Starting phenix.real_space_refine on Wed Feb 14 08:10:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phe_17659/02_2024/8phe_17659.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phe_17659/02_2024/8phe_17659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phe_17659/02_2024/8phe_17659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phe_17659/02_2024/8phe_17659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phe_17659/02_2024/8phe_17659.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phe_17659/02_2024/8phe_17659.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.119 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 5656 2.51 5 N 1498 2.21 5 O 1714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 58": "OE1" <-> "OE2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8914 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4304 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 15, 'TRANS': 535} Chain breaks: 1 Chain: "B" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4304 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 15, 'TRANS': 535} Chain breaks: 1 Chain: "C" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 134 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 2, 'TRANS': 12} Chain: "D" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 134 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 2, 'TRANS': 12} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Time building chain proxies: 5.15, per 1000 atoms: 0.58 Number of scatterers: 8914 At special positions: 0 Unit cell: (91.797, 121.569, 76.084, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1714 8.00 N 1498 7.00 C 5656 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: 3.20 Conformation dependent library (CDL) restraints added in 1.6 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 5 sheets defined 62.6% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 39 through 44 removed outlier: 3.537A pdb=" N PHE A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 71 Processing helix chain 'A' and resid 74 through 81 Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 121 through 133 removed outlier: 3.526A pdb=" N SER A 126 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 147 removed outlier: 3.719A pdb=" N THR A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 143 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.654A pdb=" N LYS A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Proline residue: A 167 - end of helix removed outlier: 3.508A pdb=" N SER A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 292 through 303 removed outlier: 3.820A pdb=" N GLY A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 328 removed outlier: 3.785A pdb=" N ARG A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 338 Processing helix chain 'A' and resid 339 through 368 removed outlier: 3.994A pdb=" N LYS A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 401 removed outlier: 3.976A pdb=" N ALA A 379 " --> pdb=" O CYS A 375 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 405 Processing helix chain 'A' and resid 412 through 419 Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'A' and resid 428 through 453 removed outlier: 3.711A pdb=" N MET A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 493 No H-bonds generated for 'chain 'A' and resid 491 through 493' Processing helix chain 'A' and resid 494 through 520 removed outlier: 3.748A pdb=" N ALA A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS A 500 " --> pdb=" O ASP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 526 through 557 removed outlier: 3.584A pdb=" N LEU A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 585 removed outlier: 3.918A pdb=" N GLU A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 609 removed outlier: 3.832A pdb=" N LYS A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 60 through 81 Proline residue: B 73 - end of helix Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 106 through 109 removed outlier: 4.167A pdb=" N LEU B 109 " --> pdb=" O LEU B 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 106 through 109' Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 121 through 133 removed outlier: 3.589A pdb=" N LEU B 128 " --> pdb=" O MET B 124 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 147 removed outlier: 3.570A pdb=" N THR B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 143 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 158 through 171 removed outlier: 3.510A pdb=" N ALA B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 164 " --> pdb=" O GLU B 160 " (cutoff:3.500A) Proline residue: B 167 - end of helix removed outlier: 3.502A pdb=" N SER B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 291 through 302 removed outlier: 4.274A pdb=" N VAL B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 327 removed outlier: 4.009A pdb=" N GLY B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER B 309 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 323 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 368 removed outlier: 4.010A pdb=" N LYS B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 401 removed outlier: 3.646A pdb=" N LEU B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 405 Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'B' and resid 420 through 424 Processing helix chain 'B' and resid 428 through 453 removed outlier: 3.867A pdb=" N MET B 434 " --> pdb=" O GLU B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 493 No H-bonds generated for 'chain 'B' and resid 491 through 493' Processing helix chain 'B' and resid 494 through 519 removed outlier: 3.730A pdb=" N ALA B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS B 500 " --> pdb=" O ASP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.854A pdb=" N MET B 524 " --> pdb=" O LYS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 557 removed outlier: 3.567A pdb=" N ARG B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU B 547 " --> pdb=" O MET B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.820A pdb=" N GLU B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 574 " --> pdb=" O THR B 570 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 585 " --> pdb=" O PHE B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 609 Processing helix chain 'C' and resid 321 through 327 Processing helix chain 'D' and resid 323 through 327 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 179 removed outlier: 6.952A pdb=" N ALA A 177 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N PHE A 226 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N CYS A 179 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N LYS A 228 " --> pdb=" O CYS A 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 198 removed outlier: 6.415A pdb=" N TYR A 205 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS A 279 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU A 207 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP A 213 " --> pdb=" O CYS A 271 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N CYS A 271 " --> pdb=" O TRP A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 176 through 179 removed outlier: 7.038A pdb=" N ALA B 177 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N PHE B 226 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N CYS B 179 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N LYS B 228 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU B 230 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 198 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TYR B 205 " --> pdb=" O LYS B 279 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS B 279 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU B 207 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP B 213 " --> pdb=" O CYS B 271 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N CYS B 271 " --> pdb=" O TRP B 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 176 through 179 removed outlier: 7.038A pdb=" N ALA B 177 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N PHE B 226 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N CYS B 179 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N LYS B 228 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ALA B 244 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 330 through 331 493 hydrogen bonds defined for protein. 1401 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: 2.57 Time building geometry restraints manager: 3.52 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: 2917 1.34 - 1.46: 1777 1.46 - 1.58: 4262 1.58 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 9030 Sorted by residual: bond pdb=" C GLU B 182 " pdb=" N PRO B 183 " ideal model delta sigma weight residual 1.333 1.345 -0.012 1.17e-02 7.31e+03 1.14e+00 bond pdb=" CA GLY B 287 " pdb=" C GLY B 287 " ideal model delta sigma weight residual 1.514 1.529 -0.015 1.41e-02 5.03e+03 1.13e+00 bond pdb=" N ILE B 265 " pdb=" CA ILE B 265 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.11e+00 bond pdb=" N GLY B 287 " pdb=" CA GLY B 287 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.02e+00 bond pdb=" CB MET A 381 " pdb=" CG MET A 381 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.40e-01 ... (remaining 9025 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.47: 130 105.47 - 112.61: 4696 112.61 - 119.75: 3088 119.75 - 126.89: 4190 126.89 - 134.03: 70 Bond angle restraints: 12174 Sorted by residual: angle pdb=" N ILE B 265 " pdb=" CA ILE B 265 " pdb=" C ILE B 265 " ideal model delta sigma weight residual 106.21 109.98 -3.77 1.07e+00 8.73e-01 1.24e+01 angle pdb=" N ILE B 148 " pdb=" CA ILE B 148 " pdb=" C ILE B 148 " ideal model delta sigma weight residual 113.53 110.28 3.25 9.80e-01 1.04e+00 1.10e+01 angle pdb=" C LYS B 50 " pdb=" N LYS B 51 " pdb=" CA LYS B 51 " ideal model delta sigma weight residual 121.54 126.58 -5.04 1.91e+00 2.74e-01 6.95e+00 angle pdb=" C GLY B 303 " pdb=" N ARG B 304 " pdb=" CA ARG B 304 " ideal model delta sigma weight residual 121.54 126.51 -4.97 1.91e+00 2.74e-01 6.78e+00 angle pdb=" CA LYS B 51 " pdb=" CB LYS B 51 " pdb=" CG LYS B 51 " ideal model delta sigma weight residual 114.10 119.17 -5.07 2.00e+00 2.50e-01 6.41e+00 ... (remaining 12169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 4882 17.10 - 34.21: 449 34.21 - 51.31: 89 51.31 - 68.42: 21 68.42 - 85.52: 17 Dihedral angle restraints: 5458 sinusoidal: 2208 harmonic: 3250 Sorted by residual: dihedral pdb=" CB GLU B 592 " pdb=" CG GLU B 592 " pdb=" CD GLU B 592 " pdb=" OE1 GLU B 592 " ideal model delta sinusoidal sigma weight residual 0.00 85.52 -85.52 1 3.00e+01 1.11e-03 9.83e+00 dihedral pdb=" CB GLU A 58 " pdb=" CG GLU A 58 " pdb=" CD GLU A 58 " pdb=" OE1 GLU A 58 " ideal model delta sinusoidal sigma weight residual 0.00 -85.10 85.10 1 3.00e+01 1.11e-03 9.76e+00 dihedral pdb=" CB MET B 434 " pdb=" CG MET B 434 " pdb=" SD MET B 434 " pdb=" CE MET B 434 " ideal model delta sinusoidal sigma weight residual 60.00 116.47 -56.47 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 5455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 822 0.028 - 0.056: 385 0.056 - 0.084: 109 0.084 - 0.112: 39 0.112 - 0.140: 25 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CA VAL A 111 " pdb=" N VAL A 111 " pdb=" C VAL A 111 " pdb=" CB VAL A 111 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA ILE A 280 " pdb=" N ILE A 280 " pdb=" C ILE A 280 " pdb=" CB ILE A 280 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA ILE B 280 " pdb=" N ILE B 280 " pdb=" C ILE B 280 " pdb=" CB ILE B 280 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1377 not shown) Planarity restraints: 1562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 491 " 0.041 5.00e-02 4.00e+02 6.28e-02 6.31e+00 pdb=" N PRO B 492 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 492 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 492 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 320 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO D 321 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 321 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 321 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 304 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C ARG B 304 " -0.026 2.00e-02 2.50e+03 pdb=" O ARG B 304 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE B 305 " 0.009 2.00e-02 2.50e+03 ... (remaining 1559 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 170 2.70 - 3.25: 8802 3.25 - 3.80: 13747 3.80 - 4.35: 19172 4.35 - 4.90: 32373 Nonbonded interactions: 74264 Sorted by model distance: nonbonded pdb=" NH1 ARG A 193 " pdb=" O HOH A 701 " model vdw 2.148 2.520 nonbonded pdb=" OG1 THR A 363 " pdb=" OH TYR A 541 " model vdw 2.220 2.440 nonbonded pdb=" OD2 ASP B 88 " pdb=" NH2 ARG B 417 " model vdw 2.268 2.520 nonbonded pdb=" OD2 ASP A 88 " pdb=" NH2 ARG A 417 " model vdw 2.285 2.520 nonbonded pdb=" O ASP A 188 " pdb=" O HOH A 701 " model vdw 2.286 2.440 ... (remaining 74259 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' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 4.010 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.850 Find NCS groups from input model: 0.440 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 : 0.003 0.030 9030 Z= 0.164 Angle : 0.501 7.056 12174 Z= 0.282 Chirality : 0.039 0.140 1380 Planarity : 0.004 0.063 1562 Dihedral : 14.633 85.519 3370 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 0.27 (0.26), residues: 1120 helix: 0.33 (0.21), residues: 644 sheet: -0.69 (0.50), residues: 76 loop : 0.41 (0.36), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 391 HIS 0.003 0.001 HIS A 491 PHE 0.008 0.001 PHE A 54 TYR 0.016 0.001 TYR B 506 ARG 0.009 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.945 Fit side-chains REVERT: A 47 LYS cc_start: 0.7592 (mmtm) cc_final: 0.7291 (ptmt) REVERT: A 521 LYS cc_start: 0.8577 (mppt) cc_final: 0.8310 (mptt) REVERT: A 555 ARG cc_start: 0.7612 (ttp-110) cc_final: 0.7076 (ttp-110) REVERT: B 65 ASN cc_start: 0.7728 (m-40) cc_final: 0.7403 (m110) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.3323 time to fit residues: 61.0310 Evaluate side-chains 111 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9030 Z= 0.259 Angle : 0.526 10.707 12174 Z= 0.274 Chirality : 0.041 0.158 1380 Planarity : 0.005 0.060 1562 Dihedral : 3.930 17.159 1214 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.15 % Allowed : 8.75 % Favored : 90.10 % 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: 0.85 (0.26), residues: 1120 helix: 0.96 (0.21), residues: 640 sheet: -0.32 (0.51), residues: 76 loop : 0.32 (0.34), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 213 HIS 0.003 0.001 HIS A 561 PHE 0.012 0.001 PHE A 571 TYR 0.015 0.001 TYR B 361 ARG 0.008 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7592 (mmtm) cc_final: 0.7252 (ptmt) REVERT: A 521 LYS cc_start: 0.8538 (mppt) cc_final: 0.7836 (mtmm) REVERT: A 599 LYS cc_start: 0.7752 (mtmt) cc_final: 0.7276 (mttm) REVERT: B 522 THR cc_start: 0.8723 (t) cc_final: 0.8302 (p) REVERT: B 551 SER cc_start: 0.8427 (t) cc_final: 0.8001 (m) REVERT: B 599 LYS cc_start: 0.7681 (mttp) cc_final: 0.7363 (mttp) outliers start: 11 outliers final: 10 residues processed: 129 average time/residue: 0.3161 time to fit residues: 51.7622 Evaluate side-chains 119 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 607 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.0170 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 110 optimal weight: 0.1980 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN B 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9030 Z= 0.146 Angle : 0.439 8.377 12174 Z= 0.232 Chirality : 0.038 0.128 1380 Planarity : 0.004 0.057 1562 Dihedral : 3.655 16.898 1214 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.67 % Allowed : 10.31 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.26), residues: 1120 helix: 1.47 (0.21), residues: 636 sheet: -0.02 (0.52), residues: 76 loop : 0.28 (0.35), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 213 HIS 0.003 0.001 HIS A 491 PHE 0.009 0.001 PHE B 54 TYR 0.011 0.001 TYR B 361 ARG 0.006 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7600 (mmtm) cc_final: 0.7295 (ptmt) REVERT: A 521 LYS cc_start: 0.8479 (mppt) cc_final: 0.7766 (mtmm) REVERT: A 596 GLU cc_start: 0.6865 (mp0) cc_final: 0.6597 (mp0) REVERT: B 65 ASN cc_start: 0.7872 (m-40) cc_final: 0.7483 (m110) REVERT: B 83 ASP cc_start: 0.5654 (OUTLIER) cc_final: 0.5410 (m-30) REVERT: B 260 GLU cc_start: 0.6746 (mt-10) cc_final: 0.6513 (mt-10) REVERT: B 335 ARG cc_start: 0.7647 (mpt180) cc_final: 0.7382 (mpt180) REVERT: B 522 THR cc_start: 0.8679 (t) cc_final: 0.8262 (p) REVERT: B 551 SER cc_start: 0.8451 (t) cc_final: 0.8075 (m) REVERT: B 599 LYS cc_start: 0.7698 (mttp) cc_final: 0.7378 (mttp) outliers start: 16 outliers final: 9 residues processed: 126 average time/residue: 0.2859 time to fit residues: 46.5040 Evaluate side-chains 124 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 490 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 HIS ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9030 Z= 0.200 Angle : 0.469 9.731 12174 Z= 0.244 Chirality : 0.039 0.129 1380 Planarity : 0.004 0.057 1562 Dihedral : 3.724 16.411 1214 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.88 % Allowed : 11.77 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.26), residues: 1120 helix: 1.42 (0.21), residues: 644 sheet: 0.06 (0.53), residues: 76 loop : 0.41 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 213 HIS 0.003 0.001 HIS A 204 PHE 0.024 0.001 PHE A 425 TYR 0.016 0.001 TYR A 506 ARG 0.007 0.000 ARG B 446 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7578 (mmtm) cc_final: 0.7236 (ptmt) REVERT: A 521 LYS cc_start: 0.8509 (mppt) cc_final: 0.7757 (mtmm) REVERT: A 596 GLU cc_start: 0.6939 (mp0) cc_final: 0.6670 (mp0) REVERT: B 65 ASN cc_start: 0.7867 (m-40) cc_final: 0.7436 (m110) REVERT: B 260 GLU cc_start: 0.6727 (mt-10) cc_final: 0.6490 (mt-10) REVERT: B 335 ARG cc_start: 0.7819 (mpt180) cc_final: 0.7592 (mmt-90) REVERT: B 522 THR cc_start: 0.8659 (t) cc_final: 0.8240 (p) REVERT: B 551 SER cc_start: 0.8421 (t) cc_final: 0.8019 (m) REVERT: B 599 LYS cc_start: 0.7713 (mttp) cc_final: 0.7448 (mttm) outliers start: 18 outliers final: 16 residues processed: 123 average time/residue: 0.2962 time to fit residues: 47.3484 Evaluate side-chains 127 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9030 Z= 0.398 Angle : 0.602 11.602 12174 Z= 0.305 Chirality : 0.044 0.199 1380 Planarity : 0.005 0.060 1562 Dihedral : 4.182 19.590 1214 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.40 % Allowed : 13.44 % Favored : 84.17 % 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: 0.92 (0.26), residues: 1120 helix: 0.95 (0.20), residues: 642 sheet: -0.20 (0.52), residues: 76 loop : 0.46 (0.35), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 324 HIS 0.005 0.001 HIS A 561 PHE 0.021 0.002 PHE A 425 TYR 0.019 0.002 TYR A 361 ARG 0.007 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 1.074 Fit side-chains REVERT: A 47 LYS cc_start: 0.7627 (mmtm) cc_final: 0.7411 (mttt) REVERT: A 64 LEU cc_start: 0.8287 (tp) cc_final: 0.8086 (tp) REVERT: A 193 ARG cc_start: 0.7428 (mtm-85) cc_final: 0.7095 (mtm-85) REVERT: A 521 LYS cc_start: 0.8629 (mppt) cc_final: 0.7870 (mtmm) REVERT: B 260 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6626 (mm-30) REVERT: B 522 THR cc_start: 0.8659 (t) cc_final: 0.8275 (p) REVERT: B 551 SER cc_start: 0.8415 (t) cc_final: 0.7882 (m) REVERT: B 599 LYS cc_start: 0.7757 (mttp) cc_final: 0.7476 (mttm) outliers start: 23 outliers final: 16 residues processed: 127 average time/residue: 0.2808 time to fit residues: 46.7320 Evaluate side-chains 123 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 607 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 560 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9030 Z= 0.175 Angle : 0.463 8.937 12174 Z= 0.241 Chirality : 0.039 0.132 1380 Planarity : 0.004 0.059 1562 Dihedral : 3.803 17.239 1214 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.60 % Allowed : 13.85 % Favored : 83.54 % 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: 1.35 (0.26), residues: 1120 helix: 1.37 (0.21), residues: 644 sheet: 0.00 (0.53), residues: 76 loop : 0.49 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 213 HIS 0.002 0.001 HIS A 561 PHE 0.022 0.001 PHE A 425 TYR 0.018 0.001 TYR A 506 ARG 0.008 0.000 ARG B 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.046 Fit side-chains REVERT: A 47 LYS cc_start: 0.7607 (mmtm) cc_final: 0.7373 (tttt) REVERT: A 521 LYS cc_start: 0.8552 (mppt) cc_final: 0.7870 (mtmm) REVERT: A 555 ARG cc_start: 0.7711 (ttp-110) cc_final: 0.7220 (ttp-110) REVERT: B 65 ASN cc_start: 0.7875 (m110) cc_final: 0.7387 (m110) REVERT: B 260 GLU cc_start: 0.6789 (mt-10) cc_final: 0.6470 (mt-10) REVERT: B 522 THR cc_start: 0.8598 (t) cc_final: 0.8158 (p) REVERT: B 551 SER cc_start: 0.8420 (t) cc_final: 0.7972 (m) REVERT: B 599 LYS cc_start: 0.7660 (mttp) cc_final: 0.7397 (mttm) outliers start: 25 outliers final: 13 residues processed: 126 average time/residue: 0.2957 time to fit residues: 48.1108 Evaluate side-chains 123 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 0.0000 chunk 67 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9030 Z= 0.157 Angle : 0.456 9.222 12174 Z= 0.237 Chirality : 0.039 0.137 1380 Planarity : 0.004 0.058 1562 Dihedral : 3.693 17.242 1214 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.56 % Allowed : 14.48 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.26), residues: 1120 helix: 1.57 (0.21), residues: 646 sheet: 0.11 (0.54), residues: 76 loop : 0.53 (0.35), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 213 HIS 0.002 0.001 HIS A 561 PHE 0.020 0.001 PHE A 425 TYR 0.017 0.001 TYR B 506 ARG 0.009 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 1.020 Fit side-chains REVERT: A 47 LYS cc_start: 0.7563 (mmtm) cc_final: 0.7342 (tttt) REVERT: A 65 ASN cc_start: 0.8030 (m110) cc_final: 0.7410 (m110) REVERT: A 521 LYS cc_start: 0.8568 (mppt) cc_final: 0.7871 (mtmm) REVERT: A 555 ARG cc_start: 0.7665 (ttp-110) cc_final: 0.7156 (ttp-110) REVERT: B 65 ASN cc_start: 0.7840 (m110) cc_final: 0.7364 (m110) REVERT: B 260 GLU cc_start: 0.6769 (mt-10) cc_final: 0.6452 (mt-10) REVERT: B 522 THR cc_start: 0.8575 (t) cc_final: 0.8121 (p) REVERT: B 551 SER cc_start: 0.8433 (t) cc_final: 0.8033 (m) REVERT: B 599 LYS cc_start: 0.7679 (mttp) cc_final: 0.7412 (mttm) outliers start: 15 outliers final: 12 residues processed: 119 average time/residue: 0.3385 time to fit residues: 51.4558 Evaluate side-chains 121 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9030 Z= 0.260 Angle : 0.511 10.804 12174 Z= 0.263 Chirality : 0.041 0.158 1380 Planarity : 0.004 0.058 1562 Dihedral : 3.846 17.522 1214 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.88 % Allowed : 14.38 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.26), residues: 1120 helix: 1.38 (0.21), residues: 644 sheet: 0.04 (0.53), residues: 76 loop : 0.51 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 213 HIS 0.003 0.001 HIS A 561 PHE 0.020 0.002 PHE A 425 TYR 0.019 0.001 TYR A 506 ARG 0.009 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 1.002 Fit side-chains REVERT: A 47 LYS cc_start: 0.7540 (mmtm) cc_final: 0.7338 (tttt) REVERT: A 521 LYS cc_start: 0.8594 (mppt) cc_final: 0.7901 (mtmm) REVERT: B 65 ASN cc_start: 0.7905 (m110) cc_final: 0.7406 (m110) REVERT: B 260 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6572 (mt-10) REVERT: B 522 THR cc_start: 0.8595 (t) cc_final: 0.8157 (p) REVERT: B 551 SER cc_start: 0.8432 (t) cc_final: 0.7976 (m) REVERT: B 580 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7872 (mp) REVERT: B 599 LYS cc_start: 0.7732 (mttp) cc_final: 0.7445 (mttm) outliers start: 18 outliers final: 14 residues processed: 117 average time/residue: 0.2926 time to fit residues: 44.2060 Evaluate side-chains 122 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 580 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9030 Z= 0.224 Angle : 0.502 10.609 12174 Z= 0.257 Chirality : 0.040 0.152 1380 Planarity : 0.004 0.058 1562 Dihedral : 3.827 17.707 1214 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.67 % Allowed : 15.10 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.26), residues: 1120 helix: 1.44 (0.21), residues: 644 sheet: 0.08 (0.53), residues: 76 loop : 0.53 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 213 HIS 0.003 0.001 HIS A 561 PHE 0.021 0.001 PHE A 425 TYR 0.019 0.001 TYR B 506 ARG 0.010 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 0.981 Fit side-chains REVERT: A 47 LYS cc_start: 0.7543 (mmtm) cc_final: 0.7325 (tttt) REVERT: A 64 LEU cc_start: 0.8253 (tp) cc_final: 0.8039 (tp) REVERT: A 65 ASN cc_start: 0.8032 (m110) cc_final: 0.7380 (m110) REVERT: A 521 LYS cc_start: 0.8617 (mppt) cc_final: 0.7923 (mtmm) REVERT: B 65 ASN cc_start: 0.7873 (m110) cc_final: 0.7380 (m110) REVERT: B 260 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6584 (mt-10) REVERT: B 422 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.7846 (mp) REVERT: B 522 THR cc_start: 0.8591 (t) cc_final: 0.8163 (p) REVERT: B 551 SER cc_start: 0.8431 (t) cc_final: 0.7984 (m) REVERT: B 599 LYS cc_start: 0.7696 (mttp) cc_final: 0.7415 (mttm) outliers start: 16 outliers final: 13 residues processed: 114 average time/residue: 0.2981 time to fit residues: 43.7618 Evaluate side-chains 121 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9030 Z= 0.214 Angle : 0.492 10.410 12174 Z= 0.254 Chirality : 0.040 0.152 1380 Planarity : 0.004 0.058 1562 Dihedral : 3.803 17.252 1214 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.98 % Allowed : 14.48 % Favored : 83.54 % 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: 1.49 (0.26), residues: 1120 helix: 1.48 (0.21), residues: 644 sheet: 0.08 (0.53), residues: 76 loop : 0.56 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 213 HIS 0.003 0.001 HIS A 561 PHE 0.021 0.001 PHE A 425 TYR 0.019 0.001 TYR A 506 ARG 0.010 0.000 ARG A 446 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 0.964 Fit side-chains REVERT: A 47 LYS cc_start: 0.7546 (mmtm) cc_final: 0.7327 (tttt) REVERT: A 64 LEU cc_start: 0.8258 (tp) cc_final: 0.8046 (tp) REVERT: A 65 ASN cc_start: 0.8032 (m110) cc_final: 0.7380 (m110) REVERT: A 206 ILE cc_start: 0.8355 (mt) cc_final: 0.8150 (mm) REVERT: A 521 LYS cc_start: 0.8590 (mppt) cc_final: 0.7887 (mtmm) REVERT: B 65 ASN cc_start: 0.7868 (m110) cc_final: 0.7380 (m110) REVERT: B 260 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6585 (mt-10) REVERT: B 422 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.7838 (mp) REVERT: B 522 THR cc_start: 0.8593 (t) cc_final: 0.8162 (p) REVERT: B 551 SER cc_start: 0.8433 (t) cc_final: 0.7989 (m) REVERT: B 580 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7910 (mp) REVERT: B 599 LYS cc_start: 0.7694 (mttp) cc_final: 0.7413 (mttm) outliers start: 19 outliers final: 15 residues processed: 115 average time/residue: 0.3039 time to fit residues: 45.0513 Evaluate side-chains 122 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 580 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.154129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.121042 restraints weight = 8780.294| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.92 r_work: 0.3180 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9030 Z= 0.204 Angle : 0.489 10.217 12174 Z= 0.252 Chirality : 0.040 0.151 1380 Planarity : 0.004 0.058 1562 Dihedral : 3.781 17.423 1214 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.88 % Allowed : 14.69 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.26), residues: 1120 helix: 1.53 (0.21), residues: 644 sheet: 0.09 (0.53), residues: 76 loop : 0.57 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 213 HIS 0.003 0.001 HIS A 561 PHE 0.021 0.001 PHE A 425 TYR 0.019 0.001 TYR B 506 ARG 0.009 0.000 ARG B 446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2086.82 seconds wall clock time: 38 minutes 45.23 seconds (2325.23 seconds total)