Starting phenix.real_space_refine on Sun Dec 10 09:54:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0r_10357/12_2023/6t0r_10357.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0r_10357/12_2023/6t0r_10357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0r_10357/12_2023/6t0r_10357.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0r_10357/12_2023/6t0r_10357.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0r_10357/12_2023/6t0r_10357.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0r_10357/12_2023/6t0r_10357.pdb" } resolution = 2.82 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= 0.004 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 20 5.49 5 S 92 5.16 5 C 8826 2.51 5 N 2460 2.21 5 O 2722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 571": "NH1" <-> "NH2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B ARG 707": "NH1" <-> "NH2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 14120 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 701, 5716 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 25, 'TRANS': 675} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 701, 5716 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 25, 'TRANS': 675} Chain breaks: 2 bond proxies already assigned to first conformer: 5828 Chain: "B" Number of atoms: 5919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 739, 5919 Classifications: {'peptide': 739} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 710} Chain breaks: 1 Chain: "C" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2016 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain: "V" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 430 Classifications: {'RNA': 20} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna2p': 10, 'rna3p': 9} Chain breaks: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "V" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 10.91, per 1000 atoms: 0.77 Number of scatterers: 14120 At special positions: 0 Unit cell: (94.2732, 118.654, 117.841, 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 92 16.00 P 20 15.00 O 2722 8.00 N 2460 7.00 C 8826 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: 5.59 Conformation dependent library (CDL) restraints added in 3.6 seconds 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3194 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 17 sheets defined 50.3% alpha, 12.5% beta 2 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 5.46 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 removed outlier: 3.648A pdb=" N ARG A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 98 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.657A pdb=" N TYR A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 185 Processing helix chain 'A' and resid 188 through 193 removed outlier: 4.046A pdb=" N ARG A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLN A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 188 through 193' Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 248 removed outlier: 3.602A pdb=" N ALA A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 330 through 347 removed outlier: 3.627A pdb=" N TYR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 365 Processing helix chain 'A' and resid 399 through 410 removed outlier: 4.548A pdb=" N GLN A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 410 " --> pdb=" O PHE A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 446 Processing helix chain 'A' and resid 448 through 471 removed outlier: 3.533A pdb=" N GLU A 452 " --> pdb=" O CYS A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 575 Processing helix chain 'A' and resid 577 through 599 removed outlier: 4.053A pdb=" N VAL A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 627 through 645 Processing helix chain 'A' and resid 647 through 669 removed outlier: 4.505A pdb=" N LYS A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 688 removed outlier: 4.072A pdb=" N CYS A 688 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 712 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 3.964A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 115 removed outlier: 3.623A pdb=" N GLN B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.786A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B 124 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 173 removed outlier: 3.524A pdb=" N PHE B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 275 through 289 removed outlier: 3.975A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.682A pdb=" N ASN B 312 " --> pdb=" O LYS B 308 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 313' Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.729A pdb=" N ALA B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.559A pdb=" N TYR B 380 " --> pdb=" O ASN B 377 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 381 " --> pdb=" O LEU B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 381' Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 427 removed outlier: 3.577A pdb=" N SER B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 473 removed outlier: 3.502A pdb=" N VAL B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 572 through 582 removed outlier: 3.514A pdb=" N GLU B 582 " --> pdb=" O ARG B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.547A pdb=" N LEU B 589 " --> pdb=" O LYS B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 683 through 700 removed outlier: 3.839A pdb=" N ARG B 687 " --> pdb=" O LEU B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 732 Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 1 through 12 Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 30 through 34 removed outlier: 3.642A pdb=" N TYR C 34 " --> pdb=" O ILE C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 52 removed outlier: 3.735A pdb=" N ALA C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 removed outlier: 3.654A pdb=" N ILE C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.891A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 removed outlier: 4.560A pdb=" N ARG C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 167 removed outlier: 4.145A pdb=" N GLN C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU C 161 " --> pdb=" O ARG C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 172 removed outlier: 3.893A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.711A pdb=" N LEU C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.820A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.564A pdb=" N GLN C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.057A pdb=" N PHE A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 147 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 155 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'A' and resid 274 through 275 removed outlier: 6.466A pdb=" N LYS A 274 " --> pdb=" O LYS A 397 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293 removed outlier: 7.235A pdb=" N TYR A 496 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU A 558 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU A 539 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 560 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL A 537 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 537 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 290 through 293 removed outlier: 5.403A pdb=" N THR A 493 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N CYS A 484 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU A 495 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR A 482 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY A 497 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 476 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR A 475 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 372 through 374 removed outlier: 4.349A pdb=" N GLN B 367 " --> pdb=" O MET A 374 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 622 through 626 removed outlier: 6.338A pdb=" N GLY A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLU A 618 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLU A 624 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP B 2 " --> pdb=" O GLU A 618 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.513A pdb=" N ARG B 135 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 180 through 183 Processing sheet with id=AB3, first strand: chain 'B' and resid 186 through 192 removed outlier: 7.877A pdb=" N ASN B 678 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG B 203 " --> pdb=" O ASN B 678 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.969A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB6, first strand: chain 'C' and resid 57 through 59 Processing sheet with id=AB7, first strand: chain 'C' and resid 129 through 133 removed outlier: 4.550A pdb=" N GLN C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.362A pdb=" N ARG C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) 665 hydrogen bonds defined for protein. 1872 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 5 hydrogen bonds 10 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 4.94 Time building geometry restraints manager: 6.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3789 1.33 - 1.45: 2601 1.45 - 1.57: 7829 1.57 - 1.69: 38 1.69 - 1.81: 160 Bond restraints: 14417 Sorted by residual: bond pdb=" C GLU A 604 " pdb=" N PRO A 605 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.35e+00 bond pdb=" CB VAL A 631 " pdb=" CG2 VAL A 631 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.30e+00 bond pdb=" CG1 ILE C 67 " pdb=" CD1 ILE C 67 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.31e+00 bond pdb=" CA SER A 504 " pdb=" CB SER A 504 " ideal model delta sigma weight residual 1.539 1.485 0.055 4.88e-02 4.20e+02 1.26e+00 bond pdb=" CG1 ILE B 389 " pdb=" CD1 ILE B 389 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.25e+00 ... (remaining 14412 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.31: 479 106.31 - 113.26: 7741 113.26 - 120.22: 5389 120.22 - 127.17: 5730 127.17 - 134.12: 192 Bond angle restraints: 19531 Sorted by residual: angle pdb=" N ILE A 79 " pdb=" CA ILE A 79 " pdb=" C ILE A 79 " ideal model delta sigma weight residual 113.42 108.10 5.32 1.17e+00 7.31e-01 2.07e+01 angle pdb=" C HIS A 297 " pdb=" N GLU A 298 " pdb=" CA GLU A 298 " ideal model delta sigma weight residual 121.54 127.38 -5.84 1.91e+00 2.74e-01 9.36e+00 angle pdb=" O4' A V 7 " pdb=" C1' A V 7 " pdb=" N9 A V 7 " ideal model delta sigma weight residual 108.20 112.66 -4.46 1.50e+00 4.44e-01 8.86e+00 angle pdb=" CA TYR B 557 " pdb=" CB TYR B 557 " pdb=" CG TYR B 557 " ideal model delta sigma weight residual 113.90 108.59 5.31 1.80e+00 3.09e-01 8.72e+00 angle pdb=" CA SER B 404 " pdb=" C SER B 404 " pdb=" N PRO B 405 " ideal model delta sigma weight residual 118.44 122.89 -4.45 1.59e+00 3.96e-01 7.82e+00 ... (remaining 19526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 7971 17.81 - 35.62: 597 35.62 - 53.43: 152 53.43 - 71.24: 51 71.24 - 89.05: 14 Dihedral angle restraints: 8785 sinusoidal: 3848 harmonic: 4937 Sorted by residual: dihedral pdb=" CA THR B 223 " pdb=" C THR B 223 " pdb=" N LEU B 224 " pdb=" CA LEU B 224 " ideal model delta harmonic sigma weight residual 180.00 159.37 20.63 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ASN A 8 " pdb=" C ASN A 8 " pdb=" N PHE A 9 " pdb=" CA PHE A 9 " ideal model delta harmonic sigma weight residual -180.00 -159.69 -20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA LEU A 219 " pdb=" C LEU A 219 " pdb=" N PRO A 220 " pdb=" CA PRO A 220 " ideal model delta harmonic sigma weight residual 180.00 161.02 18.98 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 8782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1485 0.043 - 0.086: 518 0.086 - 0.129: 122 0.129 - 0.172: 13 0.172 - 0.215: 3 Chirality restraints: 2141 Sorted by residual: chirality pdb=" CB ILE B 368 " pdb=" CA ILE B 368 " pdb=" CG1 ILE B 368 " pdb=" CG2 ILE B 368 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C1' A V 7 " pdb=" O4' A V 7 " pdb=" C2' A V 7 " pdb=" N9 A V 7 " both_signs ideal model delta sigma weight residual False 2.44 2.25 0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CB VAL A 445 " pdb=" CA VAL A 445 " pdb=" CG1 VAL A 445 " pdb=" CG2 VAL A 445 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.88e-01 ... (remaining 2138 not shown) Planarity restraints: 2439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 619 " -0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO A 620 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 620 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 620 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A V 7 " -0.031 2.00e-02 2.50e+03 1.47e-02 5.93e+00 pdb=" N9 A V 7 " 0.036 2.00e-02 2.50e+03 pdb=" C8 A V 7 " -0.000 2.00e-02 2.50e+03 pdb=" N7 A V 7 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A V 7 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A V 7 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A V 7 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A V 7 " -0.000 2.00e-02 2.50e+03 pdb=" C2 A V 7 " -0.000 2.00e-02 2.50e+03 pdb=" N3 A V 7 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A V 7 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 111 " 0.039 5.00e-02 4.00e+02 5.82e-02 5.41e+00 pdb=" N PRO C 112 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 112 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 112 " 0.033 5.00e-02 4.00e+02 ... (remaining 2436 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3824 2.80 - 3.33: 11808 3.33 - 3.85: 24720 3.85 - 4.38: 29485 4.38 - 4.90: 49848 Nonbonded interactions: 119685 Sorted by model distance: nonbonded pdb=" O THR C 224 " pdb=" OG1 THR C 224 " model vdw 2.279 2.440 nonbonded pdb=" OE1 GLU A 588 " pdb=" OG1 THR B 543 " model vdw 2.290 2.440 nonbonded pdb=" OD2 ASP B 593 " pdb=" OH TYR B 620 " model vdw 2.294 2.440 nonbonded pdb=" O ASN A 3 " pdb=" OG1 THR A 7 " model vdw 2.294 2.440 nonbonded pdb=" O ALA B 113 " pdb=" OG1 THR B 117 " model vdw 2.295 2.440 ... (remaining 119680 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.900 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 48.880 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 0.056 14417 Z= 0.303 Angle : 0.662 8.137 19531 Z= 0.389 Chirality : 0.045 0.215 2141 Planarity : 0.006 0.064 2439 Dihedral : 14.438 89.049 5591 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.99 % Allowed : 7.52 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 (0.16), residues: 1679 helix: -1.80 (0.14), residues: 764 sheet: -1.82 (0.34), residues: 189 loop : -2.07 (0.19), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 438 HIS 0.005 0.001 HIS B 32 PHE 0.020 0.002 PHE A 515 TYR 0.025 0.002 TYR B 557 ARG 0.005 0.001 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 294 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 20 residues processed: 349 average time/residue: 1.4451 time to fit residues: 546.2909 Evaluate side-chains 230 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 210 time to evaluate : 1.557 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 6 average time/residue: 0.4866 time to fit residues: 5.9242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 4.9990 chunk 128 optimal weight: 0.0970 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 133 optimal weight: 0.0270 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN B 124 GLN B 314 ASN B 452 ASN B 690 GLN C 87 ASN C 182 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14417 Z= 0.169 Angle : 0.495 6.427 19531 Z= 0.266 Chirality : 0.039 0.204 2141 Planarity : 0.004 0.046 2439 Dihedral : 9.386 75.584 2126 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.26 % Allowed : 16.37 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -1.08 (0.19), residues: 1679 helix: 0.32 (0.18), residues: 771 sheet: -1.31 (0.37), residues: 176 loop : -1.67 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 49 HIS 0.003 0.001 HIS C 127 PHE 0.014 0.001 PHE A 53 TYR 0.024 0.001 TYR B 557 ARG 0.009 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 213 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 28 residues processed: 248 average time/residue: 1.3873 time to fit residues: 374.7995 Evaluate side-chains 226 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 198 time to evaluate : 1.626 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 5 average time/residue: 0.1304 time to fit residues: 3.4376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 HIS B 158 ASN B 314 ASN B 690 GLN C 182 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14417 Z= 0.244 Angle : 0.521 7.301 19531 Z= 0.278 Chirality : 0.040 0.159 2141 Planarity : 0.004 0.044 2439 Dihedral : 9.391 75.852 2126 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.19 % Allowed : 17.17 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.32 (0.20), residues: 1679 helix: 1.04 (0.18), residues: 771 sheet: -1.12 (0.38), residues: 170 loop : -1.33 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 49 HIS 0.004 0.001 HIS A 360 PHE 0.016 0.002 PHE A 702 TYR 0.025 0.002 TYR B 557 ARG 0.010 0.001 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 197 time to evaluate : 1.751 Fit side-chains revert: symmetry clash outliers start: 63 outliers final: 36 residues processed: 240 average time/residue: 1.3219 time to fit residues: 347.7861 Evaluate side-chains 221 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 185 time to evaluate : 1.659 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 29 residues processed: 7 average time/residue: 0.3033 time to fit residues: 5.3377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN B 452 ASN B 690 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 14417 Z= 0.365 Angle : 0.589 7.957 19531 Z= 0.312 Chirality : 0.043 0.184 2141 Planarity : 0.005 0.042 2439 Dihedral : 9.498 77.335 2126 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.99 % Allowed : 17.30 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.25 (0.20), residues: 1679 helix: 1.07 (0.18), residues: 779 sheet: -1.13 (0.38), residues: 170 loop : -1.28 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 49 HIS 0.005 0.001 HIS A 360 PHE 0.020 0.002 PHE A 702 TYR 0.027 0.002 TYR B 557 ARG 0.006 0.001 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 187 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 40 residues processed: 235 average time/residue: 1.2773 time to fit residues: 330.7081 Evaluate side-chains 220 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 180 time to evaluate : 1.764 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 31 residues processed: 9 average time/residue: 0.3499 time to fit residues: 6.6674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 2 optimal weight: 0.0040 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 113 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.0040 chunk 147 optimal weight: 0.0870 chunk 41 optimal weight: 1.9990 overall best weight: 0.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 585 GLN B 127 GLN B 158 ASN B 314 ASN B 690 GLN C 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14417 Z= 0.128 Angle : 0.455 7.017 19531 Z= 0.243 Chirality : 0.037 0.149 2141 Planarity : 0.003 0.039 2439 Dihedral : 9.232 74.798 2126 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.66 % Allowed : 19.10 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 (0.21), residues: 1679 helix: 1.69 (0.19), residues: 767 sheet: -0.84 (0.37), residues: 177 loop : -1.05 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 49 HIS 0.002 0.000 HIS B 32 PHE 0.013 0.001 PHE A 46 TYR 0.018 0.001 TYR B 557 ARG 0.005 0.000 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 201 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 37 residues processed: 243 average time/residue: 1.2363 time to fit residues: 331.3620 Evaluate side-chains 225 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 188 time to evaluate : 1.776 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 35 residues processed: 3 average time/residue: 0.1383 time to fit residues: 3.0781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 314 ASN B 452 ASN B 690 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14417 Z= 0.212 Angle : 0.498 8.250 19531 Z= 0.264 Chirality : 0.039 0.152 2141 Planarity : 0.004 0.041 2439 Dihedral : 9.255 75.773 2126 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.93 % Allowed : 19.29 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.43 (0.21), residues: 1679 helix: 1.73 (0.19), residues: 768 sheet: -0.82 (0.38), residues: 170 loop : -0.99 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 49 HIS 0.003 0.001 HIS A 360 PHE 0.021 0.001 PHE C 168 TYR 0.023 0.001 TYR B 557 ARG 0.004 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 192 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 44 residues processed: 233 average time/residue: 1.1959 time to fit residues: 306.3530 Evaluate side-chains 229 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 185 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 36 residues processed: 9 average time/residue: 0.3651 time to fit residues: 5.5329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 93 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 313 GLN B 314 ASN B 452 ASN B 597 ASN B 690 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14417 Z= 0.211 Angle : 0.498 8.210 19531 Z= 0.264 Chirality : 0.040 0.195 2141 Planarity : 0.004 0.041 2439 Dihedral : 9.232 75.882 2126 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.93 % Allowed : 19.83 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.51 (0.21), residues: 1679 helix: 1.80 (0.19), residues: 762 sheet: -0.79 (0.39), residues: 170 loop : -0.93 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 49 HIS 0.003 0.001 HIS A 360 PHE 0.017 0.001 PHE C 168 TYR 0.022 0.001 TYR B 557 ARG 0.007 0.000 ARG B 707 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 188 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 41 residues processed: 231 average time/residue: 1.2318 time to fit residues: 314.1406 Evaluate side-chains 227 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 186 time to evaluate : 1.666 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 35 residues processed: 7 average time/residue: 0.6475 time to fit residues: 7.5669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS B 127 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 314 ASN B 452 ASN B 690 GLN C 39 GLN C 182 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14417 Z= 0.193 Angle : 0.487 7.533 19531 Z= 0.259 Chirality : 0.039 0.178 2141 Planarity : 0.003 0.041 2439 Dihedral : 9.190 75.658 2126 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.59 % Allowed : 19.89 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.59 (0.21), residues: 1679 helix: 1.84 (0.19), residues: 763 sheet: -0.80 (0.39), residues: 162 loop : -0.86 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 49 HIS 0.003 0.001 HIS A 360 PHE 0.025 0.001 PHE A 46 TYR 0.022 0.001 TYR B 557 ARG 0.003 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 193 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 46 residues processed: 230 average time/residue: 1.2800 time to fit residues: 324.0554 Evaluate side-chains 229 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 183 time to evaluate : 1.554 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 38 residues processed: 9 average time/residue: 0.5518 time to fit residues: 8.1579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 161 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 452 ASN B 690 GLN C 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14417 Z= 0.149 Angle : 0.465 7.752 19531 Z= 0.247 Chirality : 0.038 0.169 2141 Planarity : 0.003 0.041 2439 Dihedral : 9.095 74.854 2126 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.79 % Allowed : 21.09 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1679 helix: 1.92 (0.19), residues: 768 sheet: -0.79 (0.40), residues: 162 loop : -0.83 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 49 HIS 0.003 0.001 HIS B 32 PHE 0.012 0.001 PHE A 46 TYR 0.019 0.001 TYR B 557 ARG 0.009 0.000 ARG B 707 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 197 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 37 residues processed: 234 average time/residue: 1.2378 time to fit residues: 320.0441 Evaluate side-chains 228 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 191 time to evaluate : 1.770 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 36 residues processed: 2 average time/residue: 0.1493 time to fit residues: 2.8501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 GLN B 313 GLN B 690 GLN C 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14417 Z= 0.336 Angle : 0.560 8.494 19531 Z= 0.295 Chirality : 0.043 0.182 2141 Planarity : 0.004 0.042 2439 Dihedral : 9.247 76.685 2126 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.93 % Allowed : 20.89 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.33 (0.20), residues: 1679 helix: 1.52 (0.19), residues: 782 sheet: -0.91 (0.40), residues: 160 loop : -0.93 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 49 HIS 0.004 0.001 HIS A 360 PHE 0.016 0.002 PHE A 702 TYR 0.024 0.002 TYR B 557 ARG 0.006 0.001 ARG B 707 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 188 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 38 residues processed: 225 average time/residue: 1.2356 time to fit residues: 306.7500 Evaluate side-chains 222 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 184 time to evaluate : 1.606 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 35 residues processed: 4 average time/residue: 0.3870 time to fit residues: 4.2497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 135 optimal weight: 0.0870 chunk 56 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN B 313 GLN B 690 GLN C 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.163122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.133222 restraints weight = 19245.621| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.62 r_work: 0.3303 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14417 Z= 0.147 Angle : 0.475 8.622 19531 Z= 0.252 Chirality : 0.038 0.156 2141 Planarity : 0.003 0.041 2439 Dihedral : 9.062 74.295 2126 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.79 % Allowed : 21.42 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.61 (0.21), residues: 1679 helix: 1.80 (0.19), residues: 773 sheet: -0.75 (0.40), residues: 162 loop : -0.82 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 49 HIS 0.003 0.000 HIS B 32 PHE 0.013 0.001 PHE C 168 TYR 0.018 0.001 TYR B 557 ARG 0.005 0.000 ARG C 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5831.83 seconds wall clock time: 105 minutes 37.82 seconds (6337.82 seconds total)