Starting phenix.real_space_refine on Thu Feb 15 03:58:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrh_14914/02_2024/7zrh_14914_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrh_14914/02_2024/7zrh_14914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrh_14914/02_2024/7zrh_14914.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrh_14914/02_2024/7zrh_14914.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrh_14914/02_2024/7zrh_14914_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrh_14914/02_2024/7zrh_14914_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 K 7 8.98 5 P 5 5.49 5 S 62 5.16 5 C 7123 2.51 5 N 1822 2.21 5 O 1995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B GLU 455": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11014 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 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: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5021 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 26, 'TRANS': 649} Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Unusual residues: {' K': 6, 'CDL': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {' K': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.69, per 1000 atoms: 0.61 Number of scatterers: 11014 At special positions: 0 Unit cell: (89.056, 115.368, 144.716, 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) K 7 19.00 S 62 16.00 P 5 15.00 O 1995 8.00 N 1822 7.00 C 7123 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: 4.53 Conformation dependent library (CDL) restraints added in 2.2 seconds 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 5 sheets defined 55.8% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 2 through 31 removed outlier: 3.649A pdb=" N PHE A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Proline residue: A 22 - end of helix removed outlier: 3.756A pdb=" N ARG A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 59 through 82 Processing helix chain 'A' and resid 99 through 110 removed outlier: 3.625A pdb=" N PHE A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) 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 131 Processing helix chain 'A' and resid 134 through 156 removed outlier: 3.694A 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: 3.953A pdb=" N LEU A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.868A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 273 removed outlier: 4.388A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 277 through 303 removed outlier: 3.927A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 removed outlier: 4.135A 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 removed outlier: 3.573A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 378 through 398 removed outlier: 4.172A pdb=" N LEU A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 435 removed outlier: 4.562A 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 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 450 through 464 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 541 Processing helix chain 'A' and resid 544 through 549 Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 21 through 33 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 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'D' and resid 3 through 24 Processing helix chain 'B' and resid 12 through 21 Processing helix chain 'B' and resid 27 through 30 No H-bonds generated for 'chain 'B' and resid 27 through 30' Processing helix chain 'B' and resid 34 through 55 removed outlier: 3.981A pdb=" N VAL B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 97 Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 216 through 245 removed outlier: 3.754A pdb=" N LEU B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 4.584A 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: 5.892A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 299 removed outlier: 3.650A pdb=" N GLY B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 343 removed outlier: 4.791A pdb=" N ALA B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 398 through 408 Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 453 through 462 Processing helix chain 'B' and resid 475 through 485 removed outlier: 3.674A pdb=" N ALA B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 508 Processing helix chain 'B' and resid 520 through 528 Proline residue: B 524 - end of helix removed outlier: 3.770A pdb=" N ALA B 527 " --> pdb=" O PRO B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 555 through 594 removed outlier: 3.960A pdb=" N LEU B 558 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE B 559 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET B 568 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN B 582 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ILE B 591 " --> pdb=" O PHE B 588 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 613 through 637 removed outlier: 3.888A pdb=" N ILE B 617 " --> pdb=" O PRO B 613 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU B 618 " --> pdb=" O ASP B 614 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.146A 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 removed outlier: 4.099A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) 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 'B' and resid 130 through 134 removed outlier: 3.699A pdb=" N ILE B 189 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL B 134 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU B 187 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU B 148 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLU B 190 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL B 146 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 152 through 154 Processing sheet with id= D, first strand: chain 'B' and resid 287 through 289 removed outlier: 7.152A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N THR B 516 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU B 305 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS B 466 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU B 306 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL B 468 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASP B 489 " --> pdb=" O MET B 469 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N THR B 471 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU B 491 " --> pdb=" O THR B 471 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 383 through 385 removed outlier: 3.626A pdb=" N VAL B 432 " --> pdb=" O GLY B 396 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 433 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY B 441 " --> pdb=" O VAL B 433 " (cutoff:3.500A) 554 hydrogen bonds defined for protein. 1551 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: 4.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1856 1.32 - 1.45: 2658 1.45 - 1.57: 6567 1.57 - 1.69: 12 1.69 - 1.81: 112 Bond restraints: 11205 Sorted by residual: bond pdb=" OA3 CDL A 607 " pdb=" PA1 CDL A 607 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.74e+00 bond pdb=" OB3 CDL A 607 " pdb=" PB2 CDL A 607 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.35e+00 bond pdb=" OB3 CDL B 801 " pdb=" PB2 CDL B 801 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.19e+00 bond pdb=" OA3 CDL B 801 " pdb=" PA1 CDL B 801 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.17e+00 bond pdb=" C51 CDL A 607 " pdb=" C52 CDL A 607 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.50e-02 4.44e+03 4.58e+00 ... (remaining 11200 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.92: 289 105.92 - 112.99: 6109 112.99 - 120.05: 3935 120.05 - 127.12: 4752 127.12 - 134.19: 119 Bond angle restraints: 15204 Sorted by residual: angle pdb=" CB LYS B 419 " pdb=" CG LYS B 419 " pdb=" CD LYS B 419 " ideal model delta sigma weight residual 111.30 120.03 -8.73 2.30e+00 1.89e-01 1.44e+01 angle pdb=" C LYS B 102 " pdb=" N THR B 103 " pdb=" CA THR B 103 " ideal model delta sigma weight residual 121.54 128.72 -7.18 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C VAL A 376 " pdb=" CA VAL A 376 " pdb=" CB VAL A 376 " ideal model delta sigma weight residual 111.23 114.94 -3.71 1.01e+00 9.80e-01 1.35e+01 angle pdb=" N GLY B 452 " pdb=" CA GLY B 452 " pdb=" C GLY B 452 " ideal model delta sigma weight residual 110.95 116.91 -5.96 1.70e+00 3.46e-01 1.23e+01 angle pdb=" N GLY A 375 " pdb=" CA GLY A 375 " pdb=" C GLY A 375 " ideal model delta sigma weight residual 111.78 117.31 -5.53 1.69e+00 3.50e-01 1.07e+01 ... (remaining 15199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5949 17.95 - 35.90: 601 35.90 - 53.85: 139 53.85 - 71.80: 35 71.80 - 89.75: 11 Dihedral angle restraints: 6735 sinusoidal: 2629 harmonic: 4106 Sorted by residual: dihedral pdb=" CA ALA A 238 " pdb=" C ALA A 238 " pdb=" N ASN A 239 " pdb=" CA ASN A 239 " ideal model delta harmonic sigma weight residual 180.00 -156.68 -23.32 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ALA A 470 " pdb=" C ALA A 470 " pdb=" N PHE A 471 " pdb=" CA PHE A 471 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LEU A 422 " pdb=" C LEU A 422 " pdb=" N VAL A 423 " pdb=" CA VAL A 423 " ideal model delta harmonic sigma weight residual 180.00 -161.35 -18.65 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 6732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1232 0.042 - 0.084: 427 0.084 - 0.126: 126 0.126 - 0.167: 21 0.167 - 0.209: 5 Chirality restraints: 1811 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 2.32 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB THR B 313 " pdb=" CA THR B 313 " pdb=" OG1 THR B 313 " pdb=" CG2 THR B 313 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA4 CDL B 801 " pdb=" CA3 CDL B 801 " pdb=" CA6 CDL B 801 " pdb=" OA6 CDL B 801 " both_signs ideal model delta sigma weight residual False -2.57 -2.38 -0.20 2.00e-01 2.50e+01 9.73e-01 ... (remaining 1808 not shown) Planarity restraints: 1909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 121 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO B 122 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 262 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.36e+00 pdb=" N PRO A 263 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 263 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 263 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 75 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO C 76 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.029 5.00e-02 4.00e+02 ... (remaining 1906 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 3208 2.82 - 3.40: 12525 3.40 - 3.98: 21551 3.98 - 4.56: 30652 4.56 - 5.14: 44405 Nonbonded interactions: 112341 Sorted by model distance: nonbonded pdb=" O LEU A 541 " pdb=" OH TYR B 587 " model vdw 2.242 2.440 nonbonded pdb=" OD1 ASP B 329 " pdb=" OG1 THR B 332 " model vdw 2.267 2.440 nonbonded pdb=" O GLN B 318 " pdb=" OG SER B 351 " model vdw 2.274 2.440 nonbonded pdb=" O LEU B 239 " pdb=" OG SER B 243 " model vdw 2.292 2.440 nonbonded pdb=" OG1 THR B 471 " pdb=" OD1 ASP B 473 " model vdw 2.298 2.440 ... (remaining 112336 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 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: 3.640 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 34.550 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11205 Z= 0.265 Angle : 0.748 8.731 15204 Z= 0.386 Chirality : 0.047 0.209 1811 Planarity : 0.006 0.065 1909 Dihedral : 15.889 89.752 4097 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -1.07 (0.20), residues: 1439 helix: 0.20 (0.16), residues: 843 sheet: -1.36 (0.74), residues: 56 loop : -2.07 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 655 HIS 0.003 0.001 HIS A 451 PHE 0.029 0.002 PHE A 260 TYR 0.023 0.002 TYR C 170 ARG 0.012 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.357 Fit side-chains REVERT: A 71 MET cc_start: 0.8244 (mmt) cc_final: 0.7738 (mmt) REVERT: A 130 MET cc_start: 0.8478 (ttp) cc_final: 0.8118 (ttm) REVERT: B 77 LEU cc_start: 0.7944 (tt) cc_final: 0.7736 (tt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2174 time to fit residues: 48.1121 Evaluate side-chains 118 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.0020 chunk 108 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 482 ASN C 80 GLN B 316 ASN B 653 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11205 Z= 0.333 Angle : 0.584 7.137 15204 Z= 0.297 Chirality : 0.041 0.145 1811 Planarity : 0.005 0.052 1909 Dihedral : 11.225 59.030 1715 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.79 % Allowed : 7.14 % Favored : 92.07 % 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: -0.54 (0.21), residues: 1439 helix: 0.64 (0.17), residues: 844 sheet: -1.26 (0.75), residues: 56 loop : -1.88 (0.24), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 31 HIS 0.004 0.001 HIS A 242 PHE 0.022 0.002 PHE A 354 TYR 0.029 0.002 TYR A 381 ARG 0.004 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 1.206 Fit side-chains REVERT: A 130 MET cc_start: 0.8369 (ttp) cc_final: 0.8003 (ttm) outliers start: 9 outliers final: 4 residues processed: 128 average time/residue: 0.1975 time to fit residues: 37.9897 Evaluate side-chains 114 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 522 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 0.0870 chunk 40 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 129 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 GLN B 80 ASN B 217 ASN B 653 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11205 Z= 0.174 Angle : 0.501 7.030 15204 Z= 0.254 Chirality : 0.038 0.144 1811 Planarity : 0.004 0.051 1909 Dihedral : 10.423 58.623 1715 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.88 % Allowed : 10.31 % Favored : 88.81 % 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: -0.16 (0.22), residues: 1439 helix: 1.04 (0.18), residues: 838 sheet: -1.44 (0.72), residues: 56 loop : -1.79 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 31 HIS 0.002 0.000 HIS A 451 PHE 0.012 0.001 PHE A 260 TYR 0.021 0.001 TYR A 381 ARG 0.003 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 1.209 Fit side-chains REVERT: A 130 MET cc_start: 0.8390 (ttp) cc_final: 0.8002 (ttm) outliers start: 10 outliers final: 6 residues processed: 123 average time/residue: 0.2105 time to fit residues: 39.3167 Evaluate side-chains 115 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 500 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 130 optimal weight: 0.4980 chunk 138 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11205 Z= 0.161 Angle : 0.485 7.016 15204 Z= 0.247 Chirality : 0.038 0.198 1811 Planarity : 0.004 0.050 1909 Dihedral : 9.929 59.548 1715 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.23 % Allowed : 12.33 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.22), residues: 1439 helix: 1.16 (0.18), residues: 842 sheet: -1.44 (0.72), residues: 56 loop : -1.65 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 31 HIS 0.002 0.000 HIS A 451 PHE 0.010 0.001 PHE A 527 TYR 0.021 0.001 TYR A 381 ARG 0.003 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.326 Fit side-chains REVERT: A 130 MET cc_start: 0.8388 (ttp) cc_final: 0.8024 (ttm) REVERT: A 413 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7197 (mt-10) REVERT: B 25 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7732 (pp) outliers start: 14 outliers final: 10 residues processed: 121 average time/residue: 0.2233 time to fit residues: 41.1175 Evaluate side-chains 119 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 322 PHE Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 522 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 11205 Z= 0.377 Angle : 0.585 7.122 15204 Z= 0.295 Chirality : 0.042 0.220 1811 Planarity : 0.004 0.049 1909 Dihedral : 9.903 59.716 1715 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.32 % Allowed : 13.13 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.22), residues: 1439 helix: 0.89 (0.18), residues: 840 sheet: -0.60 (0.78), residues: 46 loop : -1.78 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 31 HIS 0.003 0.001 HIS A 451 PHE 0.016 0.001 PHE A 354 TYR 0.023 0.002 TYR A 381 ARG 0.004 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.378 Fit side-chains REVERT: A 130 MET cc_start: 0.8455 (ttp) cc_final: 0.8130 (ttm) REVERT: A 413 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: B 25 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7803 (pp) outliers start: 15 outliers final: 10 residues processed: 125 average time/residue: 0.2268 time to fit residues: 42.0175 Evaluate side-chains 124 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 522 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 0.6980 chunk 124 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 482 ASN B 653 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11205 Z= 0.171 Angle : 0.499 6.976 15204 Z= 0.252 Chirality : 0.039 0.188 1811 Planarity : 0.004 0.051 1909 Dihedral : 9.191 59.208 1715 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.32 % Allowed : 13.74 % Favored : 84.93 % 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: 0.08 (0.22), residues: 1439 helix: 1.19 (0.18), residues: 836 sheet: -0.67 (0.76), residues: 46 loop : -1.69 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 186 HIS 0.002 0.000 HIS A 451 PHE 0.012 0.001 PHE A 260 TYR 0.021 0.001 TYR A 381 ARG 0.003 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 1.293 Fit side-chains REVERT: A 130 MET cc_start: 0.8448 (ttp) cc_final: 0.8122 (ttm) REVERT: A 413 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: B 25 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7791 (pp) REVERT: B 383 MET cc_start: 0.5889 (ttp) cc_final: 0.5250 (tmm) REVERT: B 431 LEU cc_start: 0.7070 (mm) cc_final: 0.6784 (tt) outliers start: 15 outliers final: 11 residues processed: 123 average time/residue: 0.2303 time to fit residues: 42.3026 Evaluate side-chains 120 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 608 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 78 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 116 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 86 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11205 Z= 0.233 Angle : 0.518 7.004 15204 Z= 0.261 Chirality : 0.039 0.186 1811 Planarity : 0.004 0.049 1909 Dihedral : 9.107 59.700 1715 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.23 % Allowed : 14.27 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.22), residues: 1439 helix: 1.12 (0.18), residues: 838 sheet: -0.65 (0.76), residues: 46 loop : -1.66 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 364 HIS 0.003 0.001 HIS A 451 PHE 0.011 0.001 PHE A 527 TYR 0.020 0.001 TYR A 381 ARG 0.013 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 1.321 Fit side-chains REVERT: A 130 MET cc_start: 0.8454 (ttp) cc_final: 0.8163 (ttm) REVERT: A 413 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: B 25 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7823 (pp) REVERT: B 383 MET cc_start: 0.5889 (ttp) cc_final: 0.5271 (tmm) REVERT: B 535 MET cc_start: 0.7463 (mmm) cc_final: 0.7216 (mtp) outliers start: 14 outliers final: 12 residues processed: 118 average time/residue: 0.2222 time to fit residues: 38.9785 Evaluate side-chains 123 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 608 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 87 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 108 optimal weight: 0.0570 chunk 125 optimal weight: 8.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11205 Z= 0.149 Angle : 0.482 6.958 15204 Z= 0.244 Chirality : 0.038 0.171 1811 Planarity : 0.004 0.050 1909 Dihedral : 8.693 59.169 1715 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.50 % Allowed : 14.54 % 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: 0.19 (0.22), residues: 1439 helix: 1.26 (0.18), residues: 843 sheet: -0.70 (0.76), residues: 46 loop : -1.62 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 364 HIS 0.002 0.000 HIS A 451 PHE 0.011 0.001 PHE A 527 TYR 0.020 0.001 TYR A 381 ARG 0.003 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.170 Fit side-chains REVERT: A 130 MET cc_start: 0.8455 (ttp) cc_final: 0.8129 (ttm) REVERT: A 413 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7203 (mt-10) REVERT: B 25 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7798 (pp) REVERT: B 383 MET cc_start: 0.5815 (ttp) cc_final: 0.5194 (tmm) REVERT: B 431 LEU cc_start: 0.6910 (mm) cc_final: 0.6705 (tt) REVERT: B 535 MET cc_start: 0.7335 (mmm) cc_final: 0.7119 (mtp) outliers start: 17 outliers final: 14 residues processed: 125 average time/residue: 0.2017 time to fit residues: 37.8920 Evaluate side-chains 123 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11205 Z= 0.245 Angle : 0.524 7.010 15204 Z= 0.264 Chirality : 0.040 0.180 1811 Planarity : 0.004 0.049 1909 Dihedral : 8.742 58.978 1715 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.50 % Allowed : 14.71 % Favored : 83.79 % 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: 0.16 (0.22), residues: 1439 helix: 1.16 (0.18), residues: 844 sheet: -0.76 (0.76), residues: 46 loop : -1.51 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 300 HIS 0.003 0.001 HIS A 451 PHE 0.010 0.001 PHE A 373 TYR 0.019 0.001 TYR A 381 ARG 0.003 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 1.224 Fit side-chains REVERT: A 130 MET cc_start: 0.8464 (ttp) cc_final: 0.8176 (ttm) REVERT: A 413 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: B 25 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7841 (pp) REVERT: B 383 MET cc_start: 0.5968 (ttp) cc_final: 0.5313 (tmm) REVERT: B 535 MET cc_start: 0.7448 (mmm) cc_final: 0.7122 (mtp) outliers start: 17 outliers final: 14 residues processed: 121 average time/residue: 0.2086 time to fit residues: 38.1102 Evaluate side-chains 123 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 30.0000 chunk 142 optimal weight: 0.0030 chunk 131 optimal weight: 0.7980 chunk 113 optimal weight: 0.0000 chunk 11 optimal weight: 0.0770 chunk 87 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.3152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 GLN A 482 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11205 Z= 0.132 Angle : 0.491 7.669 15204 Z= 0.247 Chirality : 0.038 0.165 1811 Planarity : 0.004 0.050 1909 Dihedral : 8.293 59.893 1715 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.32 % Allowed : 15.07 % Favored : 83.61 % 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: 0.35 (0.22), residues: 1439 helix: 1.41 (0.18), residues: 839 sheet: -1.69 (0.68), residues: 56 loop : -1.45 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 364 HIS 0.002 0.000 HIS A 451 PHE 0.010 0.001 PHE A 527 TYR 0.019 0.001 TYR A 381 ARG 0.002 0.000 ARG B 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.253 Fit side-chains REVERT: A 130 MET cc_start: 0.8428 (ttp) cc_final: 0.8125 (ttm) REVERT: A 413 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7173 (mt-10) REVERT: B 25 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7749 (pp) REVERT: B 383 MET cc_start: 0.5820 (ttp) cc_final: 0.5163 (tmm) REVERT: B 431 LEU cc_start: 0.6910 (mm) cc_final: 0.6700 (tt) outliers start: 15 outliers final: 13 residues processed: 125 average time/residue: 0.2148 time to fit residues: 40.8858 Evaluate side-chains 123 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 99 optimal weight: 0.3980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 GLN A 482 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.140968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108313 restraints weight = 14497.840| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.35 r_work: 0.2947 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11205 Z= 0.214 Angle : 0.519 11.280 15204 Z= 0.259 Chirality : 0.039 0.227 1811 Planarity : 0.004 0.050 1909 Dihedral : 8.328 58.162 1715 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.50 % Allowed : 14.98 % Favored : 83.52 % 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: 0.29 (0.22), residues: 1439 helix: 1.39 (0.18), residues: 831 sheet: -1.47 (0.68), residues: 56 loop : -1.53 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 364 HIS 0.003 0.001 HIS A 451 PHE 0.010 0.001 PHE A 527 TYR 0.019 0.001 TYR A 381 ARG 0.002 0.000 ARG B 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2351.27 seconds wall clock time: 44 minutes 42.02 seconds (2682.02 seconds total)