Starting phenix.real_space_refine on Mon Mar 11 00:07:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o84_0650/03_2024/6o84_0650.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o84_0650/03_2024/6o84_0650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o84_0650/03_2024/6o84_0650.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o84_0650/03_2024/6o84_0650.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o84_0650/03_2024/6o84_0650.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o84_0650/03_2024/6o84_0650.pdb" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 54 5.16 5 C 4054 2.51 5 N 1032 2.21 5 O 1084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 112": "NH1" <-> "NH2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A ARG 506": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "B ARG 112": "NH1" <-> "NH2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B ARG 506": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6224 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3112 Classifications: {'peptide': 415} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 5, 'TRANS': 409} Chain breaks: 5 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'UNK:plan-1': 59} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 3112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3112 Classifications: {'peptide': 415} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 5, 'TRANS': 409} Chain breaks: 5 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'UNK:plan-1': 59} Unresolved non-hydrogen planarities: 59 Time building chain proxies: 4.02, per 1000 atoms: 0.65 Number of scatterers: 6224 At special positions: 0 Unit cell: (86.67, 88.81, 79.18, 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 54 16.00 O 1084 8.00 N 1032 7.00 C 4054 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: 2.30 Conformation dependent library (CDL) restraints added in 1.2 seconds 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1568 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 94.5% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 109 through 137 removed outlier: 4.205A pdb=" N PHE A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 166 removed outlier: 3.861A pdb=" N GLN A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 209 removed outlier: 3.543A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 196 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 239 removed outlier: 3.524A pdb=" N SER A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 271 removed outlier: 3.530A pdb=" N THR A 251 " --> pdb=" O HIS A 247 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 removed outlier: 3.768A pdb=" N LEU A 308 " --> pdb=" O MET A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.998A pdb=" N GLU A 321 " --> pdb=" O PRO A 317 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 380 removed outlier: 4.484A pdb=" N UNK A 365 " --> pdb=" O UNK A 361 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N UNK A 366 " --> pdb=" O UNK A 362 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N UNK A 367 " --> pdb=" O UNK A 363 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N UNK A 369 " --> pdb=" O UNK A 365 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N UNK A 370 " --> pdb=" O UNK A 366 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N UNK A 376 " --> pdb=" O UNK A 372 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N UNK A 378 " --> pdb=" O UNK A 374 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N UNK A 379 " --> pdb=" O UNK A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 421 removed outlier: 3.831A pdb=" N UNK A 400 " --> pdb=" O UNK A 396 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N UNK A 406 " --> pdb=" O UNK A 402 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N UNK A 407 " --> pdb=" O UNK A 403 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N UNK A 409 " --> pdb=" O UNK A 405 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N UNK A 412 " --> pdb=" O UNK A 408 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N UNK A 413 " --> pdb=" O UNK A 409 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N UNK A 416 " --> pdb=" O UNK A 412 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N UNK A 418 " --> pdb=" O UNK A 414 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N UNK A 419 " --> pdb=" O UNK A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 516 removed outlier: 3.619A pdb=" N LEU A 512 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A 514 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 533 removed outlier: 5.178A pdb=" N ILE A 523 " --> pdb=" O GLY A 519 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N SER A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 526 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 571 removed outlier: 3.601A pdb=" N ILE A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 574 No H-bonds generated for 'chain 'A' and resid 572 through 574' Processing helix chain 'A' and resid 607 through 631 removed outlier: 3.624A pdb=" N PHE A 618 " --> pdb=" O GLU A 614 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 621 " --> pdb=" O MET A 617 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 629 " --> pdb=" O MET A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 647 Processing helix chain 'A' and resid 648 through 683 removed outlier: 4.581A pdb=" N ALA A 654 " --> pdb=" O GLY A 650 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 655 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Proline residue: A 661 - end of helix removed outlier: 3.985A pdb=" N GLY A 672 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 673 " --> pdb=" O HIS A 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 137 removed outlier: 4.205A pdb=" N PHE B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 166 removed outlier: 3.861A pdb=" N GLN B 146 " --> pdb=" O GLU B 142 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 209 removed outlier: 3.543A pdb=" N LEU B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS B 206 " --> pdb=" O PHE B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 239 removed outlier: 3.524A pdb=" N SER B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 removed outlier: 3.530A pdb=" N THR B 251 " --> pdb=" O HIS B 247 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 310 removed outlier: 3.768A pdb=" N LEU B 308 " --> pdb=" O MET B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.998A pdb=" N GLU B 321 " --> pdb=" O PRO B 317 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE B 332 " --> pdb=" O THR B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 380 removed outlier: 4.484A pdb=" N UNK B 365 " --> pdb=" O UNK B 361 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N UNK B 366 " --> pdb=" O UNK B 362 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N UNK B 367 " --> pdb=" O UNK B 363 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N UNK B 369 " --> pdb=" O UNK B 365 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N UNK B 370 " --> pdb=" O UNK B 366 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N UNK B 376 " --> pdb=" O UNK B 372 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N UNK B 378 " --> pdb=" O UNK B 374 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N UNK B 379 " --> pdb=" O UNK B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 421 removed outlier: 3.831A pdb=" N UNK B 400 " --> pdb=" O UNK B 396 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N UNK B 406 " --> pdb=" O UNK B 402 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N UNK B 407 " --> pdb=" O UNK B 403 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N UNK B 409 " --> pdb=" O UNK B 405 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N UNK B 412 " --> pdb=" O UNK B 408 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N UNK B 413 " --> pdb=" O UNK B 409 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N UNK B 416 " --> pdb=" O UNK B 412 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N UNK B 418 " --> pdb=" O UNK B 414 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N UNK B 419 " --> pdb=" O UNK B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 516 removed outlier: 3.619A pdb=" N LEU B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE B 514 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 533 removed outlier: 5.178A pdb=" N ILE B 523 " --> pdb=" O GLY B 519 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N SER B 524 " --> pdb=" O GLN B 520 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 526 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 571 removed outlier: 3.601A pdb=" N ILE B 552 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 553 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET B 560 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 574 No H-bonds generated for 'chain 'B' and resid 572 through 574' Processing helix chain 'B' and resid 607 through 631 removed outlier: 3.624A pdb=" N PHE B 618 " --> pdb=" O GLU B 614 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 621 " --> pdb=" O MET B 617 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 629 " --> pdb=" O MET B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 647 Processing helix chain 'B' and resid 648 through 683 removed outlier: 4.581A pdb=" N ALA B 654 " --> pdb=" O GLY B 650 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE B 655 " --> pdb=" O ILE B 651 " (cutoff:3.500A) Proline residue: B 661 - end of helix removed outlier: 3.985A pdb=" N GLY B 672 " --> pdb=" O MET B 668 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE B 673 " --> pdb=" O HIS B 669 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 175 Processing sheet with id=AA2, first strand: chain 'B' and resid 173 through 175 433 hydrogen bonds defined for protein. 1299 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: 1.82 Time building geometry restraints manager: 2.50 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: 1954 1.34 - 1.46: 1522 1.46 - 1.58: 2776 1.58 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 6342 Sorted by residual: bond pdb=" CA THR A 535 " pdb=" C THR A 535 " ideal model delta sigma weight residual 1.521 1.537 -0.016 1.14e-02 7.69e+03 1.93e+00 bond pdb=" CA THR B 535 " pdb=" C THR B 535 " ideal model delta sigma weight residual 1.521 1.537 -0.016 1.14e-02 7.69e+03 1.93e+00 bond pdb=" C SER A 145 " pdb=" O SER A 145 " ideal model delta sigma weight residual 1.237 1.250 -0.014 1.16e-02 7.43e+03 1.36e+00 bond pdb=" C SER B 145 " pdb=" O SER B 145 " ideal model delta sigma weight residual 1.237 1.250 -0.014 1.16e-02 7.43e+03 1.36e+00 bond pdb=" CA SER B 145 " pdb=" C SER B 145 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.26e-02 6.30e+03 1.32e+00 ... (remaining 6337 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.82: 120 106.82 - 113.61: 3670 113.61 - 120.40: 2522 120.40 - 127.19: 2226 127.19 - 133.99: 72 Bond angle restraints: 8610 Sorted by residual: angle pdb=" C ASP A 144 " pdb=" N SER A 145 " pdb=" CA SER A 145 " ideal model delta sigma weight residual 120.44 114.21 6.23 1.36e+00 5.41e-01 2.10e+01 angle pdb=" C ASP B 144 " pdb=" N SER B 145 " pdb=" CA SER B 145 " ideal model delta sigma weight residual 120.44 114.21 6.23 1.36e+00 5.41e-01 2.10e+01 angle pdb=" N ILE B 151 " pdb=" CA ILE B 151 " pdb=" CB ILE B 151 " ideal model delta sigma weight residual 110.54 116.67 -6.13 1.36e+00 5.41e-01 2.03e+01 angle pdb=" N ILE A 151 " pdb=" CA ILE A 151 " pdb=" CB ILE A 151 " ideal model delta sigma weight residual 110.54 116.67 -6.13 1.36e+00 5.41e-01 2.03e+01 angle pdb=" N GLN A 146 " pdb=" CA GLN A 146 " pdb=" C GLN A 146 " ideal model delta sigma weight residual 111.36 116.22 -4.86 1.09e+00 8.42e-01 1.99e+01 ... (remaining 8605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 3322 17.33 - 34.66: 306 34.66 - 51.99: 60 51.99 - 69.32: 6 69.32 - 86.65: 4 Dihedral angle restraints: 3698 sinusoidal: 1292 harmonic: 2406 Sorted by residual: dihedral pdb=" CA ASP B 177 " pdb=" C ASP B 177 " pdb=" N HIS B 178 " pdb=" CA HIS B 178 " ideal model delta harmonic sigma weight residual -180.00 -157.09 -22.91 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA ASP A 177 " pdb=" C ASP A 177 " pdb=" N HIS A 178 " pdb=" CA HIS A 178 " ideal model delta harmonic sigma weight residual 180.00 -157.09 -22.91 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA ILE B 215 " pdb=" C ILE B 215 " pdb=" N LEU B 216 " pdb=" CA LEU B 216 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 3695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 678 0.041 - 0.083: 310 0.083 - 0.124: 36 0.124 - 0.165: 12 0.165 - 0.206: 10 Chirality restraints: 1046 Sorted by residual: chirality pdb=" CA GLN A 146 " pdb=" N GLN A 146 " pdb=" C GLN A 146 " pdb=" CB GLN A 146 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA GLN B 146 " pdb=" N GLN B 146 " pdb=" C GLN B 146 " pdb=" CB GLN B 146 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE B 151 " pdb=" N ILE B 151 " pdb=" C ILE B 151 " pdb=" CB ILE B 151 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1043 not shown) Planarity restraints: 1048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 140 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO B 141 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 141 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 141 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 140 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A 141 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 141 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 141 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 660 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO B 661 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 661 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 661 " 0.020 5.00e-02 4.00e+02 ... (remaining 1045 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 2188 2.86 - 3.37: 6179 3.37 - 3.88: 9577 3.88 - 4.39: 10860 4.39 - 4.90: 17928 Nonbonded interactions: 46732 Sorted by model distance: nonbonded pdb=" O PHE B 124 " pdb=" OG1 THR B 128 " model vdw 2.350 2.440 nonbonded pdb=" O PHE A 124 " pdb=" OG1 THR A 128 " model vdw 2.350 2.440 nonbonded pdb=" O LEU A 257 " pdb=" OG1 THR A 261 " model vdw 2.359 2.440 nonbonded pdb=" O LEU B 257 " pdb=" OG1 THR B 261 " model vdw 2.359 2.440 nonbonded pdb=" OG SER B 115 " pdb=" O ARG B 252 " model vdw 2.374 2.440 ... (remaining 46727 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.340 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: 1.630 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.810 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.005 0.039 6342 Z= 0.316 Angle : 0.838 7.820 8610 Z= 0.480 Chirality : 0.047 0.206 1046 Planarity : 0.004 0.041 1048 Dihedral : 14.014 86.651 2130 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.64 % Allowed : 7.99 % Favored : 91.37 % 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: -5.68 (0.20), residues: 696 helix: -3.51 (0.13), residues: 508 sheet: -5.32 (0.58), residues: 20 loop : -3.46 (0.37), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 159 HIS 0.004 0.001 HIS B 635 PHE 0.010 0.002 PHE A 665 TYR 0.010 0.002 TYR B 647 ARG 0.001 0.000 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 187 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8355 (mttt) cc_final: 0.7869 (pttm) REVERT: A 150 CYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8861 (p) REVERT: A 153 MET cc_start: 0.9200 (mtm) cc_final: 0.8968 (mtm) REVERT: A 162 TYR cc_start: 0.8387 (t80) cc_final: 0.8187 (t80) REVERT: A 508 LEU cc_start: 0.8490 (tp) cc_final: 0.8214 (tt) REVERT: A 639 MET cc_start: 0.7665 (mmt) cc_final: 0.6495 (tmm) REVERT: B 109 LYS cc_start: 0.8337 (mttt) cc_final: 0.7902 (pttm) REVERT: B 150 CYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8864 (p) REVERT: B 153 MET cc_start: 0.9236 (mtm) cc_final: 0.8987 (mtm) REVERT: B 255 ILE cc_start: 0.9660 (mt) cc_final: 0.9457 (mm) REVERT: B 617 MET cc_start: 0.8417 (tpt) cc_final: 0.7987 (tpt) REVERT: B 639 MET cc_start: 0.7614 (mmt) cc_final: 0.6428 (tmm) outliers start: 4 outliers final: 2 residues processed: 191 average time/residue: 0.1594 time to fit residues: 41.6907 Evaluate side-chains 148 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 151 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 3.9990 chunk 62 optimal weight: 30.0000 chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 64 optimal weight: 30.0000 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 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 245 GLN ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 HIS ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 HIS ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 6342 Z= 0.367 Angle : 0.706 5.698 8610 Z= 0.372 Chirality : 0.040 0.163 1046 Planarity : 0.004 0.036 1048 Dihedral : 5.493 40.383 868 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.83 % Allowed : 19.17 % Favored : 77.00 % 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: -1.83 (0.29), residues: 696 helix: -0.41 (0.20), residues: 528 sheet: -5.65 (0.40), residues: 20 loop : -3.13 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 159 HIS 0.005 0.002 HIS B 669 PHE 0.014 0.002 PHE B 221 TYR 0.011 0.002 TYR A 647 ARG 0.002 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8298 (mttt) cc_final: 0.7927 (pttm) REVERT: A 150 CYS cc_start: 0.9266 (OUTLIER) cc_final: 0.9061 (p) REVERT: A 153 MET cc_start: 0.9276 (mtm) cc_final: 0.8851 (mtp) REVERT: A 170 GLN cc_start: 0.8179 (mp10) cc_final: 0.7923 (mp10) REVERT: A 319 ASN cc_start: 0.9337 (OUTLIER) cc_final: 0.8972 (p0) REVERT: A 508 LEU cc_start: 0.8589 (tp) cc_final: 0.8080 (tt) REVERT: A 613 LYS cc_start: 0.8258 (tmtt) cc_final: 0.7842 (tmtt) REVERT: A 639 MET cc_start: 0.7639 (mmt) cc_final: 0.6556 (tmm) REVERT: B 109 LYS cc_start: 0.8335 (mttt) cc_final: 0.7949 (pttm) REVERT: B 150 CYS cc_start: 0.9264 (OUTLIER) cc_final: 0.9055 (p) REVERT: B 153 MET cc_start: 0.9277 (mtm) cc_final: 0.8856 (mtp) REVERT: B 170 GLN cc_start: 0.8192 (mp10) cc_final: 0.7939 (mp10) REVERT: B 216 LEU cc_start: 0.8453 (mt) cc_final: 0.8235 (tp) REVERT: B 319 ASN cc_start: 0.9340 (OUTLIER) cc_final: 0.8976 (p0) REVERT: B 508 LEU cc_start: 0.8591 (tp) cc_final: 0.8231 (tt) REVERT: B 613 LYS cc_start: 0.8250 (tmtt) cc_final: 0.7832 (tmtt) REVERT: B 639 MET cc_start: 0.7716 (mmt) cc_final: 0.6635 (tmm) outliers start: 24 outliers final: 11 residues processed: 161 average time/residue: 0.1499 time to fit residues: 33.2656 Evaluate side-chains 153 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 323 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 30.0000 chunk 61 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 20 optimal weight: 0.0870 chunk 74 optimal weight: 0.0770 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 137 ASN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6342 Z= 0.138 Angle : 0.507 6.838 8610 Z= 0.262 Chirality : 0.034 0.139 1046 Planarity : 0.003 0.026 1048 Dihedral : 4.726 40.888 868 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.24 % Allowed : 23.48 % Favored : 74.28 % 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: -0.36 (0.32), residues: 696 helix: 0.67 (0.22), residues: 544 sheet: -5.45 (0.38), residues: 20 loop : -3.03 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 184 HIS 0.001 0.000 HIS B 178 PHE 0.010 0.001 PHE A 221 TYR 0.010 0.001 TYR B 555 ARG 0.001 0.000 ARG A 644 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 182 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8293 (mttt) cc_final: 0.7734 (pttm) REVERT: A 137 ASN cc_start: 0.7180 (m-40) cc_final: 0.6969 (m-40) REVERT: A 150 CYS cc_start: 0.9251 (OUTLIER) cc_final: 0.9004 (p) REVERT: A 153 MET cc_start: 0.9179 (mtm) cc_final: 0.8678 (mtp) REVERT: A 335 LYS cc_start: 0.9185 (ttpt) cc_final: 0.8925 (ttpp) REVERT: A 508 LEU cc_start: 0.8432 (tp) cc_final: 0.7975 (tt) REVERT: A 617 MET cc_start: 0.8347 (tpt) cc_final: 0.7799 (tpp) REVERT: A 639 MET cc_start: 0.7548 (mmt) cc_final: 0.6496 (tmm) REVERT: A 676 GLU cc_start: 0.7966 (tp30) cc_final: 0.7471 (tp30) REVERT: B 109 LYS cc_start: 0.8452 (mttt) cc_final: 0.7555 (mtmm) REVERT: B 150 CYS cc_start: 0.9260 (OUTLIER) cc_final: 0.9023 (p) REVERT: B 153 MET cc_start: 0.9180 (mtm) cc_final: 0.8680 (mtp) REVERT: B 216 LEU cc_start: 0.8329 (mt) cc_final: 0.8026 (tp) REVERT: B 256 MET cc_start: 0.9056 (mmm) cc_final: 0.8769 (mmm) REVERT: B 333 MET cc_start: 0.8388 (ttm) cc_final: 0.8165 (ttm) REVERT: B 508 LEU cc_start: 0.8561 (tp) cc_final: 0.8196 (tt) REVERT: B 617 MET cc_start: 0.8161 (tpt) cc_final: 0.7638 (tpp) REVERT: B 639 MET cc_start: 0.7551 (mmt) cc_final: 0.6525 (tmm) REVERT: B 676 GLU cc_start: 0.7980 (tp30) cc_final: 0.7469 (tp30) outliers start: 14 outliers final: 7 residues processed: 188 average time/residue: 0.1527 time to fit residues: 38.9839 Evaluate side-chains 150 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 141 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 511 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 30.0000 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 146 GLN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN B 146 GLN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6342 Z= 0.144 Angle : 0.511 8.206 8610 Z= 0.263 Chirality : 0.034 0.136 1046 Planarity : 0.003 0.025 1048 Dihedral : 4.444 39.394 864 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.40 % Allowed : 25.56 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.32), residues: 696 helix: 1.12 (0.22), residues: 544 sheet: -5.29 (0.40), residues: 20 loop : -2.95 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 184 HIS 0.002 0.000 HIS B 206 PHE 0.015 0.001 PHE B 222 TYR 0.017 0.001 TYR B 678 ARG 0.000 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8426 (mttt) cc_final: 0.7804 (pttm) REVERT: A 150 CYS cc_start: 0.9279 (OUTLIER) cc_final: 0.9041 (p) REVERT: A 153 MET cc_start: 0.9208 (mtm) cc_final: 0.8767 (mtp) REVERT: A 170 GLN cc_start: 0.8280 (mp10) cc_final: 0.7926 (mp10) REVERT: A 335 LYS cc_start: 0.9181 (ttpt) cc_final: 0.8931 (ttpp) REVERT: A 508 LEU cc_start: 0.8480 (tp) cc_final: 0.7971 (tt) REVERT: A 617 MET cc_start: 0.8402 (tpt) cc_final: 0.7490 (tpp) REVERT: A 639 MET cc_start: 0.7463 (mmt) cc_final: 0.6381 (tmm) REVERT: A 666 TYR cc_start: 0.9442 (t80) cc_final: 0.9065 (t80) REVERT: A 676 GLU cc_start: 0.8011 (tp30) cc_final: 0.7481 (tp30) REVERT: B 109 LYS cc_start: 0.8427 (mttt) cc_final: 0.7566 (mtmm) REVERT: B 150 CYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8995 (p) REVERT: B 153 MET cc_start: 0.9202 (mtm) cc_final: 0.8760 (mtp) REVERT: B 170 GLN cc_start: 0.8262 (mp10) cc_final: 0.7957 (mp10) REVERT: B 216 LEU cc_start: 0.8366 (mt) cc_final: 0.8036 (tp) REVERT: B 256 MET cc_start: 0.9094 (mmm) cc_final: 0.8760 (mmm) REVERT: B 310 GLN cc_start: 0.7580 (mt0) cc_final: 0.7263 (mp10) REVERT: B 333 MET cc_start: 0.8399 (ttm) cc_final: 0.8052 (ttm) REVERT: B 508 LEU cc_start: 0.8566 (tp) cc_final: 0.8128 (tt) REVERT: B 617 MET cc_start: 0.8352 (tpt) cc_final: 0.7441 (tpp) REVERT: B 639 MET cc_start: 0.7453 (mmt) cc_final: 0.6382 (tmm) REVERT: B 666 TYR cc_start: 0.9445 (t80) cc_final: 0.9159 (t80) REVERT: B 676 GLU cc_start: 0.8015 (tp30) cc_final: 0.7484 (tp30) outliers start: 15 outliers final: 10 residues processed: 168 average time/residue: 0.1579 time to fit residues: 36.0418 Evaluate side-chains 155 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 511 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 67 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 HIS A 558 GLN A 645 GLN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 645 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6342 Z= 0.160 Angle : 0.505 6.876 8610 Z= 0.265 Chirality : 0.035 0.145 1046 Planarity : 0.002 0.024 1048 Dihedral : 4.347 39.503 864 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.67 % Allowed : 24.60 % Favored : 71.73 % 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: 0.56 (0.32), residues: 696 helix: 1.39 (0.22), residues: 544 sheet: -5.34 (0.38), residues: 20 loop : -3.02 (0.46), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 184 HIS 0.002 0.001 HIS B 206 PHE 0.030 0.001 PHE A 222 TYR 0.009 0.001 TYR A 647 ARG 0.001 0.000 ARG B 667 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 150 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8472 (mttt) cc_final: 0.7935 (pttm) REVERT: A 123 MET cc_start: 0.8699 (tmm) cc_final: 0.8208 (tmm) REVERT: A 150 CYS cc_start: 0.9228 (OUTLIER) cc_final: 0.9015 (p) REVERT: A 153 MET cc_start: 0.9205 (mtm) cc_final: 0.8790 (mtp) REVERT: A 262 ASP cc_start: 0.8539 (m-30) cc_final: 0.8291 (m-30) REVERT: A 310 GLN cc_start: 0.7643 (mt0) cc_final: 0.7289 (mp10) REVERT: A 333 MET cc_start: 0.8843 (tpp) cc_final: 0.8222 (ttm) REVERT: A 335 LYS cc_start: 0.9261 (ttpt) cc_final: 0.9037 (ttpp) REVERT: A 508 LEU cc_start: 0.8486 (tp) cc_final: 0.7968 (tt) REVERT: A 617 MET cc_start: 0.8412 (tpt) cc_final: 0.7871 (tpp) REVERT: A 639 MET cc_start: 0.7330 (mmt) cc_final: 0.6191 (tmm) REVERT: A 645 GLN cc_start: 0.8800 (tt0) cc_final: 0.8595 (tp40) REVERT: A 676 GLU cc_start: 0.8011 (tp30) cc_final: 0.7671 (tp30) REVERT: B 109 LYS cc_start: 0.8393 (mttt) cc_final: 0.7566 (mtmm) REVERT: B 123 MET cc_start: 0.8714 (tmm) cc_final: 0.8308 (tmm) REVERT: B 150 CYS cc_start: 0.9228 (OUTLIER) cc_final: 0.9011 (p) REVERT: B 153 MET cc_start: 0.9195 (mtm) cc_final: 0.8794 (mtp) REVERT: B 170 GLN cc_start: 0.8231 (mp10) cc_final: 0.8031 (mp10) REVERT: B 310 GLN cc_start: 0.7620 (mt0) cc_final: 0.7262 (mp10) REVERT: B 333 MET cc_start: 0.8490 (ttm) cc_final: 0.8288 (ttm) REVERT: B 508 LEU cc_start: 0.8577 (tp) cc_final: 0.8122 (tt) REVERT: B 617 MET cc_start: 0.8416 (tpt) cc_final: 0.7877 (tpp) REVERT: B 639 MET cc_start: 0.7349 (mmt) cc_final: 0.6243 (tmm) REVERT: B 645 GLN cc_start: 0.8794 (tt0) cc_final: 0.8579 (tp40) REVERT: B 676 GLU cc_start: 0.8014 (tp30) cc_final: 0.7675 (tp30) outliers start: 23 outliers final: 16 residues processed: 164 average time/residue: 0.1537 time to fit residues: 34.2380 Evaluate side-chains 159 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 511 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 HIS B 137 ASN B 206 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6342 Z= 0.334 Angle : 0.636 6.555 8610 Z= 0.333 Chirality : 0.038 0.156 1046 Planarity : 0.003 0.023 1048 Dihedral : 4.720 41.889 864 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 5.91 % Allowed : 24.44 % Favored : 69.65 % 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: 0.67 (0.32), residues: 696 helix: 1.42 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -2.88 (0.42), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP B 184 HIS 0.010 0.002 HIS A 206 PHE 0.014 0.002 PHE A 222 TYR 0.012 0.002 TYR B 647 ARG 0.001 0.000 ARG B 610 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8517 (mttt) cc_final: 0.7739 (mtmm) REVERT: A 150 CYS cc_start: 0.9226 (OUTLIER) cc_final: 0.9009 (p) REVERT: A 153 MET cc_start: 0.9192 (mtm) cc_final: 0.8642 (mtp) REVERT: A 262 ASP cc_start: 0.8693 (m-30) cc_final: 0.8483 (m-30) REVERT: A 310 GLN cc_start: 0.7619 (mt0) cc_final: 0.7337 (mp10) REVERT: A 319 ASN cc_start: 0.9359 (OUTLIER) cc_final: 0.9023 (p0) REVERT: A 333 MET cc_start: 0.8855 (tpp) cc_final: 0.8456 (ttm) REVERT: A 508 LEU cc_start: 0.8554 (tp) cc_final: 0.8191 (tt) REVERT: A 617 MET cc_start: 0.8450 (tpt) cc_final: 0.7559 (tpp) REVERT: A 639 MET cc_start: 0.7553 (mmt) cc_final: 0.6363 (tmm) REVERT: A 676 GLU cc_start: 0.8097 (tp30) cc_final: 0.7730 (tp30) REVERT: B 109 LYS cc_start: 0.8606 (mttt) cc_final: 0.7840 (mtmm) REVERT: B 150 CYS cc_start: 0.9224 (OUTLIER) cc_final: 0.9010 (p) REVERT: B 153 MET cc_start: 0.9195 (mtm) cc_final: 0.8651 (mtp) REVERT: B 310 GLN cc_start: 0.7639 (mt0) cc_final: 0.7366 (mp10) REVERT: B 319 ASN cc_start: 0.9356 (OUTLIER) cc_final: 0.9023 (p0) REVERT: B 508 LEU cc_start: 0.8659 (tp) cc_final: 0.8172 (tt) REVERT: B 617 MET cc_start: 0.8451 (tpt) cc_final: 0.7563 (tpp) REVERT: B 639 MET cc_start: 0.7532 (mmt) cc_final: 0.6332 (tmm) REVERT: B 676 GLU cc_start: 0.8103 (tp30) cc_final: 0.7728 (tp30) outliers start: 37 outliers final: 24 residues processed: 155 average time/residue: 0.1561 time to fit residues: 32.9359 Evaluate side-chains 159 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 511 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 44 optimal weight: 0.0020 chunk 66 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6342 Z= 0.143 Angle : 0.536 9.654 8610 Z= 0.270 Chirality : 0.035 0.153 1046 Planarity : 0.002 0.024 1048 Dihedral : 4.512 41.281 864 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.72 % Allowed : 28.27 % Favored : 69.01 % 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: 1.18 (0.34), residues: 696 helix: 1.85 (0.23), residues: 532 sheet: -5.53 (0.34), residues: 20 loop : -2.41 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 184 HIS 0.005 0.001 HIS B 206 PHE 0.011 0.001 PHE A 222 TYR 0.008 0.001 TYR A 162 ARG 0.001 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8482 (mttt) cc_final: 0.7623 (mtmm) REVERT: A 150 CYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8993 (p) REVERT: A 153 MET cc_start: 0.9196 (mtm) cc_final: 0.8773 (mtp) REVERT: A 333 MET cc_start: 0.8806 (tpp) cc_final: 0.8234 (ttm) REVERT: A 508 LEU cc_start: 0.8485 (tp) cc_final: 0.8144 (tt) REVERT: A 617 MET cc_start: 0.8362 (tpt) cc_final: 0.7825 (tpp) REVERT: A 639 MET cc_start: 0.7358 (mmt) cc_final: 0.6241 (tmm) REVERT: A 676 GLU cc_start: 0.8022 (tp30) cc_final: 0.7653 (tp30) REVERT: B 109 LYS cc_start: 0.8338 (mttt) cc_final: 0.7626 (mtmm) REVERT: B 150 CYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8990 (p) REVERT: B 153 MET cc_start: 0.9193 (mtm) cc_final: 0.8780 (mtp) REVERT: B 170 GLN cc_start: 0.8234 (mp10) cc_final: 0.7932 (mp10) REVERT: B 508 LEU cc_start: 0.8583 (tp) cc_final: 0.8111 (tt) REVERT: B 617 MET cc_start: 0.8362 (tpt) cc_final: 0.7823 (tpp) REVERT: B 639 MET cc_start: 0.7347 (mmt) cc_final: 0.6247 (tmm) REVERT: B 676 GLU cc_start: 0.8030 (tp30) cc_final: 0.7654 (tp30) outliers start: 17 outliers final: 12 residues processed: 158 average time/residue: 0.1524 time to fit residues: 32.8001 Evaluate side-chains 157 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 511 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 30.0000 chunk 15 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 30.0000 chunk 71 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.8224 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6342 Z= 0.160 Angle : 0.561 10.330 8610 Z= 0.276 Chirality : 0.034 0.152 1046 Planarity : 0.002 0.023 1048 Dihedral : 4.355 39.612 864 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.19 % Allowed : 28.59 % Favored : 68.21 % 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: 1.36 (0.33), residues: 696 helix: 1.96 (0.23), residues: 532 sheet: -5.45 (0.35), residues: 20 loop : -2.28 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP B 184 HIS 0.002 0.000 HIS B 635 PHE 0.007 0.001 PHE B 222 TYR 0.008 0.001 TYR A 162 ARG 0.002 0.000 ARG A 644 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8525 (mttt) cc_final: 0.7705 (mtmm) REVERT: A 150 CYS cc_start: 0.9269 (OUTLIER) cc_final: 0.9025 (p) REVERT: A 153 MET cc_start: 0.9205 (mtm) cc_final: 0.8771 (mtp) REVERT: A 310 GLN cc_start: 0.7608 (mt0) cc_final: 0.7281 (mp10) REVERT: A 333 MET cc_start: 0.8832 (tpp) cc_final: 0.8041 (ttm) REVERT: A 508 LEU cc_start: 0.8485 (tp) cc_final: 0.8148 (tt) REVERT: A 617 MET cc_start: 0.8383 (tpt) cc_final: 0.7735 (tpp) REVERT: A 639 MET cc_start: 0.7263 (mmt) cc_final: 0.6122 (tmm) REVERT: A 676 GLU cc_start: 0.8071 (tp30) cc_final: 0.7685 (tp30) REVERT: B 109 LYS cc_start: 0.8371 (mttt) cc_final: 0.7549 (mtmm) REVERT: B 150 CYS cc_start: 0.9263 (OUTLIER) cc_final: 0.9015 (p) REVERT: B 153 MET cc_start: 0.9206 (mtm) cc_final: 0.8712 (mtp) REVERT: B 170 GLN cc_start: 0.8221 (mp10) cc_final: 0.7949 (mp10) REVERT: B 186 LYS cc_start: 0.9171 (tttt) cc_final: 0.8906 (mtpt) REVERT: B 310 GLN cc_start: 0.7656 (mt0) cc_final: 0.7303 (mp10) REVERT: B 508 LEU cc_start: 0.8613 (tp) cc_final: 0.8130 (tt) REVERT: B 617 MET cc_start: 0.8387 (tpt) cc_final: 0.7734 (tpp) REVERT: B 639 MET cc_start: 0.7252 (mmt) cc_final: 0.6240 (tmm) REVERT: B 676 GLU cc_start: 0.8072 (tp30) cc_final: 0.7680 (tp30) outliers start: 20 outliers final: 15 residues processed: 163 average time/residue: 0.1586 time to fit residues: 34.9321 Evaluate side-chains 165 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 511 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 chunk 32 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 30.0000 chunk 66 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 645 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6342 Z= 0.181 Angle : 0.568 10.754 8610 Z= 0.280 Chirality : 0.035 0.154 1046 Planarity : 0.002 0.024 1048 Dihedral : 4.357 40.015 864 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.51 % Allowed : 28.59 % Favored : 67.89 % 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: 1.63 (0.33), residues: 696 helix: 2.15 (0.23), residues: 520 sheet: None (None), residues: 0 loop : -2.41 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP B 184 HIS 0.002 0.001 HIS B 206 PHE 0.006 0.001 PHE B 331 TYR 0.010 0.001 TYR B 647 ARG 0.001 0.000 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 149 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8565 (mttt) cc_final: 0.7740 (mtmm) REVERT: A 150 CYS cc_start: 0.9242 (OUTLIER) cc_final: 0.9006 (p) REVERT: A 153 MET cc_start: 0.9182 (mtm) cc_final: 0.8752 (mtp) REVERT: A 310 GLN cc_start: 0.7724 (mt0) cc_final: 0.7340 (mp10) REVERT: A 333 MET cc_start: 0.8839 (tpp) cc_final: 0.8218 (ttm) REVERT: A 508 LEU cc_start: 0.8486 (tp) cc_final: 0.8120 (tt) REVERT: A 617 MET cc_start: 0.8407 (tpt) cc_final: 0.7769 (tpp) REVERT: A 639 MET cc_start: 0.7310 (mmt) cc_final: 0.6257 (tmm) REVERT: A 676 GLU cc_start: 0.8087 (tp30) cc_final: 0.7711 (tp30) REVERT: B 109 LYS cc_start: 0.8376 (mttt) cc_final: 0.7686 (mtmm) REVERT: B 150 CYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8986 (p) REVERT: B 153 MET cc_start: 0.9186 (mtm) cc_final: 0.8698 (mtp) REVERT: B 170 GLN cc_start: 0.8205 (mp10) cc_final: 0.7926 (mp10) REVERT: B 186 LYS cc_start: 0.9187 (tttt) cc_final: 0.8932 (mtpt) REVERT: B 310 GLN cc_start: 0.7699 (mt0) cc_final: 0.7322 (mp10) REVERT: B 508 LEU cc_start: 0.8622 (tp) cc_final: 0.8102 (tt) REVERT: B 617 MET cc_start: 0.8403 (tpt) cc_final: 0.7765 (tpp) REVERT: B 639 MET cc_start: 0.7329 (mmt) cc_final: 0.6265 (tmm) REVERT: B 676 GLU cc_start: 0.8104 (tp30) cc_final: 0.7722 (tp30) outliers start: 22 outliers final: 18 residues processed: 158 average time/residue: 0.1564 time to fit residues: 33.3365 Evaluate side-chains 165 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 511 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 6 optimal weight: 0.0980 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 6342 Z= 0.147 Angle : 0.577 11.384 8610 Z= 0.277 Chirality : 0.034 0.152 1046 Planarity : 0.002 0.024 1048 Dihedral : 4.262 39.492 864 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.56 % Allowed : 29.71 % Favored : 67.73 % 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: 1.59 (0.33), residues: 696 helix: 2.26 (0.23), residues: 520 sheet: -5.26 (0.40), residues: 20 loop : -2.41 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP B 184 HIS 0.002 0.000 HIS B 206 PHE 0.009 0.001 PHE B 221 TYR 0.010 0.001 TYR B 555 ARG 0.002 0.000 ARG B 644 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8553 (mttt) cc_final: 0.7696 (mtmm) REVERT: A 150 CYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9061 (p) REVERT: A 153 MET cc_start: 0.9177 (mtm) cc_final: 0.8664 (mtp) REVERT: A 310 GLN cc_start: 0.7721 (mt0) cc_final: 0.7374 (mp10) REVERT: A 333 MET cc_start: 0.8815 (tpp) cc_final: 0.8226 (ttm) REVERT: A 508 LEU cc_start: 0.8435 (tp) cc_final: 0.8091 (tt) REVERT: A 617 MET cc_start: 0.8395 (tpt) cc_final: 0.7781 (tpp) REVERT: A 639 MET cc_start: 0.7183 (mmt) cc_final: 0.6034 (tmm) REVERT: A 676 GLU cc_start: 0.8074 (tp30) cc_final: 0.7687 (tp30) REVERT: B 109 LYS cc_start: 0.8467 (mttt) cc_final: 0.7648 (mtmm) REVERT: B 150 CYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9055 (p) REVERT: B 153 MET cc_start: 0.9182 (mtm) cc_final: 0.8693 (mtp) REVERT: B 170 GLN cc_start: 0.8183 (mp10) cc_final: 0.7704 (mp10) REVERT: B 186 LYS cc_start: 0.9130 (tttt) cc_final: 0.8837 (tttt) REVERT: B 310 GLN cc_start: 0.7686 (mt0) cc_final: 0.7361 (mp10) REVERT: B 508 LEU cc_start: 0.8566 (tp) cc_final: 0.8060 (tt) REVERT: B 617 MET cc_start: 0.8383 (tpt) cc_final: 0.7757 (tpp) REVERT: B 639 MET cc_start: 0.7178 (mmt) cc_final: 0.6027 (tmm) REVERT: B 676 GLU cc_start: 0.8078 (tp30) cc_final: 0.7693 (tp30) outliers start: 16 outliers final: 14 residues processed: 162 average time/residue: 0.1708 time to fit residues: 37.0565 Evaluate side-chains 163 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 511 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 27 optimal weight: 0.0050 chunk 66 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 3 optimal weight: 0.0020 chunk 47 optimal weight: 9.9990 overall best weight: 0.5606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 HIS ** 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 = 0.3566 r_free = 0.3566 target = 0.106461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.086379 restraints weight = 15614.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.088166 restraints weight = 9967.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.089816 restraints weight = 7631.497| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6342 Z= 0.146 Angle : 0.572 11.273 8610 Z= 0.273 Chirality : 0.034 0.155 1046 Planarity : 0.002 0.024 1048 Dihedral : 4.167 38.805 864 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.40 % Allowed : 30.19 % Favored : 67.41 % 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: 1.76 (0.33), residues: 696 helix: 2.40 (0.22), residues: 520 sheet: -4.87 (0.49), residues: 20 loop : -2.47 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP B 184 HIS 0.001 0.000 HIS B 635 PHE 0.008 0.001 PHE B 221 TYR 0.010 0.001 TYR A 162 ARG 0.002 0.000 ARG B 644 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1390.69 seconds wall clock time: 25 minutes 54.65 seconds (1554.65 seconds total)