Starting phenix.real_space_refine on Fri Jul 19 21:02:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4x_17429/07_2024/8p4x_17429_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4x_17429/07_2024/8p4x_17429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4x_17429/07_2024/8p4x_17429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4x_17429/07_2024/8p4x_17429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4x_17429/07_2024/8p4x_17429_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4x_17429/07_2024/8p4x_17429_neut.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.189 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 78 5.16 5 C 5564 2.51 5 N 1456 2.21 5 O 1652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 118": "OE1" <-> "OE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 497": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8756 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4282 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 39, 'TRANS': 486} Chain: "B" Number of atoms: 4282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4282 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 39, 'TRANS': 486} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' MG': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' MG': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Time building chain proxies: 5.50, per 1000 atoms: 0.63 Number of scatterers: 8756 At special positions: 0 Unit cell: (95.682, 104.302, 95.682, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 4 15.00 Mg 2 11.99 O 1652 8.00 N 1456 7.00 C 5564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.5 seconds 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 2 sheets defined 56.7% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 77 through 99 removed outlier: 3.626A pdb=" N LYS A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 121 removed outlier: 4.228A pdb=" N LYS A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 148 removed outlier: 3.663A pdb=" N ASP A 139 " --> pdb=" O TRP A 135 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 141 " --> pdb=" O PRO A 137 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 171 Processing helix chain 'A' and resid 178 through 190 removed outlier: 3.871A pdb=" N LEU A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.762A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 removed outlier: 3.528A pdb=" N GLY A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.710A pdb=" N GLU A 234 " --> pdb=" O CYS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 265 Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 293 through 309 removed outlier: 3.559A pdb=" N HIS A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.646A pdb=" N LEU A 317 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 318 " --> pdb=" O GLY A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 314 through 318' Processing helix chain 'A' and resid 319 through 331 removed outlier: 3.880A pdb=" N TRP A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET A 330 " --> pdb=" O TYR A 326 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 368 through 381 removed outlier: 3.555A pdb=" N CYS A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 Processing helix chain 'A' and resid 404 through 416 removed outlier: 3.845A pdb=" N GLY A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 432 removed outlier: 4.093A pdb=" N ALA A 425 " --> pdb=" O TRP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 442 removed outlier: 3.909A pdb=" N CYS A 442 " --> pdb=" O CYS A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 456 Processing helix chain 'A' and resid 459 through 466 removed outlier: 3.614A pdb=" N TYR A 465 " --> pdb=" O PHE A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 470 Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.625A pdb=" N ALA A 483 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 492 Processing helix chain 'A' and resid 505 through 524 removed outlier: 3.588A pdb=" N SER A 511 " --> pdb=" O LYS A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 544 removed outlier: 3.536A pdb=" N VAL A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'B' and resid 77 through 99 removed outlier: 3.627A pdb=" N LYS B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 121 removed outlier: 4.228A pdb=" N LYS B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.663A pdb=" N ASP B 139 " --> pdb=" O TRP B 135 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 141 " --> pdb=" O PRO B 137 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 171 Processing helix chain 'B' and resid 178 through 190 removed outlier: 3.871A pdb=" N LEU B 188 " --> pdb=" O GLN B 184 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 removed outlier: 3.763A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 removed outlier: 3.528A pdb=" N GLY B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 3.709A pdb=" N GLU B 234 " --> pdb=" O CYS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 265 Processing helix chain 'B' and resid 283 through 290 Processing helix chain 'B' and resid 293 through 309 removed outlier: 3.559A pdb=" N HIS B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 308 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 removed outlier: 3.646A pdb=" N LEU B 317 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 318 " --> pdb=" O GLY B 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 314 through 318' Processing helix chain 'B' and resid 319 through 331 removed outlier: 3.881A pdb=" N TRP B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG B 324 " --> pdb=" O GLN B 320 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET B 330 " --> pdb=" O TYR B 326 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 368 through 381 removed outlier: 3.556A pdb=" N CYS B 374 " --> pdb=" O TRP B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 397 Processing helix chain 'B' and resid 404 through 416 removed outlier: 3.844A pdb=" N GLY B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 410 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 432 removed outlier: 4.093A pdb=" N ALA B 425 " --> pdb=" O TRP B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 442 removed outlier: 3.909A pdb=" N CYS B 442 " --> pdb=" O CYS B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 456 Processing helix chain 'B' and resid 459 through 466 removed outlier: 3.615A pdb=" N TYR B 465 " --> pdb=" O PHE B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 470 Processing helix chain 'B' and resid 479 through 483 removed outlier: 3.625A pdb=" N ALA B 483 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 492 Processing helix chain 'B' and resid 505 through 524 removed outlier: 3.587A pdb=" N SER B 511 " --> pdb=" O LYS B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 544 removed outlier: 3.537A pdb=" N VAL B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 106 removed outlier: 6.299A pdb=" N VAL A 33 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N THR A 126 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 35 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N GLU A 128 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N TRP A 37 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 106 removed outlier: 6.300A pdb=" N VAL B 33 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N THR B 126 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 35 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N GLU B 128 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N TRP B 37 " --> pdb=" O GLU B 128 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2744 1.34 - 1.46: 2088 1.46 - 1.58: 4014 1.58 - 1.69: 4 1.69 - 1.81: 114 Bond restraints: 8964 Sorted by residual: bond pdb=" O3P FAD A 601 " pdb=" P FAD A 601 " ideal model delta sigma weight residual 1.660 1.585 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" O3P FAD B 601 " pdb=" P FAD B 601 " ideal model delta sigma weight residual 1.660 1.585 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" O5' FAD B 601 " pdb=" P FAD B 601 " ideal model delta sigma weight residual 1.637 1.574 0.063 2.00e-02 2.50e+03 9.95e+00 bond pdb=" O5' FAD A 601 " pdb=" P FAD A 601 " ideal model delta sigma weight residual 1.637 1.574 0.063 2.00e-02 2.50e+03 9.95e+00 bond pdb=" O5B FAD A 601 " pdb=" PA FAD A 601 " ideal model delta sigma weight residual 1.634 1.572 0.062 2.00e-02 2.50e+03 9.49e+00 ... (remaining 8959 not shown) Histogram of bond angle deviations from ideal: 99.08 - 106.08: 325 106.08 - 113.07: 4584 113.07 - 120.06: 3345 120.06 - 127.05: 3726 127.05 - 134.05: 214 Bond angle restraints: 12194 Sorted by residual: angle pdb=" O1P FAD B 601 " pdb=" P FAD B 601 " pdb=" O2P FAD B 601 " ideal model delta sigma weight residual 122.50 115.09 7.41 3.00e+00 1.11e-01 6.10e+00 angle pdb=" O1P FAD A 601 " pdb=" P FAD A 601 " pdb=" O2P FAD A 601 " ideal model delta sigma weight residual 122.50 115.10 7.40 3.00e+00 1.11e-01 6.08e+00 angle pdb=" O1A FAD B 601 " pdb=" PA FAD B 601 " pdb=" O5B FAD B 601 " ideal model delta sigma weight residual 104.10 111.17 -7.07 3.00e+00 1.11e-01 5.55e+00 angle pdb=" O1A FAD A 601 " pdb=" PA FAD A 601 " pdb=" O5B FAD A 601 " ideal model delta sigma weight residual 104.10 111.16 -7.06 3.00e+00 1.11e-01 5.54e+00 angle pdb=" O1A FAD B 601 " pdb=" PA FAD B 601 " pdb=" O2A FAD B 601 " ideal model delta sigma weight residual 121.20 114.74 6.46 3.00e+00 1.11e-01 4.64e+00 ... (remaining 12189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 5002 18.12 - 36.25: 212 36.25 - 54.37: 62 54.37 - 72.50: 30 72.50 - 90.62: 12 Dihedral angle restraints: 5318 sinusoidal: 2270 harmonic: 3048 Sorted by residual: dihedral pdb=" CA ARG B 39 " pdb=" C ARG B 39 " pdb=" N HIS B 40 " pdb=" CA HIS B 40 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ARG A 39 " pdb=" C ARG A 39 " pdb=" N HIS A 40 " pdb=" CA HIS A 40 " ideal model delta harmonic sigma weight residual 180.00 163.28 16.72 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" O5' FAD A 601 " pdb=" O3P FAD A 601 " pdb=" P FAD A 601 " pdb=" PA FAD A 601 " ideal model delta sinusoidal sigma weight residual -61.77 -152.39 90.62 1 3.00e+01 1.11e-03 1.08e+01 ... (remaining 5315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 662 0.025 - 0.049: 346 0.049 - 0.074: 114 0.074 - 0.098: 42 0.098 - 0.123: 56 Chirality restraints: 1220 Sorted by residual: chirality pdb=" CA VAL A 76 " pdb=" N VAL A 76 " pdb=" C VAL A 76 " pdb=" CB VAL A 76 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA VAL B 33 " pdb=" N VAL B 33 " pdb=" C VAL B 33 " pdb=" CB VAL B 33 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" C2B FAD A 601 " pdb=" C1B FAD A 601 " pdb=" C3B FAD A 601 " pdb=" O2B FAD A 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.66 0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 1217 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 526 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO B 527 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 526 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO A 527 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 533 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO A 534 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 534 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 534 " 0.017 5.00e-02 4.00e+02 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 120 2.67 - 3.23: 7683 3.23 - 3.78: 12540 3.78 - 4.34: 18624 4.34 - 4.90: 30825 Nonbonded interactions: 69792 Sorted by model distance: nonbonded pdb=" O HOH B 717 " pdb=" O HOH B 740 " model vdw 2.112 2.440 nonbonded pdb=" O HOH A 717 " pdb=" O HOH A 740 " model vdw 2.114 2.440 nonbonded pdb=" OD2 ASP B 420 " pdb=" O HOH B 701 " model vdw 2.116 2.440 nonbonded pdb=" OD2 ASP A 420 " pdb=" O HOH A 701 " model vdw 2.116 2.440 nonbonded pdb=" NH1 ARG A 324 " pdb=" O HOH A 701 " model vdw 2.125 2.520 ... (remaining 69787 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 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.520 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.004 0.075 8964 Z= 0.273 Angle : 0.561 7.407 12194 Z= 0.284 Chirality : 0.040 0.123 1220 Planarity : 0.004 0.040 1552 Dihedral : 13.116 90.621 3362 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % 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: -0.11 (0.26), residues: 1048 helix: 0.99 (0.24), residues: 528 sheet: 0.00 (0.58), residues: 70 loop : -1.38 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 430 HIS 0.003 0.001 HIS A 45 PHE 0.012 0.001 PHE B 543 TYR 0.012 0.001 TYR B 326 ARG 0.003 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.064 Fit side-chains REVERT: A 115 GLN cc_start: 0.7079 (tt0) cc_final: 0.6857 (tt0) REVERT: A 200 ASP cc_start: 0.7123 (t70) cc_final: 0.6896 (t0) REVERT: B 115 GLN cc_start: 0.7076 (tt0) cc_final: 0.6854 (tt0) REVERT: B 200 ASP cc_start: 0.7121 (t70) cc_final: 0.6893 (t0) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 1.2596 time to fit residues: 194.2701 Evaluate side-chains 127 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 0.0060 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 0.2980 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN B 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8964 Z= 0.183 Angle : 0.575 7.556 12194 Z= 0.287 Chirality : 0.044 0.166 1220 Planarity : 0.005 0.037 1552 Dihedral : 9.688 89.116 1232 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.86 % Allowed : 8.53 % Favored : 90.60 % 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: 0.30 (0.26), residues: 1048 helix: 1.33 (0.24), residues: 530 sheet: 0.24 (0.58), residues: 70 loop : -1.20 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 430 HIS 0.004 0.001 HIS B 45 PHE 0.011 0.001 PHE A 543 TYR 0.008 0.001 TYR B 298 ARG 0.003 0.000 ARG B 515 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 1.036 Fit side-chains REVERT: A 275 ASP cc_start: 0.7897 (t0) cc_final: 0.7655 (t0) REVERT: B 275 ASP cc_start: 0.7881 (t0) cc_final: 0.7650 (t0) outliers start: 8 outliers final: 2 residues processed: 138 average time/residue: 1.3868 time to fit residues: 202.4620 Evaluate side-chains 129 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain B residue 110 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 538 ASN B 32 HIS B 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8964 Z= 0.203 Angle : 0.582 7.987 12194 Z= 0.292 Chirality : 0.044 0.126 1220 Planarity : 0.005 0.043 1552 Dihedral : 9.824 108.040 1232 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.84 % Allowed : 8.53 % Favored : 89.63 % 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: 0.32 (0.26), residues: 1048 helix: 1.24 (0.23), residues: 542 sheet: 0.59 (0.59), residues: 70 loop : -1.18 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 430 HIS 0.004 0.001 HIS A 45 PHE 0.015 0.002 PHE B 543 TYR 0.008 0.001 TYR A 326 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.019 Fit side-chains REVERT: A 118 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7267 (mt-10) REVERT: A 188 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8001 (mp) REVERT: A 249 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7387 (mt-10) REVERT: A 341 GLU cc_start: 0.6157 (OUTLIER) cc_final: 0.5242 (mp0) REVERT: B 118 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7277 (mt-10) REVERT: B 188 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7998 (mp) REVERT: B 249 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7386 (mt-10) REVERT: B 341 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.5247 (mp0) outliers start: 17 outliers final: 4 residues processed: 137 average time/residue: 1.5090 time to fit residues: 218.2281 Evaluate side-chains 136 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 490 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 3.9990 chunk 71 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 538 ASN B 32 HIS B 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8964 Z= 0.157 Angle : 0.529 7.703 12194 Z= 0.261 Chirality : 0.041 0.121 1220 Planarity : 0.005 0.039 1552 Dihedral : 9.079 107.096 1232 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.16 % Allowed : 9.83 % Favored : 88.01 % 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: 0.47 (0.26), residues: 1048 helix: 1.38 (0.23), residues: 542 sheet: 0.69 (0.60), residues: 70 loop : -1.13 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 430 HIS 0.003 0.001 HIS A 45 PHE 0.012 0.001 PHE B 543 TYR 0.008 0.001 TYR A 298 ARG 0.002 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 1.003 Fit side-chains REVERT: A 341 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.5218 (mp0) REVERT: A 512 LYS cc_start: 0.7748 (pttp) cc_final: 0.7399 (mmtm) REVERT: B 341 GLU cc_start: 0.6161 (OUTLIER) cc_final: 0.5246 (mp0) REVERT: B 512 LYS cc_start: 0.7728 (pttp) cc_final: 0.7364 (mmtm) outliers start: 20 outliers final: 9 residues processed: 134 average time/residue: 1.4956 time to fit residues: 211.3507 Evaluate side-chains 133 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8964 Z= 0.312 Angle : 0.693 9.729 12194 Z= 0.350 Chirality : 0.048 0.156 1220 Planarity : 0.006 0.045 1552 Dihedral : 11.092 118.035 1232 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.16 % Allowed : 11.56 % Favored : 86.29 % 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: 0.03 (0.25), residues: 1048 helix: 0.96 (0.22), residues: 542 sheet: 0.65 (0.59), residues: 70 loop : -1.28 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 430 HIS 0.006 0.002 HIS A 385 PHE 0.016 0.002 PHE A 543 TYR 0.012 0.002 TYR B 465 ARG 0.003 0.001 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.006 Fit side-chains REVERT: A 110 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7482 (p0) REVERT: A 118 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7258 (mt-10) REVERT: A 188 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7965 (mp) REVERT: A 341 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.5569 (mp0) REVERT: B 110 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7482 (p0) REVERT: B 118 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: B 188 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7962 (mp) REVERT: B 341 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.5568 (mp0) outliers start: 20 outliers final: 6 residues processed: 138 average time/residue: 1.4929 time to fit residues: 217.1871 Evaluate side-chains 141 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 0.0570 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 538 ASN B 538 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8964 Z= 0.336 Angle : 0.721 9.406 12194 Z= 0.365 Chirality : 0.049 0.156 1220 Planarity : 0.006 0.045 1552 Dihedral : 11.093 118.323 1232 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.48 % Allowed : 12.31 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1048 helix: 0.76 (0.22), residues: 540 sheet: 1.01 (0.61), residues: 66 loop : -1.44 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 430 HIS 0.007 0.002 HIS A 385 PHE 0.017 0.003 PHE B 543 TYR 0.013 0.002 TYR A 465 ARG 0.003 0.001 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 0.999 Fit side-chains REVERT: A 110 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7358 (p0) REVERT: A 118 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: A 341 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.5594 (mp0) REVERT: B 110 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7358 (p0) REVERT: B 118 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: B 341 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.5595 (mp0) outliers start: 23 outliers final: 11 residues processed: 138 average time/residue: 1.4844 time to fit residues: 216.1666 Evaluate side-chains 141 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 73 optimal weight: 0.0470 chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8964 Z= 0.153 Angle : 0.538 7.805 12194 Z= 0.269 Chirality : 0.041 0.148 1220 Planarity : 0.005 0.039 1552 Dihedral : 9.409 110.079 1232 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.94 % Allowed : 13.07 % Favored : 84.99 % 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: 0.27 (0.26), residues: 1048 helix: 1.20 (0.23), residues: 542 sheet: 0.83 (0.61), residues: 70 loop : -1.27 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 430 HIS 0.003 0.001 HIS A 45 PHE 0.012 0.001 PHE A 543 TYR 0.009 0.001 TYR A 326 ARG 0.002 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.063 Fit side-chains REVERT: A 110 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7421 (p0) REVERT: A 118 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7144 (mt-10) REVERT: A 188 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7927 (mp) REVERT: A 222 LYS cc_start: 0.7475 (mptt) cc_final: 0.6893 (mmmt) REVERT: A 341 GLU cc_start: 0.6227 (OUTLIER) cc_final: 0.5231 (mp0) REVERT: B 110 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7425 (p0) REVERT: B 118 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7142 (mt-10) REVERT: B 188 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7924 (mp) REVERT: B 222 LYS cc_start: 0.7502 (mptt) cc_final: 0.6916 (mmmt) REVERT: B 341 GLU cc_start: 0.6226 (OUTLIER) cc_final: 0.5230 (mp0) outliers start: 18 outliers final: 9 residues processed: 123 average time/residue: 1.4594 time to fit residues: 189.6345 Evaluate side-chains 132 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8964 Z= 0.288 Angle : 0.668 8.816 12194 Z= 0.338 Chirality : 0.047 0.162 1220 Planarity : 0.006 0.041 1552 Dihedral : 10.669 117.951 1232 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.27 % Allowed : 12.53 % Favored : 85.21 % 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 (0.25), residues: 1048 helix: 0.99 (0.22), residues: 542 sheet: 1.12 (0.62), residues: 66 loop : -1.39 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 430 HIS 0.005 0.001 HIS A 45 PHE 0.016 0.002 PHE B 543 TYR 0.012 0.002 TYR A 465 ARG 0.002 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 1.036 Fit side-chains REVERT: A 110 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7424 (p0) REVERT: A 118 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7210 (mt-10) REVERT: A 188 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7962 (mp) REVERT: A 341 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.5561 (mp0) REVERT: B 110 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7379 (p0) REVERT: B 118 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7211 (mt-10) REVERT: B 188 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7958 (mp) REVERT: B 341 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5558 (mp0) outliers start: 21 outliers final: 8 residues processed: 130 average time/residue: 1.5172 time to fit residues: 208.5094 Evaluate side-chains 137 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8964 Z= 0.258 Angle : 0.651 8.830 12194 Z= 0.330 Chirality : 0.046 0.192 1220 Planarity : 0.006 0.040 1552 Dihedral : 10.619 117.882 1232 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.16 % Allowed : 12.85 % Favored : 84.99 % 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: 0.01 (0.25), residues: 1048 helix: 0.95 (0.22), residues: 542 sheet: 1.09 (0.62), residues: 66 loop : -1.38 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 430 HIS 0.004 0.001 HIS A 385 PHE 0.015 0.002 PHE B 543 TYR 0.011 0.002 TYR B 326 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 0.974 Fit side-chains REVERT: A 110 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7370 (p0) REVERT: A 188 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7953 (mp) REVERT: A 222 LYS cc_start: 0.7539 (mptt) cc_final: 0.6931 (ptpp) REVERT: A 341 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.5568 (mp0) REVERT: B 110 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7372 (p0) REVERT: B 188 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7950 (mp) REVERT: B 222 LYS cc_start: 0.7537 (mptt) cc_final: 0.6929 (ptpp) REVERT: B 341 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.5566 (mp0) outliers start: 20 outliers final: 11 residues processed: 128 average time/residue: 1.4645 time to fit residues: 198.2407 Evaluate side-chains 137 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8964 Z= 0.174 Angle : 0.569 8.807 12194 Z= 0.284 Chirality : 0.042 0.185 1220 Planarity : 0.005 0.038 1552 Dihedral : 9.550 112.413 1232 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.94 % Allowed : 13.07 % Favored : 84.99 % 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: 0.28 (0.26), residues: 1048 helix: 1.20 (0.23), residues: 542 sheet: 1.16 (0.62), residues: 66 loop : -1.27 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 430 HIS 0.003 0.001 HIS B 36 PHE 0.013 0.001 PHE A 543 TYR 0.009 0.001 TYR B 326 ARG 0.002 0.000 ARG A 281 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.985 Fit side-chains REVERT: A 110 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7360 (p0) REVERT: A 188 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7897 (mp) REVERT: A 222 LYS cc_start: 0.7429 (mptt) cc_final: 0.6886 (ptpp) REVERT: A 341 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.5209 (mp0) REVERT: B 110 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7362 (p0) REVERT: B 188 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7894 (mp) REVERT: B 222 LYS cc_start: 0.7427 (mptt) cc_final: 0.6884 (ptpp) REVERT: B 341 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5192 (mp0) outliers start: 18 outliers final: 9 residues processed: 124 average time/residue: 1.4896 time to fit residues: 194.9981 Evaluate side-chains 133 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.0770 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 10 optimal weight: 0.0170 chunk 15 optimal weight: 2.9990 chunk 72 optimal weight: 0.0980 chunk 4 optimal weight: 0.3980 chunk 59 optimal weight: 3.9990 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 171 ASN A 538 ASN B 171 ASN B 538 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.147698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.123377 restraints weight = 8515.374| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.60 r_work: 0.3270 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8964 Z= 0.125 Angle : 0.483 9.058 12194 Z= 0.238 Chirality : 0.039 0.146 1220 Planarity : 0.004 0.036 1552 Dihedral : 7.739 101.368 1232 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.19 % Allowed : 13.61 % Favored : 85.21 % 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: 0.62 (0.26), residues: 1048 helix: 1.47 (0.23), residues: 544 sheet: 0.70 (0.59), residues: 74 loop : -1.02 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 299 HIS 0.002 0.000 HIS B 36 PHE 0.007 0.001 PHE A 212 TYR 0.007 0.001 TYR A 326 ARG 0.002 0.000 ARG B 281 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3701.60 seconds wall clock time: 65 minutes 3.60 seconds (3903.60 seconds total)