Starting phenix.real_space_refine on Fri Mar 15 08:42:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnp_12482/03_2024/7nnp_12482_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnp_12482/03_2024/7nnp_12482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnp_12482/03_2024/7nnp_12482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnp_12482/03_2024/7nnp_12482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnp_12482/03_2024/7nnp_12482_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnp_12482/03_2024/7nnp_12482_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 Rb 8 11.75 5 P 7 5.49 5 S 63 5.16 5 C 7167 2.51 5 N 1837 2.21 5 O 2014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 33": "OD1" <-> "OD2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A ASP 54": "OD1" <-> "OD2" Residue "A PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 439": "OD1" <-> "OD2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 417": "OD1" <-> "OD2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11096 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4159 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 5067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5067 Classifications: {'peptide': 682} Link IDs: {'PTRANS': 26, 'TRANS': 655} Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Unusual residues: {' RB': 6, 'CDL': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 133 Unusual residues: {' RB': 2, 'ACP': 1, 'CDL': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.32, per 1000 atoms: 0.57 Number of scatterers: 11096 At special positions: 0 Unit cell: (83.996, 105.248, 153.824, 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) Rb 8 36.98 S 63 16.00 P 7 15.00 O 2014 8.00 N 1837 7.00 C 7167 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: 4.66 Conformation dependent library (CDL) restraints added in 2.3 seconds 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2652 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 8 sheets defined 55.8% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 2 through 31 Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 42 through 50 removed outlier: 3.541A pdb=" N ARG A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 82 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 135 through 156 removed outlier: 3.766A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 178 through 192 removed outlier: 3.765A pdb=" N LEU A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.746A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 274 removed outlier: 4.477A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix removed outlier: 3.604A pdb=" N CYS A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 304 removed outlier: 4.244A pdb=" N MET A 282 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 289 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 removed outlier: 4.132A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 311' Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 356 through 367 Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 378 through 398 removed outlier: 4.139A pdb=" N LEU A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 388 " --> pdb=" O MET A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 436 removed outlier: 3.753A pdb=" N VAL A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 439 through 444 removed outlier: 4.573A pdb=" N ALA A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.553A pdb=" N GLY A 452 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 457 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 494 Processing helix chain 'A' and resid 497 through 507 Processing helix chain 'A' and resid 524 through 547 removed outlier: 3.827A pdb=" N PHE A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'C' and resid 5 through 19 Processing helix chain 'C' and resid 21 through 33 Processing helix chain 'C' and resid 35 through 38 No H-bonds generated for 'chain 'C' and resid 35 through 38' Processing helix chain 'C' and resid 92 through 108 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 152 through 161 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'D' and resid 3 through 24 Processing helix chain 'B' and resid 14 through 22 removed outlier: 4.339A pdb=" N ALA B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 55 Processing helix chain 'B' and resid 62 through 96 removed outlier: 3.696A pdb=" N GLU B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 216 through 246 removed outlier: 4.081A pdb=" N LEU B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 265 through 284 removed outlier: 5.726A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 removed outlier: 3.897A pdb=" N GLY B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 347 through 360 removed outlier: 3.728A pdb=" N VAL B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLN B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 408 Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 454 through 463 Processing helix chain 'B' and resid 477 through 485 Processing helix chain 'B' and resid 496 through 508 Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 558 through 594 removed outlier: 4.011A pdb=" N ASP B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS B 586 " --> pdb=" O ASN B 582 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 600 through 605 removed outlier: 3.879A pdb=" N ASN B 603 " --> pdb=" O PRO B 600 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 637 removed outlier: 4.329A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 646 through 679 Proline residue: B 665 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 202 through 205 Processing sheet with id= B, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.486A pdb=" N GLU C 45 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 106 through 108 removed outlier: 4.188A pdb=" N ASP B 119 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 131 through 134 removed outlier: 3.586A pdb=" N ILE B 189 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 151 through 153 Processing sheet with id= F, first strand: chain 'B' and resid 287 through 289 Processing sheet with id= G, first strand: chain 'B' and resid 531 through 534 removed outlier: 6.414A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR B 516 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU B 305 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS B 466 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LEU B 306 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL B 468 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ASP B 489 " --> pdb=" O MET B 469 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 321 through 324 removed outlier: 3.623A pdb=" N GLU B 321 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B 444 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 323 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL B 442 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU B 431 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA B 444 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N THR B 429 " --> pdb=" O ALA B 444 " (cutoff:3.500A) 559 hydrogen bonds defined for protein. 1554 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: 3.19 Time building geometry restraints manager: 4.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1784 1.31 - 1.44: 2758 1.44 - 1.57: 6618 1.57 - 1.70: 12 1.70 - 1.83: 116 Bond restraints: 11288 Sorted by residual: bond pdb=" CB7 CDL B 703 " pdb=" OB8 CDL B 703 " ideal model delta sigma weight residual 1.334 1.423 -0.089 1.10e-02 8.26e+03 6.59e+01 bond pdb=" CB7 CDL A 607 " pdb=" OB8 CDL A 607 " ideal model delta sigma weight residual 1.334 1.422 -0.088 1.10e-02 8.26e+03 6.43e+01 bond pdb=" CA7 CDL B 703 " pdb=" OA8 CDL B 703 " ideal model delta sigma weight residual 1.334 1.417 -0.083 1.10e-02 8.26e+03 5.66e+01 bond pdb=" CA7 CDL A 607 " pdb=" OA8 CDL A 607 " ideal model delta sigma weight residual 1.334 1.415 -0.081 1.10e-02 8.26e+03 5.46e+01 bond pdb=" OB2 CDL A 607 " pdb=" PB2 CDL A 607 " ideal model delta sigma weight residual 1.579 1.667 -0.088 1.50e-02 4.44e+03 3.47e+01 ... (remaining 11283 not shown) Histogram of bond angle deviations from ideal: 98.45 - 105.59: 273 105.59 - 112.72: 6154 112.72 - 119.86: 3679 119.86 - 127.00: 5091 127.00 - 134.14: 123 Bond angle restraints: 15320 Sorted by residual: angle pdb=" C51 CDL B 703 " pdb=" CB5 CDL B 703 " pdb=" OB6 CDL B 703 " ideal model delta sigma weight residual 111.33 120.68 -9.35 1.32e+00 5.72e-01 5.00e+01 angle pdb=" C51 CDL A 607 " pdb=" CB5 CDL A 607 " pdb=" OB6 CDL A 607 " ideal model delta sigma weight residual 111.33 120.13 -8.80 1.32e+00 5.72e-01 4.43e+01 angle pdb=" C11 CDL B 703 " pdb=" CA5 CDL B 703 " pdb=" OA6 CDL B 703 " ideal model delta sigma weight residual 111.33 119.93 -8.60 1.32e+00 5.72e-01 4.23e+01 angle pdb=" C11 CDL A 607 " pdb=" CA5 CDL A 607 " pdb=" OA6 CDL A 607 " ideal model delta sigma weight residual 111.33 119.90 -8.57 1.32e+00 5.72e-01 4.21e+01 angle pdb=" C71 CDL B 703 " pdb=" CB7 CDL B 703 " pdb=" OB8 CDL B 703 " ideal model delta sigma weight residual 111.64 120.24 -8.60 1.65e+00 3.69e-01 2.73e+01 ... (remaining 15315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.03: 6042 19.03 - 38.07: 570 38.07 - 57.10: 142 57.10 - 76.13: 36 76.13 - 95.17: 14 Dihedral angle restraints: 6804 sinusoidal: 2678 harmonic: 4126 Sorted by residual: dihedral pdb=" CA GLU B 364 " pdb=" C GLU B 364 " pdb=" N ARG B 365 " pdb=" CA ARG B 365 " ideal model delta harmonic sigma weight residual -180.00 -157.46 -22.54 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ASN A 239 " pdb=" C ASN A 239 " pdb=" N SER A 240 " pdb=" CA SER A 240 " ideal model delta harmonic sigma weight residual 180.00 160.15 19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ARG C 44 " pdb=" C ARG C 44 " pdb=" N GLU C 45 " pdb=" CA GLU C 45 " ideal model delta harmonic sigma weight residual 180.00 160.46 19.54 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 6801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1249 0.040 - 0.080: 406 0.080 - 0.120: 129 0.120 - 0.160: 35 0.160 - 0.200: 4 Chirality restraints: 1823 Sorted by residual: chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB VAL B 207 " pdb=" CA VAL B 207 " pdb=" CG1 VAL B 207 " pdb=" CG2 VAL B 207 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB VAL A 376 " pdb=" CA VAL A 376 " pdb=" CG1 VAL A 376 " pdb=" CG2 VAL A 376 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 1820 not shown) Planarity restraints: 1919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 245 " -0.018 2.00e-02 2.50e+03 1.75e-02 7.65e+00 pdb=" CG TRP B 245 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 245 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 245 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 245 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 245 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 245 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 245 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 245 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 245 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 121 " -0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO B 122 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 612 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO B 613 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 613 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 613 " 0.030 5.00e-02 4.00e+02 ... (remaining 1916 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.87: 3892 2.87 - 3.51: 14989 3.51 - 4.15: 24680 4.15 - 4.80: 42728 4.80 - 5.44: 53032 Nonbonded interactions: 139321 Sorted by model distance: nonbonded pdb=" O VAL C 118 " pdb=" OG1 THR C 122 " model vdw 2.223 2.440 nonbonded pdb=" OG1 THR C 72 " pdb=" O MET C 75 " model vdw 2.247 2.440 nonbonded pdb=" OE2 GLU A 321 " pdb=" OG SER C 85 " model vdw 2.250 2.440 nonbonded pdb=" OD1 ASP A 352 " pdb=" NE2 HIS A 451 " model vdw 2.264 2.520 nonbonded pdb=" OG1 THR A 401 " pdb=" OD2 ASP B 300 " model vdw 2.303 2.440 ... (remaining 139316 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.650 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 34.270 Find NCS groups from input model: 0.270 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.006 0.089 11288 Z= 0.381 Angle : 0.958 13.459 15320 Z= 0.485 Chirality : 0.046 0.200 1823 Planarity : 0.005 0.066 1919 Dihedral : 16.849 95.167 4152 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: -0.72 (0.20), residues: 1448 helix: 0.15 (0.16), residues: 879 sheet: -0.71 (0.58), residues: 90 loop : -1.44 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 245 HIS 0.009 0.001 HIS B 563 PHE 0.033 0.002 PHE A 260 TYR 0.029 0.002 TYR A 381 ARG 0.007 0.000 ARG B 402 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.159 Fit side-chains REVERT: A 350 MET cc_start: 0.8429 (mmp) cc_final: 0.8035 (mmp) REVERT: C 9 SER cc_start: 0.8684 (m) cc_final: 0.8330 (m) REVERT: B 358 GLN cc_start: 0.7537 (tt0) cc_final: 0.7025 (pt0) REVERT: B 463 MET cc_start: 0.7936 (mtp) cc_final: 0.7732 (mtp) REVERT: B 536 ASN cc_start: 0.6951 (t0) cc_final: 0.6626 (t0) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2339 time to fit residues: 50.0959 Evaluate side-chains 120 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 112 optimal weight: 40.0000 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11288 Z= 0.315 Angle : 0.595 6.544 15320 Z= 0.301 Chirality : 0.042 0.145 1823 Planarity : 0.005 0.055 1919 Dihedral : 12.925 89.903 1751 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.88 % Allowed : 8.06 % Favored : 91.07 % 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 (0.21), residues: 1448 helix: 0.56 (0.17), residues: 878 sheet: -0.61 (0.58), residues: 76 loop : -1.35 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 186 HIS 0.006 0.001 HIS A 451 PHE 0.023 0.002 PHE A 373 TYR 0.022 0.002 TYR A 381 ARG 0.004 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 1.221 Fit side-chains REVERT: A 350 MET cc_start: 0.8575 (mmp) cc_final: 0.8074 (mmp) REVERT: A 397 MET cc_start: 0.8457 (mtp) cc_final: 0.8164 (mtp) REVERT: A 413 GLU cc_start: 0.8116 (mp0) cc_final: 0.7869 (mp0) REVERT: C 9 SER cc_start: 0.8683 (m) cc_final: 0.8342 (m) REVERT: B 339 LEU cc_start: 0.7759 (mm) cc_final: 0.7517 (mm) REVERT: B 358 GLN cc_start: 0.7584 (tt0) cc_final: 0.7149 (pt0) REVERT: B 564 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7657 (mt) outliers start: 10 outliers final: 7 residues processed: 129 average time/residue: 0.2219 time to fit residues: 41.9640 Evaluate side-chains 130 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 506 TYR Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 580 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 30.0000 chunk 89 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 chunk 129 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11288 Z= 0.203 Angle : 0.520 6.466 15320 Z= 0.262 Chirality : 0.039 0.136 1823 Planarity : 0.004 0.052 1919 Dihedral : 11.779 88.703 1751 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.70 % Allowed : 11.03 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1448 helix: 0.95 (0.17), residues: 861 sheet: -0.52 (0.57), residues: 81 loop : -1.28 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 186 HIS 0.005 0.001 HIS A 451 PHE 0.020 0.001 PHE A 373 TYR 0.021 0.001 TYR A 381 ARG 0.003 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 1.239 Fit side-chains REVERT: A 350 MET cc_start: 0.8558 (mmp) cc_final: 0.8041 (mmt) REVERT: C 98 ILE cc_start: 0.8877 (mt) cc_final: 0.8658 (mt) REVERT: B 339 LEU cc_start: 0.7763 (mm) cc_final: 0.7495 (mm) REVERT: B 358 GLN cc_start: 0.7570 (tt0) cc_final: 0.7165 (pt0) REVERT: B 564 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7587 (mt) REVERT: B 599 TYR cc_start: 0.8673 (m-80) cc_final: 0.8435 (m-80) outliers start: 8 outliers final: 7 residues processed: 131 average time/residue: 0.2553 time to fit residues: 48.6447 Evaluate side-chains 128 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 506 TYR Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 618 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 chunk 67 optimal weight: 0.4980 chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 87 optimal weight: 20.0000 chunk 131 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11288 Z= 0.143 Angle : 0.482 5.861 15320 Z= 0.243 Chirality : 0.038 0.137 1823 Planarity : 0.004 0.050 1919 Dihedral : 10.769 85.839 1751 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.49 % Allowed : 12.17 % Favored : 86.34 % 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: 0.48 (0.22), residues: 1448 helix: 1.23 (0.18), residues: 866 sheet: -0.31 (0.58), residues: 82 loop : -1.17 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 245 HIS 0.004 0.000 HIS A 451 PHE 0.017 0.001 PHE A 373 TYR 0.020 0.001 TYR A 381 ARG 0.003 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 1.179 Fit side-chains REVERT: A 350 MET cc_start: 0.8523 (mmp) cc_final: 0.7946 (mmt) REVERT: B 339 LEU cc_start: 0.7809 (mm) cc_final: 0.7538 (mm) REVERT: B 358 GLN cc_start: 0.7528 (tt0) cc_final: 0.7139 (pt0) REVERT: B 536 ASN cc_start: 0.7067 (t0) cc_final: 0.6750 (t0) REVERT: B 564 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7576 (mt) outliers start: 17 outliers final: 10 residues processed: 136 average time/residue: 0.2285 time to fit residues: 45.4483 Evaluate side-chains 127 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 506 TYR Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 580 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11288 Z= 0.244 Angle : 0.532 6.322 15320 Z= 0.269 Chirality : 0.040 0.134 1823 Planarity : 0.004 0.050 1919 Dihedral : 10.577 85.937 1751 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.19 % Allowed : 12.87 % Favored : 84.94 % 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 (0.22), residues: 1448 helix: 1.04 (0.17), residues: 867 sheet: -0.24 (0.58), residues: 81 loop : -1.11 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 186 HIS 0.004 0.001 HIS A 451 PHE 0.019 0.001 PHE A 373 TYR 0.020 0.001 TYR A 381 ARG 0.002 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 1.171 Fit side-chains REVERT: A 413 GLU cc_start: 0.8140 (mp0) cc_final: 0.7919 (mp0) REVERT: C 98 ILE cc_start: 0.8893 (mt) cc_final: 0.8659 (mt) REVERT: B 283 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8313 (tt) REVERT: B 339 LEU cc_start: 0.7805 (mm) cc_final: 0.7537 (mm) REVERT: B 358 GLN cc_start: 0.7517 (tt0) cc_final: 0.7130 (pt0) REVERT: B 522 ASP cc_start: 0.7071 (p0) cc_final: 0.6800 (p0) REVERT: B 564 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7605 (mt) outliers start: 25 outliers final: 18 residues processed: 140 average time/residue: 0.2174 time to fit residues: 45.2065 Evaluate side-chains 135 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 506 TYR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 618 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.0570 chunk 34 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN C 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11288 Z= 0.241 Angle : 0.528 6.599 15320 Z= 0.267 Chirality : 0.040 0.134 1823 Planarity : 0.004 0.048 1919 Dihedral : 10.383 85.587 1751 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.45 % Allowed : 13.13 % Favored : 84.41 % 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: 0.33 (0.22), residues: 1448 helix: 1.06 (0.17), residues: 860 sheet: -0.25 (0.58), residues: 81 loop : -1.10 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 186 HIS 0.004 0.001 HIS A 451 PHE 0.019 0.001 PHE A 373 TYR 0.020 0.001 TYR A 381 ARG 0.002 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.228 Fit side-chains REVERT: C 98 ILE cc_start: 0.8901 (mt) cc_final: 0.8671 (mt) REVERT: B 283 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8341 (tt) REVERT: B 339 LEU cc_start: 0.7785 (mm) cc_final: 0.7506 (mm) REVERT: B 358 GLN cc_start: 0.7552 (tt0) cc_final: 0.7175 (pt0) REVERT: B 522 ASP cc_start: 0.7156 (p0) cc_final: 0.6896 (p0) REVERT: B 564 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7637 (mt) outliers start: 28 outliers final: 17 residues processed: 141 average time/residue: 0.2264 time to fit residues: 47.6379 Evaluate side-chains 135 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 618 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 78 optimal weight: 0.0030 chunk 117 optimal weight: 7.9990 chunk 77 optimal weight: 0.4980 chunk 138 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 85 optimal weight: 0.0870 overall best weight: 0.4368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11288 Z= 0.132 Angle : 0.481 6.901 15320 Z= 0.243 Chirality : 0.038 0.137 1823 Planarity : 0.003 0.048 1919 Dihedral : 9.750 85.924 1751 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.84 % Allowed : 14.10 % Favored : 84.06 % 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: 0.74 (0.22), residues: 1448 helix: 1.43 (0.18), residues: 861 sheet: -0.18 (0.57), residues: 82 loop : -1.00 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 186 HIS 0.003 0.000 HIS A 451 PHE 0.016 0.001 PHE A 373 TYR 0.019 0.001 TYR A 381 ARG 0.002 0.000 ARG B 402 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.239 Fit side-chains REVERT: B 339 LEU cc_start: 0.7823 (mm) cc_final: 0.7550 (mm) REVERT: B 358 GLN cc_start: 0.7583 (tt0) cc_final: 0.7214 (pt0) REVERT: B 522 ASP cc_start: 0.7130 (p0) cc_final: 0.6849 (p0) REVERT: B 536 ASN cc_start: 0.7040 (t0) cc_final: 0.6774 (t0) REVERT: B 564 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7563 (mt) outliers start: 21 outliers final: 12 residues processed: 140 average time/residue: 0.2202 time to fit residues: 45.2593 Evaluate side-chains 130 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 547 ASN Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 618 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 chunk 12 optimal weight: 0.5980 chunk 109 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11288 Z= 0.145 Angle : 0.483 6.790 15320 Z= 0.243 Chirality : 0.038 0.136 1823 Planarity : 0.003 0.049 1919 Dihedral : 9.560 86.666 1751 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.58 % Allowed : 14.89 % 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: 0.79 (0.22), residues: 1448 helix: 1.45 (0.18), residues: 863 sheet: -0.08 (0.57), residues: 81 loop : -0.98 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 186 HIS 0.003 0.000 HIS A 451 PHE 0.016 0.001 PHE A 373 TYR 0.019 0.001 TYR A 381 ARG 0.002 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 1.350 Fit side-chains REVERT: B 168 GLU cc_start: 0.6280 (tt0) cc_final: 0.5940 (tt0) REVERT: B 339 LEU cc_start: 0.7819 (mm) cc_final: 0.7551 (mm) REVERT: B 358 GLN cc_start: 0.7438 (tt0) cc_final: 0.7110 (pt0) REVERT: B 522 ASP cc_start: 0.7114 (p0) cc_final: 0.6745 (p0) REVERT: B 536 ASN cc_start: 0.7021 (t0) cc_final: 0.6718 (t0) REVERT: B 564 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7578 (mt) outliers start: 18 outliers final: 14 residues processed: 134 average time/residue: 0.2117 time to fit residues: 42.2935 Evaluate side-chains 133 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 547 ASN Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 618 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 122 optimal weight: 0.0870 chunk 128 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11288 Z= 0.180 Angle : 0.502 7.205 15320 Z= 0.252 Chirality : 0.039 0.135 1823 Planarity : 0.004 0.049 1919 Dihedral : 9.529 87.169 1751 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.75 % Allowed : 15.06 % Favored : 83.19 % 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: 0.74 (0.22), residues: 1448 helix: 1.40 (0.18), residues: 859 sheet: -0.09 (0.57), residues: 81 loop : -0.96 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 186 HIS 0.003 0.000 HIS A 451 PHE 0.016 0.001 PHE A 373 TYR 0.019 0.001 TYR A 381 ARG 0.001 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 1.116 Fit side-chains REVERT: B 168 GLU cc_start: 0.6301 (tt0) cc_final: 0.5915 (tt0) REVERT: B 339 LEU cc_start: 0.7806 (mm) cc_final: 0.7543 (mm) REVERT: B 358 GLN cc_start: 0.7433 (tt0) cc_final: 0.7106 (pt0) REVERT: B 522 ASP cc_start: 0.7169 (p0) cc_final: 0.6802 (p0) REVERT: B 536 ASN cc_start: 0.7051 (t0) cc_final: 0.6770 (t0) REVERT: B 564 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7584 (mt) outliers start: 20 outliers final: 16 residues processed: 131 average time/residue: 0.2197 time to fit residues: 42.6741 Evaluate side-chains 131 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 547 ASN Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11288 Z= 0.164 Angle : 0.498 7.386 15320 Z= 0.249 Chirality : 0.038 0.133 1823 Planarity : 0.003 0.048 1919 Dihedral : 9.402 87.595 1751 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.93 % Allowed : 14.97 % Favored : 83.10 % 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: 0.79 (0.22), residues: 1448 helix: 1.45 (0.18), residues: 858 sheet: -0.05 (0.56), residues: 81 loop : -0.95 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 186 HIS 0.003 0.000 HIS A 451 PHE 0.017 0.001 PHE A 373 TYR 0.019 0.001 TYR A 381 ARG 0.002 0.000 ARG B 359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 1.212 Fit side-chains REVERT: B 168 GLU cc_start: 0.6293 (tt0) cc_final: 0.5915 (tt0) REVERT: B 339 LEU cc_start: 0.7806 (mm) cc_final: 0.7547 (mm) REVERT: B 358 GLN cc_start: 0.7430 (tt0) cc_final: 0.7102 (pt0) REVERT: B 522 ASP cc_start: 0.7191 (p0) cc_final: 0.6817 (p0) REVERT: B 536 ASN cc_start: 0.7035 (t0) cc_final: 0.6732 (t0) REVERT: B 564 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7567 (mt) outliers start: 22 outliers final: 16 residues processed: 138 average time/residue: 0.2053 time to fit residues: 42.6098 Evaluate side-chains 137 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 547 ASN Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 618 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 0.0980 chunk 100 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.152570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115097 restraints weight = 11233.282| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.18 r_work: 0.3142 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11288 Z= 0.147 Angle : 0.501 13.919 15320 Z= 0.247 Chirality : 0.038 0.183 1823 Planarity : 0.003 0.048 1919 Dihedral : 9.276 89.820 1751 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.75 % Allowed : 15.06 % Favored : 83.19 % 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: 0.88 (0.22), residues: 1448 helix: 1.52 (0.18), residues: 858 sheet: 0.00 (0.56), residues: 81 loop : -0.93 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 186 HIS 0.003 0.000 HIS A 451 PHE 0.016 0.001 PHE A 373 TYR 0.019 0.001 TYR A 381 ARG 0.002 0.000 ARG B 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2231.80 seconds wall clock time: 41 minutes 5.12 seconds (2465.12 seconds total)