Starting phenix.real_space_refine on Mon Mar 11 10:21:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocy_12816/03_2024/7ocy_12816_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocy_12816/03_2024/7ocy_12816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocy_12816/03_2024/7ocy_12816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocy_12816/03_2024/7ocy_12816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocy_12816/03_2024/7ocy_12816_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocy_12816/03_2024/7ocy_12816_neut.pdb" } resolution = 4.25 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= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 5051 2.51 5 N 1423 2.21 5 O 1488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 41": "OE1" <-> "OE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "B TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7994 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 3613 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 206} Link IDs: {'PTRANS': 13, 'TRANS': 543} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 715 Unresolved non-hydrogen angles: 909 Unresolved non-hydrogen dihedrals: 569 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 15, 'TYR:plan': 5, 'ASN:plan1': 6, 'HIS:plan': 5, 'PHE:plan': 8, 'GLU:plan': 25, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 383 Chain: "B" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 3852 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 10, 'TRANS': 567} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 742 Unresolved non-hydrogen angles: 955 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 83 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 16, 'TYR:plan': 5, 'ASN:plan1': 16, 'HIS:plan': 7, 'PHE:plan': 9, 'GLU:plan': 27, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 414 Chain: "C" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 529 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 3, 'TRANS': 104} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 291 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 222 Time building chain proxies: 5.13, per 1000 atoms: 0.64 Number of scatterers: 7994 At special positions: 0 Unit cell: (76.96, 83.2, 165.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1488 8.00 N 1423 7.00 C 5051 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.98 Conformation dependent library (CDL) restraints added in 2.1 seconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 7 sheets defined 66.5% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 11 through 46 removed outlier: 4.019A pdb=" N ILE A 17 " --> pdb=" O GLY A 13 " (cutoff:3.500A) Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 47 through 97 Processing helix chain 'A' and resid 99 through 105 Processing helix chain 'A' and resid 107 through 132 removed outlier: 4.268A pdb=" N ASP A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 151 removed outlier: 4.034A pdb=" N PHE A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 200 removed outlier: 3.732A pdb=" N ILE A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE A 182 " --> pdb=" O LYS A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 208 through 258 removed outlier: 4.304A pdb=" N ASN A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Proline residue: A 240 - end of helix removed outlier: 4.033A pdb=" N SER A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 311 removed outlier: 4.357A pdb=" N ALA A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER A 296 " --> pdb=" O MET A 292 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG A 297 " --> pdb=" O MET A 293 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A 298 " --> pdb=" O MET A 294 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.987A pdb=" N ILE A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 405 removed outlier: 3.530A pdb=" N LEU A 402 " --> pdb=" O ASN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 Processing helix chain 'A' and resid 432 through 444 Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 468 through 483 removed outlier: 4.646A pdb=" N GLY A 483 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.705A pdb=" N VAL A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 555 removed outlier: 4.040A pdb=" N ALA A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 563 removed outlier: 4.411A pdb=" N GLN A 559 " --> pdb=" O ASN A 555 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU A 560 " --> pdb=" O PRO A 556 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 561 " --> pdb=" O VAL A 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 16 removed outlier: 3.772A pdb=" N TYR B 14 " --> pdb=" O PHE B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 60 removed outlier: 3.857A pdb=" N PHE B 26 " --> pdb=" O PHE B 22 " (cutoff:3.500A) Proline residue: B 40 - end of helix removed outlier: 3.674A pdb=" N GLN B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 112 Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.581A pdb=" N PHE B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 133 Processing helix chain 'B' and resid 133 through 167 removed outlier: 4.753A pdb=" N LEU B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU B 147 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN B 148 " --> pdb=" O GLN B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 177 through 224 removed outlier: 6.567A pdb=" N ARG B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 220 " --> pdb=" O GLY B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 253 Processing helix chain 'B' and resid 253 through 280 Processing helix chain 'B' and resid 283 through 330 Proline residue: B 304 - end of helix removed outlier: 4.155A pdb=" N SER B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N MET B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 397 removed outlier: 4.430A pdb=" N MET B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 394 " --> pdb=" O THR B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 425 Processing helix chain 'B' and resid 439 through 446 Processing helix chain 'B' and resid 454 through 463 removed outlier: 3.941A pdb=" N GLN B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 Processing helix chain 'B' and resid 474 through 478 Processing helix chain 'B' and resid 488 through 504 removed outlier: 3.726A pdb=" N LYS B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN B 493 " --> pdb=" O THR B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 536 removed outlier: 4.194A pdb=" N GLY B 535 " --> pdb=" O GLU B 531 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 549 removed outlier: 3.568A pdb=" N LEU B 549 " --> pdb=" O LYS B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 574 Processing helix chain 'B' and resid 576 through 583 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 353 removed outlier: 5.941A pdb=" N LYS A 347 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SER A 335 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE A 349 " --> pdb=" O HIS A 333 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL A 334 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLU A 384 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 406 through 408 removed outlier: 6.764A pdb=" N MET A 358 " --> pdb=" O ARG A 533 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU A 535 " --> pdb=" O MET A 358 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLY A 360 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU A 537 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL A 362 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 534 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLU A 545 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 536 " --> pdb=" O VAL A 543 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 418 through 419 Processing sheet with id=AA4, first strand: chain 'B' and resid 366 through 369 removed outlier: 4.749A pdb=" N VAL B 355 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL B 355 " --> pdb=" O GLU B 404 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU B 404 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 426 through 429 removed outlier: 5.931A pdb=" N LEU B 508 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE B 541 " --> pdb=" O LEU B 508 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 510 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N MET B 378 " --> pdb=" O ARG B 553 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ILE B 555 " --> pdb=" O MET B 378 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ALA B 380 " --> pdb=" O ILE B 555 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU B 557 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B 382 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU B 564 " --> pdb=" O VAL B 556 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 7 through 10 Processing sheet with id=AA7, first strand: chain 'C' and resid 14 through 16 removed outlier: 6.997A pdb=" N VAL C 15 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE C 98 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ARG C 33 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ARG C 38 " --> pdb=" O MET C 47 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N MET C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1947 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.81 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2776 1.34 - 1.46: 1649 1.46 - 1.58: 3585 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 8074 Sorted by residual: bond pdb=" N THR B 2 " pdb=" CA THR B 2 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.12e+00 bond pdb=" N GLN C 6 " pdb=" CA GLN C 6 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N ASP A 2 " pdb=" CA ASP A 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" C GLU A 484 " pdb=" O GLU A 484 " ideal model delta sigma weight residual 1.233 1.241 -0.008 4.80e-03 4.34e+04 2.80e+00 bond pdb=" CA THR B 363 " pdb=" C THR B 363 " ideal model delta sigma weight residual 1.531 1.524 0.008 7.40e-03 1.83e+04 1.03e+00 ... (remaining 8069 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.89: 103 106.89 - 113.66: 4618 113.66 - 120.43: 3050 120.43 - 127.19: 3221 127.19 - 133.96: 27 Bond angle restraints: 11019 Sorted by residual: angle pdb=" N ILE A 561 " pdb=" CA ILE A 561 " pdb=" C ILE A 561 " ideal model delta sigma weight residual 111.90 107.47 4.43 8.10e-01 1.52e+00 2.98e+01 angle pdb=" N VAL C 48 " pdb=" CA VAL C 48 " pdb=" C VAL C 48 " ideal model delta sigma weight residual 111.62 108.56 3.06 7.90e-01 1.60e+00 1.50e+01 angle pdb=" N ILE A 376 " pdb=" CA ILE A 376 " pdb=" C ILE A 376 " ideal model delta sigma weight residual 112.35 107.76 4.59 1.20e+00 6.94e-01 1.46e+01 angle pdb=" C ILE A 136 " pdb=" CA ILE A 136 " pdb=" CB ILE A 136 " ideal model delta sigma weight residual 114.00 109.50 4.50 1.31e+00 5.83e-01 1.18e+01 angle pdb=" N ARG B 558 " pdb=" CA ARG B 558 " pdb=" C ARG B 558 " ideal model delta sigma weight residual 110.80 104.59 6.21 2.13e+00 2.20e-01 8.51e+00 ... (remaining 11014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4463 17.53 - 35.05: 260 35.05 - 52.58: 43 52.58 - 70.11: 6 70.11 - 87.64: 6 Dihedral angle restraints: 4778 sinusoidal: 1208 harmonic: 3570 Sorted by residual: dihedral pdb=" CA ASN C 32 " pdb=" C ASN C 32 " pdb=" N ARG C 33 " pdb=" CA ARG C 33 " ideal model delta harmonic sigma weight residual 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA LEU B 557 " pdb=" C LEU B 557 " pdb=" N ARG B 558 " pdb=" CA ARG B 558 " ideal model delta harmonic sigma weight residual 180.00 160.17 19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLY A 270 " pdb=" C GLY A 270 " pdb=" N VAL A 271 " pdb=" CA VAL A 271 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 4775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 892 0.031 - 0.062: 338 0.062 - 0.093: 107 0.093 - 0.124: 45 0.124 - 0.156: 4 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA ILE B 541 " pdb=" N ILE B 541 " pdb=" C ILE B 541 " pdb=" CB ILE B 541 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA ILE A 519 " pdb=" N ILE A 519 " pdb=" C ILE A 519 " pdb=" CB ILE A 519 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA VAL B 356 " pdb=" N VAL B 356 " pdb=" C VAL B 356 " pdb=" CB VAL B 356 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1383 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 303 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO B 304 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 304 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 304 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 31 " 0.012 2.00e-02 2.50e+03 9.44e-03 2.23e+00 pdb=" CG TRP A 31 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 31 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 31 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 31 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 31 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 31 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 31 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 31 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 31 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 210 " -0.007 2.00e-02 2.50e+03 1.41e-02 2.00e+00 pdb=" C MET B 210 " 0.024 2.00e-02 2.50e+03 pdb=" O MET B 210 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP B 211 " -0.008 2.00e-02 2.50e+03 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 77 2.56 - 3.15: 7525 3.15 - 3.73: 12918 3.73 - 4.32: 15305 4.32 - 4.90: 25084 Nonbonded interactions: 60909 Sorted by model distance: nonbonded pdb=" O GLU A 222 " pdb=" OG1 THR A 225 " model vdw 1.980 2.440 nonbonded pdb=" O VAL A 250 " pdb=" OG SER A 253 " model vdw 2.047 2.440 nonbonded pdb=" OE2 GLU A 89 " pdb=" NE ARG A 93 " model vdw 2.077 2.520 nonbonded pdb=" O LYS A 219 " pdb=" OE1 GLU A 223 " model vdw 2.158 3.040 nonbonded pdb=" NZ LYS A 94 " pdb=" O MET A 309 " model vdw 2.255 2.520 ... (remaining 60904 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 group one per residue 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.320 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 28.300 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:3.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8074 Z= 0.203 Angle : 0.616 6.212 11019 Z= 0.391 Chirality : 0.039 0.156 1386 Planarity : 0.003 0.042 1450 Dihedral : 12.493 87.635 2462 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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 (0.24), residues: 1231 helix: 0.68 (0.18), residues: 756 sheet: -0.97 (0.45), residues: 119 loop : -1.15 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 31 HIS 0.001 0.000 HIS A 179 PHE 0.015 0.001 PHE B 86 TYR 0.017 0.002 TYR B 12 ARG 0.002 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9616 (mm) cc_final: 0.9406 (mp) REVERT: A 118 ASP cc_start: 0.9208 (m-30) cc_final: 0.8883 (m-30) REVERT: A 196 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8312 (tm-30) REVERT: A 277 TYR cc_start: 0.8650 (m-80) cc_final: 0.8375 (m-80) REVERT: A 287 ILE cc_start: 0.9531 (tt) cc_final: 0.9298 (tt) REVERT: A 307 GLU cc_start: 0.9332 (pt0) cc_final: 0.8659 (pp20) REVERT: B 67 PHE cc_start: 0.9357 (t80) cc_final: 0.9142 (t80) REVERT: B 71 ILE cc_start: 0.9676 (mm) cc_final: 0.9471 (mm) REVERT: B 136 ASP cc_start: 0.9160 (m-30) cc_final: 0.8897 (m-30) REVERT: B 210 MET cc_start: 0.9661 (mtp) cc_final: 0.9297 (mtp) REVERT: B 225 LEU cc_start: 0.9082 (mt) cc_final: 0.8786 (mt) REVERT: B 327 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8572 (mt-10) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1633 time to fit residues: 36.6215 Evaluate side-chains 121 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 110 optimal weight: 20.0000 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8074 Z= 0.313 Angle : 0.659 8.115 11019 Z= 0.369 Chirality : 0.042 0.174 1386 Planarity : 0.003 0.030 1450 Dihedral : 4.450 22.257 1274 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.18 % Allowed : 8.71 % Favored : 91.11 % 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: 0.14 (0.23), residues: 1231 helix: 0.73 (0.18), residues: 765 sheet: -0.69 (0.45), residues: 118 loop : -0.86 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 31 HIS 0.002 0.001 HIS A 7 PHE 0.023 0.002 PHE B 86 TYR 0.031 0.002 TYR B 88 ARG 0.005 0.001 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9176 (tpt) cc_final: 0.8954 (tpp) REVERT: A 118 ASP cc_start: 0.9231 (m-30) cc_final: 0.8915 (m-30) REVERT: A 151 LEU cc_start: 0.9332 (mt) cc_final: 0.9015 (mp) REVERT: A 196 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8455 (tm-30) REVERT: A 223 GLU cc_start: 0.8974 (mp0) cc_final: 0.8706 (mp0) REVERT: A 277 TYR cc_start: 0.8810 (m-80) cc_final: 0.8556 (m-80) REVERT: A 287 ILE cc_start: 0.9530 (tt) cc_final: 0.9305 (tt) REVERT: B 35 LEU cc_start: 0.8895 (tp) cc_final: 0.8541 (tp) REVERT: B 58 MET cc_start: 0.9413 (mmp) cc_final: 0.9157 (mmm) REVERT: B 71 ILE cc_start: 0.9718 (mm) cc_final: 0.9483 (mm) REVERT: B 122 HIS cc_start: 0.8423 (m90) cc_final: 0.7950 (m90) REVERT: B 136 ASP cc_start: 0.9199 (m-30) cc_final: 0.8929 (m-30) REVERT: B 210 MET cc_start: 0.9647 (mtp) cc_final: 0.9252 (mtp) REVERT: B 225 LEU cc_start: 0.9058 (mt) cc_final: 0.8786 (mt) REVERT: B 293 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.8138 (ppp) REVERT: B 324 ARG cc_start: 0.9450 (mtt90) cc_final: 0.8742 (mtt90) REVERT: B 327 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8565 (mt-10) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.1598 time to fit residues: 32.3896 Evaluate side-chains 124 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 30 optimal weight: 0.0980 chunk 110 optimal weight: 10.0000 chunk 119 optimal weight: 40.0000 chunk 98 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8074 Z= 0.347 Angle : 0.681 9.148 11019 Z= 0.382 Chirality : 0.043 0.195 1386 Planarity : 0.003 0.036 1450 Dihedral : 4.440 22.455 1274 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.24), residues: 1231 helix: 0.62 (0.18), residues: 767 sheet: -0.68 (0.48), residues: 114 loop : -0.90 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 31 HIS 0.003 0.001 HIS B 13 PHE 0.024 0.002 PHE B 86 TYR 0.031 0.003 TYR B 12 ARG 0.002 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8507 (t0) cc_final: 0.8290 (t0) REVERT: A 118 ASP cc_start: 0.9267 (m-30) cc_final: 0.8945 (m-30) REVERT: A 196 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8381 (tm-30) REVERT: A 275 MET cc_start: 0.9322 (ppp) cc_final: 0.9088 (ppp) REVERT: A 277 TYR cc_start: 0.8894 (m-80) cc_final: 0.8423 (m-80) REVERT: A 287 ILE cc_start: 0.9458 (tt) cc_final: 0.9258 (tt) REVERT: B 35 LEU cc_start: 0.9010 (tp) cc_final: 0.8769 (tp) REVERT: B 58 MET cc_start: 0.9428 (mmp) cc_final: 0.9156 (mmm) REVERT: B 71 ILE cc_start: 0.9767 (mm) cc_final: 0.9481 (mm) REVERT: B 122 HIS cc_start: 0.8419 (m90) cc_final: 0.7946 (m90) REVERT: B 136 ASP cc_start: 0.9161 (m-30) cc_final: 0.8868 (m-30) REVERT: B 210 MET cc_start: 0.9655 (mtp) cc_final: 0.9271 (mtp) REVERT: B 225 LEU cc_start: 0.9029 (mt) cc_final: 0.8799 (mt) REVERT: B 324 ARG cc_start: 0.9413 (mtt90) cc_final: 0.8932 (mtt90) REVERT: B 327 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8570 (mt-10) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1539 time to fit residues: 32.4840 Evaluate side-chains 119 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 98 optimal weight: 0.0050 overall best weight: 1.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8074 Z= 0.199 Angle : 0.573 8.197 11019 Z= 0.315 Chirality : 0.041 0.185 1386 Planarity : 0.003 0.034 1450 Dihedral : 4.150 20.443 1274 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.24), residues: 1231 helix: 1.03 (0.19), residues: 770 sheet: -0.47 (0.48), residues: 114 loop : -0.86 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 31 HIS 0.002 0.001 HIS B 13 PHE 0.025 0.002 PHE B 67 TYR 0.025 0.002 TYR B 12 ARG 0.002 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.9189 (m-30) cc_final: 0.8625 (m-30) REVERT: A 196 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8348 (tm-30) REVERT: A 223 GLU cc_start: 0.8853 (mp0) cc_final: 0.8560 (mp0) REVERT: A 275 MET cc_start: 0.9372 (ppp) cc_final: 0.9027 (ppp) REVERT: A 277 TYR cc_start: 0.8736 (m-80) cc_final: 0.8420 (m-80) REVERT: A 282 MET cc_start: 0.8793 (tmm) cc_final: 0.8561 (tmm) REVERT: A 287 ILE cc_start: 0.9440 (tt) cc_final: 0.9237 (tt) REVERT: A 304 ARG cc_start: 0.9264 (ptp-110) cc_final: 0.8981 (ptp90) REVERT: B 35 LEU cc_start: 0.8925 (tp) cc_final: 0.8649 (tp) REVERT: B 58 MET cc_start: 0.9442 (mmp) cc_final: 0.9152 (mmm) REVERT: B 71 ILE cc_start: 0.9763 (mm) cc_final: 0.9547 (mm) REVERT: B 122 HIS cc_start: 0.8358 (m90) cc_final: 0.7890 (m90) REVERT: B 136 ASP cc_start: 0.9108 (m-30) cc_final: 0.8879 (m-30) REVERT: B 210 MET cc_start: 0.9613 (mtp) cc_final: 0.9279 (mtp) REVERT: B 225 LEU cc_start: 0.8988 (mt) cc_final: 0.8745 (mt) REVERT: B 324 ARG cc_start: 0.9379 (mtt90) cc_final: 0.8964 (mtt90) REVERT: B 327 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8488 (mt-10) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1652 time to fit residues: 36.6011 Evaluate side-chains 134 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8074 Z= 0.183 Angle : 0.571 6.891 11019 Z= 0.308 Chirality : 0.041 0.199 1386 Planarity : 0.003 0.038 1450 Dihedral : 3.973 18.365 1274 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % 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: 0.68 (0.24), residues: 1231 helix: 1.17 (0.19), residues: 770 sheet: -0.16 (0.49), residues: 104 loop : -0.81 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 31 HIS 0.002 0.001 HIS A 179 PHE 0.021 0.002 PHE B 86 TYR 0.012 0.002 TYR B 302 ARG 0.005 0.001 ARG B 130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8672 (p0) cc_final: 0.8208 (p0) REVERT: A 118 ASP cc_start: 0.9165 (m-30) cc_final: 0.8685 (m-30) REVERT: A 196 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8225 (tm-30) REVERT: A 275 MET cc_start: 0.9375 (ppp) cc_final: 0.9000 (ppp) REVERT: A 277 TYR cc_start: 0.8426 (m-80) cc_final: 0.8140 (m-80) REVERT: A 282 MET cc_start: 0.8766 (tmm) cc_final: 0.8404 (tmm) REVERT: A 287 ILE cc_start: 0.9423 (tt) cc_final: 0.9212 (tt) REVERT: A 304 ARG cc_start: 0.9254 (ptp-110) cc_final: 0.9038 (ptp90) REVERT: B 35 LEU cc_start: 0.9004 (tp) cc_final: 0.8764 (tp) REVERT: B 58 MET cc_start: 0.9429 (mmp) cc_final: 0.9173 (mmm) REVERT: B 71 ILE cc_start: 0.9779 (mm) cc_final: 0.9559 (mm) REVERT: B 122 HIS cc_start: 0.8293 (m90) cc_final: 0.7839 (m90) REVERT: B 130 ARG cc_start: 0.8481 (tpp80) cc_final: 0.8101 (tpp80) REVERT: B 136 ASP cc_start: 0.9149 (m-30) cc_final: 0.8927 (m-30) REVERT: B 210 MET cc_start: 0.9605 (mtp) cc_final: 0.9238 (mtp) REVERT: B 327 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8486 (mt-10) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1621 time to fit residues: 35.2848 Evaluate side-chains 126 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 118 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8074 Z= 0.171 Angle : 0.580 9.151 11019 Z= 0.309 Chirality : 0.040 0.156 1386 Planarity : 0.003 0.030 1450 Dihedral : 3.875 17.099 1274 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.24), residues: 1231 helix: 1.25 (0.19), residues: 767 sheet: 0.11 (0.49), residues: 102 loop : -0.80 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 172 HIS 0.002 0.001 HIS A 179 PHE 0.020 0.001 PHE B 86 TYR 0.029 0.002 TYR B 302 ARG 0.005 0.000 ARG B 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.9182 (m-30) cc_final: 0.8740 (m-30) REVERT: A 196 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8269 (tm-30) REVERT: A 223 GLU cc_start: 0.8837 (mp0) cc_final: 0.8460 (pm20) REVERT: A 275 MET cc_start: 0.9280 (ppp) cc_final: 0.8954 (ppp) REVERT: A 282 MET cc_start: 0.8759 (tmm) cc_final: 0.8343 (tmm) REVERT: A 286 ILE cc_start: 0.9418 (pt) cc_final: 0.9195 (pt) REVERT: A 287 ILE cc_start: 0.9404 (tt) cc_final: 0.9196 (tt) REVERT: B 35 LEU cc_start: 0.9013 (tp) cc_final: 0.8642 (tp) REVERT: B 58 MET cc_start: 0.9424 (mmp) cc_final: 0.9172 (mmm) REVERT: B 67 PHE cc_start: 0.9279 (t80) cc_final: 0.8800 (t80) REVERT: B 71 ILE cc_start: 0.9769 (mm) cc_final: 0.9529 (mm) REVERT: B 122 HIS cc_start: 0.8262 (m90) cc_final: 0.7819 (m90) REVERT: B 136 ASP cc_start: 0.9172 (m-30) cc_final: 0.8909 (m-30) REVERT: B 210 MET cc_start: 0.9600 (mtp) cc_final: 0.9226 (mtp) REVERT: B 324 ARG cc_start: 0.9471 (mtt90) cc_final: 0.8988 (mtp85) REVERT: B 327 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8496 (mt-10) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1696 time to fit residues: 36.8434 Evaluate side-chains 128 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8074 Z= 0.175 Angle : 0.570 8.151 11019 Z= 0.307 Chirality : 0.041 0.253 1386 Planarity : 0.003 0.032 1450 Dihedral : 3.799 17.242 1274 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.18 % Allowed : 1.27 % Favored : 98.55 % 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: 0.82 (0.24), residues: 1231 helix: 1.23 (0.19), residues: 771 sheet: 0.07 (0.49), residues: 104 loop : -0.69 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 31 HIS 0.002 0.001 HIS A 179 PHE 0.018 0.001 PHE B 86 TYR 0.048 0.002 TYR A 277 ARG 0.009 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8966 (tpt) cc_final: 0.8603 (tmm) REVERT: A 75 PHE cc_start: 0.9213 (m-80) cc_final: 0.8964 (m-10) REVERT: A 131 GLN cc_start: 0.8657 (tt0) cc_final: 0.8426 (tt0) REVERT: A 138 PHE cc_start: 0.8715 (t80) cc_final: 0.8460 (t80) REVERT: A 196 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8129 (tm-30) REVERT: A 223 GLU cc_start: 0.8833 (mp0) cc_final: 0.8557 (mp0) REVERT: A 282 MET cc_start: 0.8743 (tmm) cc_final: 0.8305 (tmm) REVERT: A 286 ILE cc_start: 0.9418 (pt) cc_final: 0.9176 (pt) REVERT: A 287 ILE cc_start: 0.9390 (tt) cc_final: 0.9182 (tt) REVERT: B 35 LEU cc_start: 0.9026 (tp) cc_final: 0.8647 (tp) REVERT: B 58 MET cc_start: 0.9417 (mmp) cc_final: 0.9167 (mmm) REVERT: B 67 PHE cc_start: 0.9277 (t80) cc_final: 0.8782 (t80) REVERT: B 71 ILE cc_start: 0.9769 (mm) cc_final: 0.9524 (mm) REVERT: B 122 HIS cc_start: 0.8256 (m90) cc_final: 0.7783 (m90) REVERT: B 136 ASP cc_start: 0.9186 (m-30) cc_final: 0.8896 (m-30) REVERT: B 210 MET cc_start: 0.9573 (mtp) cc_final: 0.9250 (mtp) REVERT: B 257 MET cc_start: 0.9231 (mmm) cc_final: 0.8855 (tmm) REVERT: B 324 ARG cc_start: 0.9444 (mtt90) cc_final: 0.8772 (mtm-85) REVERT: B 327 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8473 (mt-10) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.1465 time to fit residues: 33.0045 Evaluate side-chains 126 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 30.0000 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 326 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8074 Z= 0.171 Angle : 0.566 7.669 11019 Z= 0.304 Chirality : 0.040 0.146 1386 Planarity : 0.003 0.028 1450 Dihedral : 3.710 18.276 1274 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.18 % Allowed : 2.72 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.24), residues: 1231 helix: 1.28 (0.19), residues: 772 sheet: 0.25 (0.50), residues: 104 loop : -0.59 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 31 HIS 0.002 0.000 HIS A 179 PHE 0.021 0.001 PHE B 86 TYR 0.013 0.002 TYR B 302 ARG 0.006 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.9222 (m-80) cc_final: 0.8953 (m-10) REVERT: A 133 LEU cc_start: 0.9220 (mm) cc_final: 0.8754 (mm) REVERT: A 138 PHE cc_start: 0.8696 (t80) cc_final: 0.8443 (t80) REVERT: A 196 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8074 (tm-30) REVERT: A 223 GLU cc_start: 0.8791 (mp0) cc_final: 0.8499 (mp0) REVERT: A 282 MET cc_start: 0.8743 (tmm) cc_final: 0.8272 (tmm) REVERT: A 286 ILE cc_start: 0.9432 (pt) cc_final: 0.9166 (pt) REVERT: A 287 ILE cc_start: 0.9394 (tt) cc_final: 0.9187 (tt) REVERT: B 35 LEU cc_start: 0.8940 (tp) cc_final: 0.8686 (tp) REVERT: B 58 MET cc_start: 0.9418 (mmp) cc_final: 0.9168 (mmm) REVERT: B 71 ILE cc_start: 0.9762 (mm) cc_final: 0.9520 (mm) REVERT: B 122 HIS cc_start: 0.8235 (m90) cc_final: 0.7771 (m90) REVERT: B 136 ASP cc_start: 0.9182 (m-30) cc_final: 0.8900 (m-30) REVERT: B 210 MET cc_start: 0.9579 (mtp) cc_final: 0.9354 (mtp) REVERT: B 324 ARG cc_start: 0.9450 (mtt90) cc_final: 0.8970 (ttm-80) REVERT: B 327 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8462 (mt-10) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.1493 time to fit residues: 33.1321 Evaluate side-chains 133 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 30.0000 chunk 102 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 30.0000 chunk 99 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8074 Z= 0.290 Angle : 0.664 11.192 11019 Z= 0.363 Chirality : 0.042 0.250 1386 Planarity : 0.003 0.029 1450 Dihedral : 3.946 18.278 1274 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.18 % Allowed : 1.45 % Favored : 98.37 % 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: 0.71 (0.24), residues: 1231 helix: 1.04 (0.19), residues: 771 sheet: 0.33 (0.51), residues: 104 loop : -0.59 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 31 HIS 0.002 0.001 HIS A 179 PHE 0.033 0.003 PHE B 67 TYR 0.017 0.003 TYR B 12 ARG 0.004 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.9051 (ttp) cc_final: 0.8826 (ttp) REVERT: A 118 ASP cc_start: 0.9262 (m-30) cc_final: 0.8810 (m-30) REVERT: A 138 PHE cc_start: 0.8749 (t80) cc_final: 0.8498 (t80) REVERT: A 170 MET cc_start: 0.8401 (ppp) cc_final: 0.8168 (ppp) REVERT: A 196 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8109 (tm-30) REVERT: A 215 SER cc_start: 0.9746 (t) cc_final: 0.9542 (p) REVERT: A 223 GLU cc_start: 0.9026 (mp0) cc_final: 0.8655 (pm20) REVERT: A 282 MET cc_start: 0.8748 (tmm) cc_final: 0.8287 (tmm) REVERT: A 286 ILE cc_start: 0.9416 (pt) cc_final: 0.9158 (pt) REVERT: A 287 ILE cc_start: 0.9419 (tt) cc_final: 0.9210 (tt) REVERT: B 35 LEU cc_start: 0.9011 (tp) cc_final: 0.8774 (tp) REVERT: B 58 MET cc_start: 0.9444 (mmp) cc_final: 0.9184 (mmm) REVERT: B 71 ILE cc_start: 0.9782 (mm) cc_final: 0.9568 (mm) REVERT: B 122 HIS cc_start: 0.8247 (m90) cc_final: 0.7803 (m90) REVERT: B 136 ASP cc_start: 0.9192 (m-30) cc_final: 0.8918 (m-30) REVERT: B 162 MET cc_start: 0.8617 (ttm) cc_final: 0.8040 (ttm) REVERT: B 210 MET cc_start: 0.9611 (mtp) cc_final: 0.9270 (mtp) REVERT: B 261 MET cc_start: 0.9465 (tpp) cc_final: 0.8660 (tpt) REVERT: B 324 ARG cc_start: 0.9467 (mtt90) cc_final: 0.8992 (mtm-85) REVERT: B 327 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8530 (mt-10) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.1674 time to fit residues: 35.9258 Evaluate side-chains 120 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8074 Z= 0.182 Angle : 0.602 11.356 11019 Z= 0.319 Chirality : 0.041 0.198 1386 Planarity : 0.003 0.032 1450 Dihedral : 3.810 17.966 1274 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.18 % Allowed : 0.36 % Favored : 99.46 % 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: 0.96 (0.25), residues: 1231 helix: 1.26 (0.19), residues: 769 sheet: 0.30 (0.50), residues: 104 loop : -0.51 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 31 HIS 0.002 0.001 HIS B 13 PHE 0.028 0.002 PHE B 67 TYR 0.019 0.002 TYR A 277 ARG 0.006 0.000 ARG A 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.9020 (ttp) cc_final: 0.8818 (ttp) REVERT: A 75 PHE cc_start: 0.9208 (m-80) cc_final: 0.9004 (m-80) REVERT: A 118 ASP cc_start: 0.9155 (m-30) cc_final: 0.8854 (m-30) REVERT: A 138 PHE cc_start: 0.8675 (t80) cc_final: 0.8474 (t80) REVERT: A 196 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8053 (tm-30) REVERT: A 223 GLU cc_start: 0.8950 (mp0) cc_final: 0.8578 (pm20) REVERT: A 282 MET cc_start: 0.8725 (tmm) cc_final: 0.8255 (tmm) REVERT: A 286 ILE cc_start: 0.9426 (pt) cc_final: 0.9154 (pt) REVERT: A 291 MET cc_start: 0.8708 (mmt) cc_final: 0.8418 (mmt) REVERT: B 35 LEU cc_start: 0.8963 (tp) cc_final: 0.8709 (tp) REVERT: B 58 MET cc_start: 0.9422 (mmp) cc_final: 0.9142 (mmm) REVERT: B 71 ILE cc_start: 0.9775 (mm) cc_final: 0.9567 (mm) REVERT: B 103 MET cc_start: 0.9249 (ptp) cc_final: 0.8987 (ptp) REVERT: B 122 HIS cc_start: 0.8270 (m90) cc_final: 0.7794 (m90) REVERT: B 136 ASP cc_start: 0.9145 (m-30) cc_final: 0.8870 (m-30) REVERT: B 210 MET cc_start: 0.9592 (mtp) cc_final: 0.9313 (mtp) REVERT: B 261 MET cc_start: 0.9452 (tpp) cc_final: 0.8639 (tpt) REVERT: B 324 ARG cc_start: 0.9483 (mtt90) cc_final: 0.9189 (mtt90) REVERT: B 327 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8462 (mt-10) outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.1476 time to fit residues: 33.2476 Evaluate side-chains 133 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 8.9990 chunk 85 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.072059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.059366 restraints weight = 37061.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.060968 restraints weight = 23755.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.062122 restraints weight = 16865.986| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8074 Z= 0.179 Angle : 0.595 11.187 11019 Z= 0.316 Chirality : 0.041 0.189 1386 Planarity : 0.003 0.030 1450 Dihedral : 3.688 18.114 1274 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: 1.03 (0.25), residues: 1231 helix: 1.30 (0.19), residues: 772 sheet: 0.34 (0.49), residues: 104 loop : -0.45 (0.36), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 31 HIS 0.002 0.001 HIS A 179 PHE 0.029 0.002 PHE B 67 TYR 0.019 0.002 TYR A 277 ARG 0.005 0.000 ARG A 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1647.58 seconds wall clock time: 30 minutes 43.21 seconds (1843.21 seconds total)