Starting phenix.real_space_refine on Wed Nov 15 07:45:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrh_14914/11_2023/7zrh_14914_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrh_14914/11_2023/7zrh_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_14914/11_2023/7zrh_14914.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrh_14914/11_2023/7zrh_14914.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrh_14914/11_2023/7zrh_14914_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrh_14914/11_2023/7zrh_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 6.93, per 1000 atoms: 0.63 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: 4.78 Conformation dependent library (CDL) restraints added in 2.4 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: 2.59 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: 3.39 Time building geometry restraints manager: 5.14 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: 5931 17.95 - 35.90: 595 35.90 - 53.85: 129 53.85 - 71.80: 29 71.80 - 89.75: 11 Dihedral angle restraints: 6695 sinusoidal: 2589 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 6692 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.010 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: 0.000 Extract box with map and model: 3.460 Check model and map are aligned: 0.220 Set scattering table: 0.170 Process input model: 37.190 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 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:3.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.120 ------------------------------------------------------------------------------- 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 : 15.558 89.752 4057 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 *********************** 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 : 1.212 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2349 time to fit residues: 52.0557 Evaluate side-chains 118 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.266 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6640 ------------------------------------------------------------------------------- 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: 10.0000 chunk 112 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 overall best weight: 2.1794 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11205 Z= 0.324 Angle : 0.582 7.214 15204 Z= 0.295 Chirality : 0.041 0.148 1811 Planarity : 0.005 0.052 1909 Dihedral : 10.345 58.510 1675 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.79 % Allowed : 7.40 % Favored : 91.81 % 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: -0.53 (0.21), residues: 1439 helix: 0.66 (0.17), residues: 844 sheet: -1.27 (0.75), residues: 56 loop : -1.87 (0.24), residues: 539 *********************** 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 134 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 1.285 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 128 average time/residue: 0.2571 time to fit residues: 47.9348 Evaluate side-chains 116 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 1.245 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1100 time to fit residues: 2.3608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 88 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN B 80 ASN ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.080 11205 Z= 0.630 Angle : 0.735 8.523 15204 Z= 0.371 Chirality : 0.047 0.222 1811 Planarity : 0.005 0.049 1909 Dihedral : 10.296 59.793 1675 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.06 % Allowed : 11.98 % Favored : 86.96 % 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: -0.98 (0.21), residues: 1439 helix: 0.26 (0.17), residues: 831 sheet: -0.71 (0.74), residues: 52 loop : -2.04 (0.24), residues: 556 *********************** 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 132 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 1.283 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 129 average time/residue: 0.2275 time to fit residues: 43.3988 Evaluate side-chains 118 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1068 time to fit residues: 2.7145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 16 GLN B 217 ASN B 361 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2129 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= 0.191 Angle : 0.526 6.923 15204 Z= 0.267 Chirality : 0.039 0.173 1811 Planarity : 0.004 0.053 1909 Dihedral : 9.530 59.834 1675 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.70 % Allowed : 13.39 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.22), residues: 1439 helix: 0.76 (0.18), residues: 843 sheet: -0.67 (0.78), residues: 46 loop : -1.74 (0.25), residues: 550 *********************** 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: 8 poor density : 117 time to evaluate : 1.566 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 123 average time/residue: 0.2239 time to fit residues: 40.8262 Evaluate side-chains 117 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 1.213 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1001 time to fit residues: 2.7246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 4.9990 chunk 78 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11205 Z= 0.201 Angle : 0.514 6.978 15204 Z= 0.261 Chirality : 0.039 0.214 1811 Planarity : 0.004 0.050 1909 Dihedral : 9.027 59.619 1675 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.79 % Allowed : 14.19 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.22), residues: 1439 helix: 0.95 (0.18), residues: 841 sheet: -0.78 (0.76), residues: 46 loop : -1.74 (0.25), residues: 552 *********************** 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 124 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 1.393 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 121 average time/residue: 0.2347 time to fit residues: 42.1372 Evaluate side-chains 113 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 110 time to evaluate : 1.238 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1139 time to fit residues: 2.3266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 138 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.8174 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11205 Z= 0.161 Angle : 0.499 7.259 15204 Z= 0.252 Chirality : 0.038 0.192 1811 Planarity : 0.004 0.051 1909 Dihedral : 8.488 59.377 1675 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.62 % Allowed : 14.98 % 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: 0.03 (0.22), residues: 1439 helix: 1.14 (0.18), residues: 835 sheet: -1.12 (0.72), residues: 51 loop : -1.64 (0.25), residues: 553 *********************** 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 121 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 1.348 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 119 average time/residue: 0.2138 time to fit residues: 38.7897 Evaluate side-chains 112 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1027 time to fit residues: 2.3026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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: 0.8216 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11205 Z= 0.256 Angle : 0.526 7.010 15204 Z= 0.268 Chirality : 0.040 0.222 1811 Planarity : 0.004 0.050 1909 Dihedral : 8.408 59.197 1675 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.79 % Allowed : 15.42 % 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: 0.05 (0.22), residues: 1439 helix: 1.09 (0.18), residues: 830 sheet: -1.11 (0.73), residues: 51 loop : -1.49 (0.25), residues: 558 *********************** 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 118 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 1.319 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 118 average time/residue: 0.2136 time to fit residues: 38.1686 Evaluate side-chains 114 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 1.208 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1031 time to fit residues: 3.0403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.8193 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11205 Z= 0.204 Angle : 0.506 6.989 15204 Z= 0.257 Chirality : 0.039 0.206 1811 Planarity : 0.004 0.051 1909 Dihedral : 8.140 59.524 1675 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.18 % Allowed : 15.59 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1439 helix: 1.16 (0.18), residues: 829 sheet: -0.69 (0.77), residues: 46 loop : -1.49 (0.25), residues: 564 *********************** 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 112 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 1.263 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 0.2200 time to fit residues: 36.7381 Evaluate side-chains 108 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 1.296 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1029 time to fit residues: 1.8405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8186 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11205 Z= 0.197 Angle : 0.512 7.072 15204 Z= 0.259 Chirality : 0.039 0.203 1811 Planarity : 0.004 0.051 1909 Dihedral : 7.961 59.613 1675 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.18 % Allowed : 15.95 % Favored : 83.88 % 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: 1.17 (0.18), residues: 831 sheet: -0.67 (0.75), residues: 46 loop : -1.48 (0.25), residues: 562 *********************** 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 110 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 1.209 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 109 average time/residue: 0.2208 time to fit residues: 35.8706 Evaluate side-chains 109 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 1.295 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1206 time to fit residues: 2.1352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 94 optimal weight: 0.0050 chunk 142 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 113 optimal weight: 0.0170 chunk 11 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 overall best weight: 0.5232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11205 Z= 0.149 Angle : 0.497 8.132 15204 Z= 0.250 Chirality : 0.038 0.190 1811 Planarity : 0.004 0.052 1909 Dihedral : 7.630 59.728 1675 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 16.48 % 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: 0.26 (0.22), residues: 1439 helix: 1.29 (0.18), residues: 839 sheet: -1.53 (0.68), residues: 56 loop : -1.44 (0.25), residues: 544 ********************** 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 113 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.337 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2263 time to fit residues: 38.7037 Evaluate side-chains 109 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.380 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.106241 restraints weight = 14549.310| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.26 r_work: 0.2950 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11205 Z= 0.245 Angle : 0.546 11.633 15204 Z= 0.271 Chirality : 0.040 0.205 1811 Planarity : 0.004 0.050 1909 Dihedral : 7.759 57.674 1675 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.18 % Allowed : 16.83 % Favored : 83.00 % 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: 0.22 (0.22), residues: 1439 helix: 1.19 (0.18), residues: 835 sheet: -0.59 (0.75), residues: 46 loop : -1.41 (0.26), residues: 558 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2228.23 seconds wall clock time: 45 minutes 3.65 seconds (2703.65 seconds total)