 helix: 1.96 (0.23), residues: 655 sheet: 0.96 (0.37), residues: 217 loop : -1.66 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 486 HIS 0.006 0.001 HIS A 277 PHE 0.012 0.001 PHE A 770 TYR 0.011 0.001 TYR A 831 ARG 0.008 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 1.194 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG A 790 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 133 average time/residue: 1.2132 time to fit residues: 176.9966 Evaluate side-chains 104 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 1203 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 40.0000 chunk 131 optimal weight: 50.0000 chunk 72 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 135 optimal weight: 30.0000 chunk 52 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 100 optimal weight: 20.0000 chunk 157 optimal weight: 50.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 GLN A 565 HIS ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 HIS A 803 ASN ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS A 976 GLN A1175 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5300 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12233 Z= 0.392 Angle : 0.701 7.887 16913 Z= 0.372 Chirality : 0.045 0.206 1991 Planarity : 0.006 0.093 2137 Dihedral : 15.326 166.727 2305 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 7.40 % Allowed : 19.29 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1690 helix: 1.53 (0.21), residues: 653 sheet: 1.22 (0.37), residues: 203 loop : -1.79 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 484 HIS 0.007 0.002 HIS A 138 PHE 0.024 0.002 PHE A 197 TYR 0.023 0.002 TYR A1108 ARG 0.010 0.001 ARG A 927 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 104 time to evaluate : 1.360 Fit side-chains TARDY: cannot create tardy model for: "ARG A 790 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 78 MET cc_start: 0.8285 (mtt) cc_final: 0.8013 (mtt) REVERT: A 146 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7206 (mt0) REVERT: A 447 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: A 612 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6007 (tm) REVERT: A 779 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6935 (tm) REVERT: A 1198 LYS cc_start: 0.6075 (OUTLIER) cc_final: 0.5785 (tmtt) outliers start: 56 outliers final: 24 residues processed: 145 average time/residue: 0.9406 time to fit residues: 152.5208 Evaluate side-chains 128 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1197 CYS Chi-restraints excluded: chain A residue 1198 LYS Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1212 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 106 optimal weight: 50.0000 chunk 43 optimal weight: 0.3980 chunk 157 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 chunk 140 optimal weight: 50.0000 chunk 156 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 126 optimal weight: 40.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5189 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12233 Z= 0.185 Angle : 0.581 9.184 16913 Z= 0.304 Chirality : 0.042 0.158 1991 Planarity : 0.004 0.073 2137 Dihedral : 15.084 160.918 2300 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 5.15 % Allowed : 21.80 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1690 helix: 1.68 (0.21), residues: 672 sheet: 1.14 (0.37), residues: 201 loop : -1.80 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 486 HIS 0.003 0.001 HIS A 84 PHE 0.010 0.001 PHE A 916 TYR 0.023 0.002 TYR A 178 ARG 0.006 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 1.231 Fit side-chains TARDY: cannot create tardy model for: "ARG A 790 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7101 (mt0) REVERT: A 295 MET cc_start: 0.7768 (mtt) cc_final: 0.7391 (mtp) REVERT: A 355 SER cc_start: 0.8234 (m) cc_final: 0.7863 (p) REVERT: A 447 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7934 (mp0) REVERT: A 594 LEU cc_start: 0.6144 (OUTLIER) cc_final: 0.5852 (mt) REVERT: A 612 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.5908 (tm) REVERT: A 1053 THR cc_start: 0.7425 (OUTLIER) cc_final: 0.6104 (m) REVERT: A 1054 GLU cc_start: 0.7006 (tp30) cc_final: 0.6615 (mp0) outliers start: 39 outliers final: 13 residues processed: 131 average time/residue: 0.9621 time to fit residues: 140.9956 Evaluate side-chains 112 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1212 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 chunk 81 optimal weight: 0.9990 chunk 17 optimal weight: 0.0370 chunk 75 optimal weight: 0.9990 chunk 105 optimal weight: 50.0000 chunk 157 optimal weight: 20.0000 chunk 167 optimal weight: 40.0000 chunk 82 optimal weight: 1.9990 chunk 149 optimal weight: 50.0000 chunk 45 optimal weight: 0.2980 overall best weight: 0.8664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 110 HIS A 803 ASN A 932 HIS A 950 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5185 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12233 Z= 0.180 Angle : 0.558 7.724 16913 Z= 0.292 Chirality : 0.041 0.158 1991 Planarity : 0.004 0.067 2137 Dihedral : 15.057 162.109 2300 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.55 % Allowed : 21.27 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.21), residues: 1690 helix: 1.66 (0.21), residues: 680 sheet: 1.09 (0.37), residues: 208 loop : -1.79 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 486 HIS 0.003 0.001 HIS A 805 PHE 0.010 0.001 PHE A 197 TYR 0.018 0.001 TYR A 178 ARG 0.009 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 99 time to evaluate : 1.306 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG A 790 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7099 (mt0) REVERT: A 295 MET cc_start: 0.7763 (mtt) cc_final: 0.7415 (mtp) REVERT: A 355 SER cc_start: 0.8247 (m) cc_final: 0.7873 (p) REVERT: A 447 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: A 457 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7750 (ptp90) REVERT: A 594 LEU cc_start: 0.6211 (OUTLIER) cc_final: 0.5940 (mp) REVERT: A 612 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.5941 (tm) REVERT: A 894 GLN cc_start: 0.7500 (tp40) cc_final: 0.7185 (tp40) REVERT: A 968 GLN cc_start: 0.7811 (mt0) cc_final: 0.7497 (mt0) REVERT: A 1053 THR cc_start: 0.7389 (OUTLIER) cc_final: 0.6998 (m) REVERT: A 1068 ASP cc_start: 0.5650 (OUTLIER) cc_final: 0.5432 (p0) outliers start: 42 outliers final: 18 residues processed: 129 average time/residue: 0.9435 time to fit residues: 137.5309 Evaluate side-chains 120 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1212 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 50.0000 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 124 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 115 optimal weight: 40.0000 chunk 0 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 150 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5303 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12233 Z= 0.346 Angle : 0.639 8.516 16913 Z= 0.336 Chirality : 0.044 0.185 1991 Planarity : 0.005 0.081 2137 Dihedral : 15.184 163.023 2300 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 6.87 % Allowed : 21.53 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1690 helix: 1.51 (0.21), residues: 672 sheet: 1.34 (0.38), residues: 195 loop : -1.94 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 486 HIS 0.006 0.002 HIS A 138 PHE 0.018 0.002 PHE A 197 TYR 0.016 0.002 TYR A 282 ARG 0.007 0.001 ARG A1071 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 106 time to evaluate : 1.323 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG A 790 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7246 (mt0) REVERT: A 355 SER cc_start: 0.8423 (OUTLIER) cc_final: 0.8015 (p) REVERT: A 439 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7502 (pt0) REVERT: A 447 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: A 612 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.5982 (tm) REVERT: A 1054 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: A 1068 ASP cc_start: 0.6084 (OUTLIER) cc_final: 0.5584 (p0) REVERT: A 1198 LYS cc_start: 0.5859 (OUTLIER) cc_final: 0.5626 (tmtt) outliers start: 52 outliers final: 24 residues processed: 141 average time/residue: 0.9895 time to fit residues: 155.4413 Evaluate side-chains 132 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1198 LYS Chi-restraints excluded: chain A residue 1212 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 0.7980 chunk 150 optimal weight: 40.0000 chunk 33 optimal weight: 4.9990 chunk 98 optimal weight: 0.0970 chunk 41 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 chunk 138 optimal weight: 40.0000 chunk 77 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 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 110 HIS ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5188 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12233 Z= 0.166 Angle : 0.567 9.542 16913 Z= 0.296 Chirality : 0.042 0.157 1991 Planarity : 0.004 0.062 2137 Dihedral : 15.030 159.903 2300 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.94 % Allowed : 22.72 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.21), residues: 1690 helix: 1.70 (0.21), residues: 678 sheet: 1.07 (0.37), residues: 208 loop : -1.83 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 486 HIS 0.003 0.001 HIS A 613 PHE 0.009 0.001 PHE A 916 TYR 0.023 0.001 TYR A 178 ARG 0.004 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 104 time to evaluate : 1.271 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG A 790 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7087 (mt0) REVERT: A 295 MET cc_start: 0.7823 (mtp) cc_final: 0.7511 (mtp) REVERT: A 355 SER cc_start: 0.8057 (m) cc_final: 0.7685 (p) REVERT: A 447 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7956 (mp0) REVERT: A 457 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7778 (ptp90) REVERT: A 594 LEU cc_start: 0.6170 (OUTLIER) cc_final: 0.5865 (mp) REVERT: A 1054 GLU cc_start: 0.7046 (tp30) cc_final: 0.6656 (mp0) outliers start: 45 outliers final: 20 residues processed: 138 average time/residue: 0.9413 time to fit residues: 145.4021 Evaluate side-chains 126 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1212 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 122 optimal weight: 30.0000 chunk 94 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 93 optimal weight: 30.0000 chunk 166 optimal weight: 50.0000 chunk 104 optimal weight: 40.0000 chunk 101 optimal weight: 6.9990 chunk 76 optimal weight: 0.4980 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 968 GLN ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5377 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 12233 Z= 0.498 Angle : 0.761 10.332 16913 Z= 0.401 Chirality : 0.048 0.288 1991 Planarity : 0.006 0.090 2137 Dihedral : 15.293 163.485 2300 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 7.00 % Allowed : 22.46 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1690 helix: 1.32 (0.21), residues: 663 sheet: 1.27 (0.38), residues: 195 loop : -2.07 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 748 HIS 0.007 0.002 HIS A 138 PHE 0.025 0.002 PHE A 88 TYR 0.030 0.003 TYR A 178 ARG 0.012 0.001 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 100 time to evaluate : 1.340 Fit side-chains TARDY: cannot create tardy model for: "ARG A 790 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7365 (mt0) REVERT: A 295 MET cc_start: 0.7938 (mtp) cc_final: 0.7609 (mtp) REVERT: A 355 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.8093 (p) REVERT: A 447 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: A 457 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7968 (ptp90) REVERT: A 612 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.5913 (tm) REVERT: A 910 MET cc_start: 0.6605 (mtm) cc_final: 0.5523 (mmm) REVERT: A 1054 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6796 (mp0) outliers start: 53 outliers final: 28 residues processed: 134 average time/residue: 0.9255 time to fit residues: 139.2475 Evaluate side-chains 128 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1197 CYS Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1212 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 50.0000 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 40.0000 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 106 optimal weight: 50.0000 chunk 113 optimal weight: 50.0000 chunk 82 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 131 optimal weight: 50.0000 chunk 151 optimal weight: 50.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5284 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 12233 Z= 0.259 Angle : 0.641 10.663 16913 Z= 0.336 Chirality : 0.043 0.164 1991 Planarity : 0.005 0.073 2137 Dihedral : 15.156 159.896 2300 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 5.55 % Allowed : 25.23 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1690 helix: 1.46 (0.21), residues: 673 sheet: 1.22 (0.38), residues: 195 loop : -2.01 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 486 HIS 0.003 0.001 HIS A 828 PHE 0.013 0.001 PHE A 949 TYR 0.034 0.002 TYR A 178 ARG 0.013 0.001 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 1.290 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG A 790 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7191 (mt0) REVERT: A 355 SER cc_start: 0.8285 (m) cc_final: 0.7924 (p) REVERT: A 447 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: A 457 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7904 (ptp90) REVERT: A 612 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.5849 (tm) REVERT: A 774 MET cc_start: 0.5724 (ttm) cc_final: 0.5487 (ttm) REVERT: A 968 GLN cc_start: 0.7884 (mt0) cc_final: 0.7493 (mp10) REVERT: A 1054 GLU cc_start: 0.7168 (tp30) cc_final: 0.6825 (mp0) outliers start: 42 outliers final: 25 residues processed: 137 average time/residue: 0.8626 time to fit residues: 133.2347 Evaluate side-chains 127 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1212 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 40.0000 chunk 145 optimal weight: 6.9990 chunk 155 optimal weight: 40.0000 chunk 93 optimal weight: 40.0000 chunk 67 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 146 optimal weight: 20.0000 chunk 154 optimal weight: 40.0000 chunk 102 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5482 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.186 12233 Z= 0.742 Angle : 0.958 14.438 16913 Z= 0.507 Chirality : 0.055 0.264 1991 Planarity : 0.008 0.107 2137 Dihedral : 15.619 163.205 2300 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 6.61 % Allowed : 25.63 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 (0.20), residues: 1690 helix: 0.54 (0.21), residues: 666 sheet: 0.59 (0.36), residues: 217 loop : -2.43 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP A 484 HIS 0.011 0.003 HIS A 106 PHE 0.032 0.004 PHE A 88 TYR 0.047 0.004 TYR A 178 ARG 0.014 0.002 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 99 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7415 (mt0) REVERT: A 447 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: A 457 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8089 (ptp90) REVERT: A 612 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.5862 (tm) REVERT: A 750 PHE cc_start: 0.2610 (OUTLIER) cc_final: 0.1883 (t80) REVERT: A 774 MET cc_start: 0.5898 (ttm) cc_final: 0.5633 (ttm) REVERT: A 910 MET cc_start: 0.6468 (mpp) cc_final: 0.5985 (mmm) REVERT: A 968 GLN cc_start: 0.7834 (mt0) cc_final: 0.7507 (mp10) REVERT: A 1054 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7087 (mp0) outliers start: 50 outliers final: 27 residues processed: 135 average time/residue: 0.9856 time to fit residues: 149.1877 Evaluate side-chains 128 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1212 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 30.0000 chunk 100 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 114 optimal weight: 40.0000 chunk 172 optimal weight: 10.0000 chunk 158 optimal weight: 0.0770 chunk 137 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 106 optimal weight: 50.0000 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS A1214 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5297 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 12233 Z= 0.238 Angle : 0.696 12.334 16913 Z= 0.363 Chirality : 0.044 0.189 1991 Planarity : 0.005 0.080 2137 Dihedral : 15.285 158.178 2300 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.62 % Allowed : 28.80 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.21), residues: 1690 helix: 1.17 (0.21), residues: 682 sheet: 0.67 (0.36), residues: 217 loop : -2.17 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP A 490 HIS 0.004 0.001 HIS A 828 PHE 0.011 0.001 PHE A 949 TYR 0.027 0.002 TYR A 178 ARG 0.011 0.001 ARG A1071 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 103 time to evaluate : 1.323 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG A 790 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7219 (mt0) REVERT: A 447 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: A 612 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.5640 (tm) REVERT: A 750 PHE cc_start: 0.2462 (OUTLIER) cc_final: 0.1714 (t80) REVERT: A 774 MET cc_start: 0.5619 (ttm) cc_final: 0.5391 (ttm) REVERT: A 910 MET cc_start: 0.6154 (mpp) cc_final: 0.5529 (mmm) REVERT: A 968 GLN cc_start: 0.7834 (mt0) cc_final: 0.7465 (mp10) REVERT: A 1054 GLU cc_start: 0.7189 (tp30) cc_final: 0.6867 (mp0) REVERT: A 1196 ASP cc_start: 0.6773 (m-30) cc_final: 0.6312 (p0) outliers start: 35 outliers final: 24 residues processed: 130 average time/residue: 0.9172 time to fit residues: 134.0413 Evaluate side-chains 124 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1212 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 50.0000 chunk 42 optimal weight: 0.7980 chunk 126 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 137 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 141 optimal weight: 50.0000 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.195444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.139419 restraints weight = 23021.335| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 3.87 r_work: 0.3894 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 12233 Z= 0.260 Angle : 0.673 12.318 16913 Z= 0.350 Chirality : 0.043 0.178 1991 Planarity : 0.005 0.073 2137 Dihedral : 15.254 160.641 2300 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 4.36 % Allowed : 28.93 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.21), residues: 1690 helix: 1.34 (0.21), residues: 677 sheet: 0.94 (0.38), residues: 197 loop : -2.09 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 486 HIS 0.004 0.001 HIS A 828 PHE 0.012 0.001 PHE A 88 TYR 0.027 0.002 TYR A 178 ARG 0.011 0.001 ARG A 101 Origin is already at (0, 0, 0), no shifts will be applied Sorry: Reduce crashed with command 'molprobity.reduce -oh -his -flip -keep -allalt -limit120 -pen9999 -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: Processing file: --standard input--