Starting phenix.real_space_refine on Sat Jul 20 21:23:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzd_41755/07_2024/8tzd_41755_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzd_41755/07_2024/8tzd_41755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzd_41755/07_2024/8tzd_41755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzd_41755/07_2024/8tzd_41755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzd_41755/07_2024/8tzd_41755_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzd_41755/07_2024/8tzd_41755_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.062 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 85 5.16 5 C 8073 2.51 5 N 1908 2.21 5 O 2108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 12175 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3971 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 18, 'TRANS': 502} Chain breaks: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "C" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'LBN': 1, 'XMO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.28, per 1000 atoms: 0.60 Number of scatterers: 12175 At special positions: 0 Unit cell: (129.6, 127.44, 79.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 1 15.00 O 2108 8.00 N 1908 7.00 C 8073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.80 Conformation dependent library (CDL) restraints added in 2.1 seconds 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 0 sheets defined 88.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 103 through 130 Processing helix chain 'A' and resid 130 through 157 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 157 through 198 Proline residue: A 167 - end of helix removed outlier: 5.021A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 204 through 223 removed outlier: 3.574A pdb=" N VAL A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 251 removed outlier: 4.309A pdb=" N VAL A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 281 removed outlier: 3.539A pdb=" N PHE A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 287 Processing helix chain 'A' and resid 288 through 312 removed outlier: 4.539A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 312 through 329 removed outlier: 3.603A pdb=" N TRP A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 343 removed outlier: 3.668A pdb=" N ILE A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 361 removed outlier: 3.555A pdb=" N ARG A 355 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Proline residue: A 356 - end of helix Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 362 through 375 Processing helix chain 'A' and resid 378 through 389 Processing helix chain 'A' and resid 391 through 414 removed outlier: 4.180A pdb=" N ALA A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 437 through 481 removed outlier: 3.963A pdb=" N ALA A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 496 Processing helix chain 'A' and resid 496 through 504 removed outlier: 3.562A pdb=" N GLY A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 Processing helix chain 'A' and resid 524 through 542 removed outlier: 3.758A pdb=" N ALA A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 571 through 586 Processing helix chain 'A' and resid 589 through 594 Processing helix chain 'A' and resid 596 through 619 Processing helix chain 'B' and resid 91 through 103 Processing helix chain 'B' and resid 103 through 130 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 157 through 203 Proline residue: B 167 - end of helix removed outlier: 4.678A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 223 removed outlier: 4.022A pdb=" N LEU B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 250 removed outlier: 4.547A pdb=" N VAL B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 271 Processing helix chain 'B' and resid 273 through 282 removed outlier: 3.768A pdb=" N PHE B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 288 through 312 removed outlier: 4.292A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Proline residue: B 296 - end of helix Processing helix chain 'B' and resid 312 through 330 removed outlier: 3.799A pdb=" N TRP B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 349 through 361 Proline residue: B 356 - end of helix Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 362 through 376 removed outlier: 3.865A pdb=" N THR B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 388 removed outlier: 3.712A pdb=" N LEU B 382 " --> pdb=" O ALA B 378 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 414 Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 437 through 480 removed outlier: 3.665A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET B 480 " --> pdb=" O TRP B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.598A pdb=" N TYR B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 504 removed outlier: 3.700A pdb=" N GLY B 504 " --> pdb=" O ALA B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 Processing helix chain 'B' and resid 524 through 542 removed outlier: 4.078A pdb=" N ALA B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 574 through 586 Processing helix chain 'B' and resid 589 through 596 removed outlier: 3.650A pdb=" N ALA B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 619 removed outlier: 3.621A pdb=" N LEU B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 602 " --> pdb=" O MET B 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 103 Processing helix chain 'C' and resid 103 through 130 Processing helix chain 'C' and resid 130 through 157 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 157 through 203 Proline residue: C 167 - end of helix removed outlier: 4.405A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYS C 201 " --> pdb=" O PHE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.825A pdb=" N LEU C 207 " --> pdb=" O GLY C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 251 removed outlier: 3.522A pdb=" N PHE C 236 " --> pdb=" O TRP C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 277 removed outlier: 4.015A pdb=" N SER C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 284 through 287 Processing helix chain 'C' and resid 288 through 312 removed outlier: 4.322A pdb=" N LEU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Proline residue: C 296 - end of helix Processing helix chain 'C' and resid 312 through 329 removed outlier: 3.697A pdb=" N TRP C 316 " --> pdb=" O GLY C 312 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 341 Processing helix chain 'C' and resid 349 through 361 Proline residue: C 356 - end of helix Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 362 through 375 Processing helix chain 'C' and resid 379 through 389 removed outlier: 4.311A pdb=" N GLY C 383 " --> pdb=" O GLY C 379 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY C 389 " --> pdb=" O TYR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 414 removed outlier: 4.217A pdb=" N ALA C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 437 through 480 removed outlier: 4.138A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET C 480 " --> pdb=" O TRP C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 496 removed outlier: 4.521A pdb=" N TYR C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 509 through 523 removed outlier: 3.550A pdb=" N VAL C 513 " --> pdb=" O ASP C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 removed outlier: 3.891A pdb=" N ALA C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 573 through 586 removed outlier: 4.410A pdb=" N ILE C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 596 removed outlier: 3.673A pdb=" N ALA C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 618 removed outlier: 3.525A pdb=" N ALA C 600 " --> pdb=" O GLY C 596 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 618 " --> pdb=" O ILE C 614 " (cutoff:3.500A) 978 hydrogen bonds defined for protein. 2892 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 5.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1821 1.29 - 1.42: 3476 1.42 - 1.55: 7045 1.55 - 1.68: 14 1.68 - 1.81: 153 Bond restraints: 12509 Sorted by residual: bond pdb=" C11 XMO A 701 " pdb=" O12 XMO A 701 " ideal model delta sigma weight residual 1.398 1.680 -0.282 2.00e-02 2.50e+03 1.98e+02 bond pdb=" C11 XMO C 701 " pdb=" O12 XMO C 701 " ideal model delta sigma weight residual 1.398 1.678 -0.280 2.00e-02 2.50e+03 1.95e+02 bond pdb=" C11 XMO B 701 " pdb=" O12 XMO B 701 " ideal model delta sigma weight residual 1.398 1.677 -0.279 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C10 XMO A 701 " pdb=" C11 XMO A 701 " ideal model delta sigma weight residual 1.534 1.289 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C10 XMO C 701 " pdb=" C11 XMO C 701 " ideal model delta sigma weight residual 1.534 1.289 0.245 2.00e-02 2.50e+03 1.50e+02 ... (remaining 12504 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.27: 307 106.27 - 113.23: 6847 113.23 - 120.19: 4729 120.19 - 127.15: 4990 127.15 - 134.11: 166 Bond angle restraints: 17039 Sorted by residual: angle pdb=" O1 LBN A 702 " pdb=" P1 LBN A 702 " pdb=" O2 LBN A 702 " ideal model delta sigma weight residual 93.45 109.54 -16.09 3.00e+00 1.11e-01 2.87e+01 angle pdb=" O3 LBN A 702 " pdb=" P1 LBN A 702 " pdb=" O4 LBN A 702 " ideal model delta sigma weight residual 119.36 109.58 9.78 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C26 LBN A 702 " pdb=" C25 LBN A 702 " pdb=" O5 LBN A 702 " ideal model delta sigma weight residual 111.43 120.73 -9.30 3.00e+00 1.11e-01 9.62e+00 angle pdb=" C02 XMO B 701 " pdb=" C04 XMO B 701 " pdb=" O06 XMO B 701 " ideal model delta sigma weight residual 111.45 120.37 -8.92 3.00e+00 1.11e-01 8.84e+00 angle pdb=" C35 LBN A 702 " pdb=" C34 LBN A 702 " pdb=" O7 LBN A 702 " ideal model delta sigma weight residual 111.21 119.63 -8.42 3.00e+00 1.11e-01 7.88e+00 ... (remaining 17034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.74: 7067 33.74 - 67.48: 104 67.48 - 101.22: 13 101.22 - 134.96: 2 134.96 - 168.70: 4 Dihedral angle restraints: 7190 sinusoidal: 2632 harmonic: 4558 Sorted by residual: dihedral pdb=" C01 XMO C 701 " pdb=" C02 XMO C 701 " pdb=" C04 XMO C 701 " pdb=" O06 XMO C 701 " ideal model delta sinusoidal sigma weight residual 296.92 128.22 168.70 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C01 XMO C 701 " pdb=" C02 XMO C 701 " pdb=" C04 XMO C 701 " pdb=" O05 XMO C 701 " ideal model delta sinusoidal sigma weight residual 116.78 -51.39 168.17 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C01 XMO B 701 " pdb=" C02 XMO B 701 " pdb=" C04 XMO B 701 " pdb=" O06 XMO B 701 " ideal model delta sinusoidal sigma weight residual 296.92 145.76 151.16 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 7187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1826 0.070 - 0.141: 144 0.141 - 0.211: 1 0.211 - 0.282: 0 0.282 - 0.352: 3 Chirality restraints: 1974 Sorted by residual: chirality pdb=" C10 XMO B 701 " pdb=" C09 XMO B 701 " pdb=" C11 XMO B 701 " pdb=" O22 XMO B 701 " both_signs ideal model delta sigma weight residual False 2.74 2.39 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" C10 XMO C 701 " pdb=" C09 XMO C 701 " pdb=" C11 XMO C 701 " pdb=" O22 XMO C 701 " both_signs ideal model delta sigma weight residual False 2.74 2.39 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C10 XMO A 701 " pdb=" C09 XMO A 701 " pdb=" C11 XMO A 701 " pdb=" O22 XMO A 701 " both_signs ideal model delta sigma weight residual False 2.74 2.39 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 1971 not shown) Planarity restraints: 2069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 233 " -0.042 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO A 234 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 233 " -0.041 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO C 234 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 234 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 234 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 403 " 0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO A 404 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 404 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 404 " 0.033 5.00e-02 4.00e+02 ... (remaining 2066 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 659 2.73 - 3.27: 12959 3.27 - 3.81: 20610 3.81 - 4.36: 22805 4.36 - 4.90: 41485 Nonbonded interactions: 98518 Sorted by model distance: nonbonded pdb=" OG SER B 380 " pdb=" O21 XMO B 701 " model vdw 2.183 2.440 nonbonded pdb=" O LEU B 195 " pdb=" OG1 THR B 199 " model vdw 2.203 2.440 nonbonded pdb=" O LEU A 248 " pdb=" OG1 THR A 252 " model vdw 2.227 2.440 nonbonded pdb=" O ALA A 275 " pdb=" OG SER A 278 " model vdw 2.266 2.440 nonbonded pdb=" OG SER C 574 " pdb=" O22 XMO C 701 " model vdw 2.322 2.440 ... (remaining 98513 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' and (resid 90 through 622 or resid 701)) selection = (chain 'B' and (resid 90 through 421 or resid 434 through 622 or resid 701)) selection = (chain 'C' and (resid 90 through 421 or resid 434 through 622 or resid 701)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 34.850 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.009 0.282 12509 Z= 0.630 Angle : 0.580 16.085 17039 Z= 0.293 Chirality : 0.039 0.352 1974 Planarity : 0.004 0.064 2069 Dihedral : 13.903 168.704 4266 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.32 % Allowed : 1.37 % Favored : 98.31 % 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: 2.98 (0.21), residues: 1579 helix: 2.47 (0.15), residues: 1291 sheet: None (None), residues: 0 loop : -0.42 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 316 HIS 0.003 0.001 HIS A 132 PHE 0.017 0.001 PHE B 413 TYR 0.008 0.001 TYR B 231 ARG 0.002 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 220 time to evaluate : 1.249 Fit side-chains REVERT: A 284 LYS cc_start: 0.8586 (mttm) cc_final: 0.8025 (mmtt) REVERT: A 307 MET cc_start: 0.8627 (mtp) cc_final: 0.8411 (mtp) REVERT: A 470 MET cc_start: 0.8183 (mmt) cc_final: 0.7782 (mmt) REVERT: A 564 TYR cc_start: 0.8569 (m-80) cc_final: 0.8171 (m-80) REVERT: B 154 MET cc_start: 0.6859 (tpt) cc_final: 0.6308 (tpt) REVERT: B 195 LEU cc_start: 0.7310 (tt) cc_final: 0.7105 (tp) REVERT: B 305 MET cc_start: 0.7951 (mmt) cc_final: 0.7665 (mmp) REVERT: B 355 ARG cc_start: 0.8011 (tmm-80) cc_final: 0.7598 (ttm170) REVERT: B 357 TYR cc_start: 0.7682 (m-80) cc_final: 0.7481 (m-80) REVERT: C 252 THR cc_start: 0.8490 (m) cc_final: 0.8171 (p) REVERT: C 423 ASN cc_start: 0.7887 (t0) cc_final: 0.7678 (t0) REVERT: C 502 MET cc_start: 0.7559 (mmp) cc_final: 0.6769 (mtp) REVERT: C 562 SER cc_start: 0.9009 (t) cc_final: 0.8619 (m) outliers start: 4 outliers final: 3 residues processed: 224 average time/residue: 0.2062 time to fit residues: 68.5884 Evaluate side-chains 180 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 177 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 571 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 0.6980 chunk 119 optimal weight: 0.4980 chunk 66 optimal weight: 0.0050 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN B 444 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12509 Z= 0.170 Angle : 0.476 6.979 17039 Z= 0.248 Chirality : 0.037 0.142 1974 Planarity : 0.004 0.050 2069 Dihedral : 10.062 158.183 1780 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.29 % Allowed : 6.85 % Favored : 91.85 % 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: 3.37 (0.21), residues: 1579 helix: 2.73 (0.14), residues: 1313 sheet: None (None), residues: 0 loop : -0.53 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 316 HIS 0.003 0.001 HIS C 394 PHE 0.015 0.001 PHE B 546 TYR 0.014 0.001 TYR A 385 ARG 0.003 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 177 time to evaluate : 1.356 Fit side-chains REVERT: A 284 LYS cc_start: 0.8515 (mttm) cc_final: 0.7898 (mmtt) REVERT: B 145 ILE cc_start: 0.7808 (mm) cc_final: 0.7598 (pt) REVERT: B 154 MET cc_start: 0.7005 (tpt) cc_final: 0.6386 (tpt) REVERT: B 305 MET cc_start: 0.8051 (mmt) cc_final: 0.7692 (mmp) REVERT: B 355 ARG cc_start: 0.8097 (tmm-80) cc_final: 0.7694 (ttm170) REVERT: B 357 TYR cc_start: 0.7675 (m-80) cc_final: 0.7461 (m-80) REVERT: B 482 ASP cc_start: 0.8839 (t0) cc_final: 0.8576 (t0) REVERT: C 502 MET cc_start: 0.7239 (mmp) cc_final: 0.6490 (mtp) REVERT: C 562 SER cc_start: 0.8928 (t) cc_final: 0.8510 (m) outliers start: 16 outliers final: 9 residues processed: 189 average time/residue: 0.2114 time to fit residues: 61.5532 Evaluate side-chains 172 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 163 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 119 optimal weight: 0.0470 chunk 97 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 143 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN C 423 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12509 Z= 0.173 Angle : 0.451 8.096 17039 Z= 0.233 Chirality : 0.036 0.145 1974 Planarity : 0.004 0.043 2069 Dihedral : 8.491 124.019 1779 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.53 % Allowed : 9.52 % Favored : 88.95 % 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: 3.47 (0.21), residues: 1579 helix: 2.82 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -0.63 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 316 HIS 0.003 0.001 HIS B 288 PHE 0.017 0.001 PHE B 546 TYR 0.011 0.001 TYR A 564 ARG 0.003 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 179 time to evaluate : 1.425 Fit side-chains REVERT: A 154 MET cc_start: 0.6523 (tpp) cc_final: 0.6251 (tpp) REVERT: A 284 LYS cc_start: 0.8508 (mttm) cc_final: 0.7905 (mmtt) REVERT: B 355 ARG cc_start: 0.8107 (tmm-80) cc_final: 0.7585 (ttm170) REVERT: B 357 TYR cc_start: 0.7701 (m-80) cc_final: 0.7357 (m-80) REVERT: B 482 ASP cc_start: 0.8823 (t0) cc_final: 0.8432 (t0) REVERT: C 502 MET cc_start: 0.7229 (mmp) cc_final: 0.6511 (mtp) REVERT: C 556 MET cc_start: 0.7278 (mtp) cc_final: 0.7077 (mtp) REVERT: C 562 SER cc_start: 0.8956 (t) cc_final: 0.8537 (m) outliers start: 19 outliers final: 13 residues processed: 193 average time/residue: 0.2059 time to fit residues: 59.6127 Evaluate side-chains 181 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 168 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12509 Z= 0.203 Angle : 0.467 8.218 17039 Z= 0.243 Chirality : 0.037 0.151 1974 Planarity : 0.004 0.043 2069 Dihedral : 8.037 105.874 1779 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.94 % Allowed : 9.52 % Favored : 88.55 % 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: 3.37 (0.21), residues: 1579 helix: 2.75 (0.14), residues: 1319 sheet: None (None), residues: 0 loop : -0.72 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 178 HIS 0.003 0.001 HIS B 288 PHE 0.018 0.001 PHE B 546 TYR 0.007 0.001 TYR A 564 ARG 0.001 0.000 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 1.368 Fit side-chains REVERT: A 133 ARG cc_start: 0.7621 (ttm170) cc_final: 0.7420 (ttp80) REVERT: A 284 LYS cc_start: 0.8518 (mttm) cc_final: 0.7899 (mmtt) REVERT: B 355 ARG cc_start: 0.8176 (tmm-80) cc_final: 0.7781 (ttm170) REVERT: B 357 TYR cc_start: 0.7749 (m-80) cc_final: 0.7378 (m-80) REVERT: B 360 TYR cc_start: 0.8060 (m-10) cc_final: 0.7852 (m-80) REVERT: C 502 MET cc_start: 0.7270 (mmp) cc_final: 0.6514 (mtp) REVERT: C 562 SER cc_start: 0.8949 (t) cc_final: 0.8546 (m) outliers start: 24 outliers final: 18 residues processed: 184 average time/residue: 0.2114 time to fit residues: 58.2870 Evaluate side-chains 181 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 0.6980 chunk 86 optimal weight: 0.0670 chunk 2 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 105 optimal weight: 40.0000 chunk 0 optimal weight: 50.0000 chunk 77 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12509 Z= 0.158 Angle : 0.441 8.070 17039 Z= 0.227 Chirality : 0.036 0.140 1974 Planarity : 0.004 0.043 2069 Dihedral : 7.650 99.787 1779 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.77 % Allowed : 10.32 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.21), residues: 1579 helix: 2.89 (0.14), residues: 1318 sheet: None (None), residues: 0 loop : -0.74 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 178 HIS 0.003 0.000 HIS B 288 PHE 0.018 0.001 PHE B 546 TYR 0.009 0.001 TYR A 564 ARG 0.001 0.000 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 1.288 Fit side-chains REVERT: A 133 ARG cc_start: 0.7582 (ttm170) cc_final: 0.7362 (ttp80) REVERT: A 284 LYS cc_start: 0.8516 (mttm) cc_final: 0.7903 (mmtt) REVERT: B 248 LEU cc_start: 0.8248 (tp) cc_final: 0.7683 (mp) REVERT: B 355 ARG cc_start: 0.8152 (tmm-80) cc_final: 0.7769 (ttm170) REVERT: B 357 TYR cc_start: 0.7721 (m-80) cc_final: 0.7333 (m-80) REVERT: B 482 ASP cc_start: 0.8747 (t0) cc_final: 0.8403 (t0) REVERT: C 502 MET cc_start: 0.7238 (mmp) cc_final: 0.6482 (mtp) REVERT: C 562 SER cc_start: 0.8920 (t) cc_final: 0.8542 (m) outliers start: 22 outliers final: 16 residues processed: 181 average time/residue: 0.2094 time to fit residues: 56.8475 Evaluate side-chains 180 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 530 GLN Chi-restraints excluded: chain B residue 562 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12509 Z= 0.231 Angle : 0.480 8.700 17039 Z= 0.249 Chirality : 0.037 0.153 1974 Planarity : 0.004 0.043 2069 Dihedral : 7.860 103.475 1779 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.42 % Allowed : 10.00 % Favored : 87.58 % 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: 3.29 (0.21), residues: 1579 helix: 2.71 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -0.84 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 150 HIS 0.003 0.001 HIS B 288 PHE 0.018 0.001 PHE B 546 TYR 0.006 0.001 TYR A 310 ARG 0.001 0.000 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 1.289 Fit side-chains REVERT: A 284 LYS cc_start: 0.8431 (mttm) cc_final: 0.7837 (mmtt) REVERT: B 355 ARG cc_start: 0.8176 (tmm-80) cc_final: 0.7770 (ttm170) REVERT: B 357 TYR cc_start: 0.7795 (m-80) cc_final: 0.7358 (m-80) REVERT: C 502 MET cc_start: 0.7271 (mmp) cc_final: 0.6451 (mtp) REVERT: C 562 SER cc_start: 0.8955 (t) cc_final: 0.8546 (m) outliers start: 30 outliers final: 23 residues processed: 184 average time/residue: 0.2066 time to fit residues: 57.4392 Evaluate side-chains 182 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 159 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 152 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN C 423 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12509 Z= 0.177 Angle : 0.456 8.390 17039 Z= 0.235 Chirality : 0.036 0.143 1974 Planarity : 0.004 0.043 2069 Dihedral : 7.580 101.277 1779 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.85 % Allowed : 10.89 % Favored : 87.26 % 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: 3.45 (0.21), residues: 1579 helix: 2.83 (0.14), residues: 1318 sheet: None (None), residues: 0 loop : -0.81 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 178 HIS 0.003 0.000 HIS B 288 PHE 0.028 0.001 PHE A 146 TYR 0.006 0.001 TYR A 564 ARG 0.004 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 1.291 Fit side-chains REVERT: A 284 LYS cc_start: 0.8440 (mttm) cc_final: 0.7841 (mmtt) REVERT: A 564 TYR cc_start: 0.8495 (m-80) cc_final: 0.8065 (m-80) REVERT: B 248 LEU cc_start: 0.8264 (tp) cc_final: 0.7709 (mp) REVERT: B 355 ARG cc_start: 0.8180 (tmm-80) cc_final: 0.7762 (ttm170) REVERT: B 357 TYR cc_start: 0.7774 (m-80) cc_final: 0.7330 (m-80) REVERT: B 482 ASP cc_start: 0.8777 (t0) cc_final: 0.8512 (t0) REVERT: C 305 MET cc_start: 0.8140 (mmp) cc_final: 0.7881 (mmp) REVERT: C 502 MET cc_start: 0.7131 (mmp) cc_final: 0.6376 (mtp) REVERT: C 562 SER cc_start: 0.8923 (t) cc_final: 0.8539 (m) outliers start: 23 outliers final: 21 residues processed: 175 average time/residue: 0.2079 time to fit residues: 54.7382 Evaluate side-chains 180 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12509 Z= 0.176 Angle : 0.455 9.430 17039 Z= 0.233 Chirality : 0.036 0.143 1974 Planarity : 0.004 0.044 2069 Dihedral : 7.466 101.066 1779 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.02 % Allowed : 11.37 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.21), residues: 1579 helix: 2.84 (0.14), residues: 1318 sheet: None (None), residues: 0 loop : -0.80 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 150 HIS 0.003 0.001 HIS B 288 PHE 0.017 0.001 PHE B 546 TYR 0.006 0.001 TYR A 564 ARG 0.004 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 1.382 Fit side-chains REVERT: A 284 LYS cc_start: 0.8441 (mttm) cc_final: 0.8138 (mttt) REVERT: A 564 TYR cc_start: 0.8500 (m-80) cc_final: 0.8093 (m-80) REVERT: B 355 ARG cc_start: 0.8206 (tmm-80) cc_final: 0.7798 (ttm170) REVERT: B 357 TYR cc_start: 0.7764 (m-80) cc_final: 0.7306 (m-80) REVERT: C 502 MET cc_start: 0.7238 (mmp) cc_final: 0.6379 (mtp) REVERT: C 562 SER cc_start: 0.8925 (t) cc_final: 0.8542 (m) outliers start: 25 outliers final: 22 residues processed: 177 average time/residue: 0.2193 time to fit residues: 58.4681 Evaluate side-chains 177 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.7664 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12509 Z= 0.187 Angle : 0.465 9.377 17039 Z= 0.238 Chirality : 0.036 0.145 1974 Planarity : 0.004 0.043 2069 Dihedral : 7.473 101.499 1779 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.94 % Allowed : 11.77 % Favored : 86.29 % 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: 3.44 (0.21), residues: 1579 helix: 2.83 (0.14), residues: 1318 sheet: None (None), residues: 0 loop : -0.84 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 178 HIS 0.003 0.001 HIS B 288 PHE 0.023 0.001 PHE C 146 TYR 0.006 0.001 TYR A 564 ARG 0.004 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 1.201 Fit side-chains REVERT: A 284 LYS cc_start: 0.8418 (mttm) cc_final: 0.8123 (mttt) REVERT: A 564 TYR cc_start: 0.8499 (m-80) cc_final: 0.8076 (m-80) REVERT: B 355 ARG cc_start: 0.8251 (tmm-80) cc_final: 0.7882 (ttm170) REVERT: B 357 TYR cc_start: 0.7791 (m-80) cc_final: 0.7327 (m-80) REVERT: C 502 MET cc_start: 0.7256 (mmp) cc_final: 0.6393 (mtp) REVERT: C 562 SER cc_start: 0.8925 (t) cc_final: 0.8546 (m) outliers start: 24 outliers final: 22 residues processed: 174 average time/residue: 0.2103 time to fit residues: 55.4599 Evaluate side-chains 178 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 0.0670 chunk 71 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 157 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 133 optimal weight: 0.0060 overall best weight: 0.4934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN C 423 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12509 Z= 0.142 Angle : 0.445 9.877 17039 Z= 0.226 Chirality : 0.035 0.135 1974 Planarity : 0.004 0.044 2069 Dihedral : 7.203 97.325 1779 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.77 % Allowed : 11.85 % Favored : 86.37 % 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: 3.71 (0.22), residues: 1579 helix: 3.03 (0.14), residues: 1313 sheet: None (None), residues: 0 loop : -0.81 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 178 HIS 0.002 0.000 HIS B 288 PHE 0.022 0.001 PHE C 146 TYR 0.004 0.001 TYR A 564 ARG 0.004 0.000 ARG A 163 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 1.257 Fit side-chains REVERT: A 154 MET cc_start: 0.6850 (tpp) cc_final: 0.6625 (mmt) REVERT: A 284 LYS cc_start: 0.8442 (mttm) cc_final: 0.8143 (mttt) REVERT: A 564 TYR cc_start: 0.8419 (m-80) cc_final: 0.8026 (m-80) REVERT: B 355 ARG cc_start: 0.8054 (tmm-80) cc_final: 0.7733 (ttm170) REVERT: B 357 TYR cc_start: 0.7754 (m-80) cc_final: 0.7294 (m-80) REVERT: B 477 LEU cc_start: 0.7731 (tt) cc_final: 0.7189 (tt) REVERT: B 485 GLN cc_start: 0.7826 (mp10) cc_final: 0.7247 (mp10) REVERT: C 502 MET cc_start: 0.7083 (mmp) cc_final: 0.6349 (mtp) REVERT: C 562 SER cc_start: 0.8894 (t) cc_final: 0.8521 (m) outliers start: 22 outliers final: 19 residues processed: 182 average time/residue: 0.2325 time to fit residues: 64.9822 Evaluate side-chains 182 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 163 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 125 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.163889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128879 restraints weight = 14468.117| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.60 r_work: 0.3332 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12509 Z= 0.167 Angle : 0.465 11.692 17039 Z= 0.235 Chirality : 0.036 0.151 1974 Planarity : 0.004 0.044 2069 Dihedral : 7.258 99.235 1779 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.69 % Allowed : 12.18 % Favored : 86.13 % 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: 3.65 (0.22), residues: 1579 helix: 2.98 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.81 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 178 HIS 0.003 0.000 HIS B 288 PHE 0.021 0.001 PHE C 146 TYR 0.005 0.001 TYR B 310 ARG 0.004 0.000 ARG A 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2519.26 seconds wall clock time: 45 minutes 54.77 seconds (2754.77 seconds total)