Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 13:45:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3v_32294/04_2023/7w3v_32294.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3v_32294/04_2023/7w3v_32294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3v_32294/04_2023/7w3v_32294.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3v_32294/04_2023/7w3v_32294.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3v_32294/04_2023/7w3v_32294.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3v_32294/04_2023/7w3v_32294.pdb" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 4755 2.51 5 N 1197 2.21 5 O 1499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 281": "OD1" <-> "OD2" Residue "C GLU 344": "OE1" <-> "OE2" Residue "C ASP 394": "OD1" <-> "OD2" Residue "C PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 464": "OD1" <-> "OD2" Residue "C TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 7480 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1675 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 5, 'TRANS': 216} Chain: "C" Number of atoms: 5487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5487 Classifications: {'peptide': 696} Link IDs: {'PTRANS': 29, 'TRANS': 666} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 4.39, per 1000 atoms: 0.59 Number of scatterers: 7480 At special positions: 0 Unit cell: (92.307, 90.185, 120.954, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 1499 8.00 N 1197 7.00 C 4755 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 64 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 621 " - pdb=" SG CYS C 644 " distance=2.03 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 Links applied ALPHA1-2 " MAN D 5 " - " MAN D 6 " ALPHA1-3 " BMA D 3 " - " MAN D 8 " " MAN D 4 " - " MAN D 7 " ALPHA1-6 " BMA D 3 " - " MAN D 4 " " MAN D 4 " - " MAN D 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG B 1 " - " ASN C 73 " " NAG C1001 " - " ASN C 159 " " NAG C1002 " - " ASN C 234 " " NAG C1003 " - " ASN C 261 " " NAG C1004 " - " ASN C 532 " " NAG C1005 " - " ASN C 542 " " NAG C1006 " - " ASN C 562 " " NAG C1007 " - " ASN C 591 " " NAG C1008 " - " ASN C 660 " " NAG D 1 " - " ASN C 143 " " NAG E 1 " - " ASN C 311 " " NAG F 1 " - " ASN C 481 " " NAG G 1 " - " ASN C 647 " Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1710 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 11 sheets defined 16.6% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'C' and resid 31 through 45 removed outlier: 3.511A pdb=" N GLY C 44 " --> pdb=" O GLU C 40 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 45 " --> pdb=" O PHE C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 105 through 111 removed outlier: 3.849A pdb=" N LEU C 108 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 136 removed outlier: 3.900A pdb=" N ILE C 133 " --> pdb=" O PRO C 130 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE C 136 " --> pdb=" O ILE C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.667A pdb=" N PHE C 157 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS C 158 " --> pdb=" O THR C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 184 removed outlier: 3.782A pdb=" N SER C 182 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS C 183 " --> pdb=" O TRP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 228 through 234 Processing helix chain 'C' and resid 256 through 263 removed outlier: 4.134A pdb=" N SER C 263 " --> pdb=" O PHE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 285 Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 337 through 340 removed outlier: 3.855A pdb=" N ARG C 340 " --> pdb=" O SER C 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 337 through 340' Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 428 through 434 removed outlier: 3.914A pdb=" N GLY C 432 " --> pdb=" O GLN C 429 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 434 " --> pdb=" O ILE C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 458 removed outlier: 3.634A pdb=" N MET C 454 " --> pdb=" O PRO C 451 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY C 455 " --> pdb=" O GLU C 452 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 457 " --> pdb=" O MET C 454 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER C 458 " --> pdb=" O GLY C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 480 removed outlier: 3.551A pdb=" N HIS C 478 " --> pdb=" O THR C 475 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 480 " --> pdb=" O SER C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 621 removed outlier: 3.687A pdb=" N CYS C 621 " --> pdb=" O SER C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 648 Processing helix chain 'C' and resid 666 through 672 removed outlier: 3.723A pdb=" N LEU C 672 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 removed outlier: 6.891A pdb=" N ALA A 64 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE A 58 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE A 63 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER A 235 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TRP A 71 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR A 227 " --> pdb=" O TRP A 71 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS A 105 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE A 236 " --> pdb=" O LYS A 103 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS A 103 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA A 238 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.561A pdb=" N TYR A 34 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 93 removed outlier: 4.300A pdb=" N LYS A 92 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE A 124 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU A 217 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASP A 122 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA A 219 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER A 120 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N THR A 221 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASP A 118 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA A 117 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ALA A 143 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 119 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLU A 136 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N PHE A 182 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N MET A 138 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ALA A 184 " --> pdb=" O MET A 138 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N TRP A 140 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 158 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 148 Processing sheet with id=AA5, first strand: chain 'C' and resid 70 through 71 removed outlier: 6.845A pdb=" N LEU C 82 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 141 through 143 removed outlier: 6.532A pdb=" N LEU C 142 " --> pdb=" O ASP C 167 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU C 166 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU C 190 " --> pdb=" O ASP C 216 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU C 215 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU C 318 " --> pdb=" O GLY C 347 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU C 346 " --> pdb=" O TYR C 370 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP C 394 " --> pdb=" O LEU C 369 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU C 393 " --> pdb=" O HIS C 417 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU C 416 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C 440 " --> pdb=" O ASP C 464 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE C 463 " --> pdb=" O ASP C 489 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU C 488 " --> pdb=" O ASN C 513 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE C 512 " --> pdb=" O ASP C 537 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU C 536 " --> pdb=" O ASN C 562 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU C 561 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE C 585 " --> pdb=" O TYR C 607 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 630 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU C 654 " --> pdb=" O TYR C 679 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.354A pdb=" N GLY C 151 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU C 173 " --> pdb=" O ASP C 196 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.408A pdb=" N LEU C 357 " --> pdb=" O MET C 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'C' and resid 569 through 570 removed outlier: 5.632A pdb=" N GLY C 570 " --> pdb=" O SER C 593 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE C 592 " --> pdb=" O GLN C 612 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE C 614 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLY C 594 " --> pdb=" O PHE C 614 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE C 613 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER C 638 " --> pdb=" O PHE C 613 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLY C 615 " --> pdb=" O SER C 638 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N PHE C 637 " --> pdb=" O ASN C 660 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N SER C 662 " --> pdb=" O PHE C 637 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLY C 639 " --> pdb=" O SER C 662 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LYS C 664 " --> pdb=" O GLY C 639 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE C 661 " --> pdb=" O SER C 684 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER C 686 " --> pdb=" O PHE C 661 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLY C 663 " --> pdb=" O SER C 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 781 through 789 removed outlier: 3.832A pdb=" N MET C 781 " --> pdb=" O TYR C 798 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY C 787 " --> pdb=" O TYR C 792 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR C 792 " --> pdb=" O GLY C 787 " (cutoff:3.500A) 133 hydrogen bonds defined for protein. 285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2323 1.34 - 1.46: 1832 1.46 - 1.58: 3441 1.58 - 1.70: 0 1.70 - 1.81: 42 Bond restraints: 7638 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.06e+00 bond pdb=" C1 NAG C1002 " pdb=" O5 NAG C1002 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.75e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.67e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 NAG C1007 " pdb=" O5 NAG C1007 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.07e+00 ... (remaining 7633 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.63: 188 106.63 - 113.47: 4341 113.47 - 120.32: 2538 120.32 - 127.16: 3218 127.16 - 134.01: 73 Bond angle restraints: 10358 Sorted by residual: angle pdb=" N ILE C 620 " pdb=" CA ILE C 620 " pdb=" C ILE C 620 " ideal model delta sigma weight residual 111.91 108.11 3.80 8.90e-01 1.26e+00 1.82e+01 angle pdb=" C PHE C 136 " pdb=" N LYS C 137 " pdb=" CA LYS C 137 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 1.00e+01 angle pdb=" C LEU C 312 " pdb=" N THR C 313 " pdb=" CA THR C 313 " ideal model delta sigma weight residual 121.54 126.40 -4.86 1.91e+00 2.74e-01 6.47e+00 angle pdb=" C ILE A 215 " pdb=" N THR A 216 " pdb=" CA THR A 216 " ideal model delta sigma weight residual 122.73 118.78 3.95 1.62e+00 3.81e-01 5.93e+00 angle pdb=" C PHE C 250 " pdb=" N SER C 251 " pdb=" CA SER C 251 " ideal model delta sigma weight residual 121.54 126.08 -4.54 1.91e+00 2.74e-01 5.65e+00 ... (remaining 10353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3958 17.98 - 35.95: 324 35.95 - 53.93: 54 53.93 - 71.91: 10 71.91 - 89.89: 4 Dihedral angle restraints: 4350 sinusoidal: 1693 harmonic: 2657 Sorted by residual: dihedral pdb=" CB CYS C 30 " pdb=" SG CYS C 30 " pdb=" SG CYS C 64 " pdb=" CB CYS C 64 " ideal model delta sinusoidal sigma weight residual 93.00 46.84 46.16 1 1.00e+01 1.00e-02 2.95e+01 dihedral pdb=" CA PHE C 260 " pdb=" C PHE C 260 " pdb=" N ASN C 261 " pdb=" CA ASN C 261 " ideal model delta harmonic sigma weight residual 180.00 158.85 21.15 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA PHE C 284 " pdb=" C PHE C 284 " pdb=" N GLY C 285 " pdb=" CA GLY C 285 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 4347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1048 0.063 - 0.126: 177 0.126 - 0.188: 12 0.188 - 0.251: 0 0.251 - 0.314: 4 Chirality restraints: 1241 Sorted by residual: chirality pdb=" C1 NAG C1003 " pdb=" ND2 ASN C 261 " pdb=" C2 NAG C1003 " pdb=" O5 NAG C1003 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C1 NAG C1004 " pdb=" ND2 ASN C 532 " pdb=" C2 NAG C1004 " pdb=" O5 NAG C1004 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN C 481 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 1238 not shown) Planarity restraints: 1293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 792 " 0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO C 793 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 793 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 793 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 261 " -0.017 2.00e-02 2.50e+03 1.58e-02 3.12e+00 pdb=" CG ASN C 261 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN C 261 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN C 261 " 0.017 2.00e-02 2.50e+03 pdb=" C1 NAG C1003 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 614 " 0.006 2.00e-02 2.50e+03 9.66e-03 1.63e+00 pdb=" CG PHE C 614 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE C 614 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 614 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 614 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 614 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 614 " -0.000 2.00e-02 2.50e+03 ... (remaining 1290 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1191 2.76 - 3.30: 6969 3.30 - 3.83: 11850 3.83 - 4.37: 14502 4.37 - 4.90: 24817 Nonbonded interactions: 59329 Sorted by model distance: nonbonded pdb=" OG1 THR C 101 " pdb=" OE2 GLU C 123 " model vdw 2.228 2.440 nonbonded pdb=" O CYS C 220 " pdb=" ND2 ASN C 248 " model vdw 2.248 2.520 nonbonded pdb=" OH TYR A 69 " pdb=" OH TYR A 108 " model vdw 2.268 2.440 nonbonded pdb=" NZ LYS A 155 " pdb=" O7 NAG D 2 " model vdw 2.272 2.520 nonbonded pdb=" OD1 ASP C 319 " pdb=" OG SER C 321 " model vdw 2.304 2.440 ... (remaining 59324 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 'B' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.630 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: 3.490 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 23.970 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 7638 Z= 0.229 Angle : 0.654 7.220 10358 Z= 0.318 Chirality : 0.048 0.314 1241 Planarity : 0.004 0.057 1280 Dihedral : 13.423 89.886 2631 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer Outliers : 0.12 % 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: -2.67 (0.27), residues: 910 helix: -2.30 (0.43), residues: 133 sheet: -2.16 (0.36), residues: 200 loop : -1.50 (0.25), residues: 577 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 0.892 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.2090 time to fit residues: 49.9535 Evaluate side-chains 161 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.901 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 GLN C 650 ASN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 7638 Z= 0.387 Angle : 0.645 8.203 10358 Z= 0.327 Chirality : 0.049 0.337 1241 Planarity : 0.004 0.038 1280 Dihedral : 5.143 20.307 970 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer Outliers : 1.35 % 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: -2.71 (0.27), residues: 910 helix: -2.23 (0.44), residues: 129 sheet: -1.89 (0.35), residues: 217 loop : -1.66 (0.26), residues: 564 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 175 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 179 average time/residue: 0.2112 time to fit residues: 50.5965 Evaluate side-chains 177 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0709 time to fit residues: 2.5284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 22 optimal weight: 0.0270 chunk 82 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 650 ASN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 7638 Z= 0.164 Angle : 0.547 8.891 10358 Z= 0.278 Chirality : 0.044 0.212 1241 Planarity : 0.003 0.031 1280 Dihedral : 4.725 16.708 970 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer Outliers : 0.86 % 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: -2.59 (0.27), residues: 910 helix: -2.11 (0.45), residues: 127 sheet: -2.00 (0.34), residues: 230 loop : -1.48 (0.26), residues: 553 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 164 time to evaluate : 0.913 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 166 average time/residue: 0.2136 time to fit residues: 47.3342 Evaluate side-chains 166 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 0.820 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0741 time to fit residues: 1.9740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.4980 chunk 42 optimal weight: 0.1980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 372 GLN ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 GLN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 7638 Z= 0.206 Angle : 0.546 6.671 10358 Z= 0.276 Chirality : 0.045 0.213 1241 Planarity : 0.003 0.030 1280 Dihedral : 4.704 16.713 970 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer Outliers : 1.48 % 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: -2.54 (0.27), residues: 910 helix: -2.13 (0.44), residues: 127 sheet: -1.93 (0.33), residues: 253 loop : -1.40 (0.27), residues: 530 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 165 average time/residue: 0.2150 time to fit residues: 47.3360 Evaluate side-chains 168 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 0.932 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0747 time to fit residues: 2.4194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 190 ASN C 86 ASN ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 7638 Z= 0.359 Angle : 0.632 8.355 10358 Z= 0.318 Chirality : 0.048 0.224 1241 Planarity : 0.004 0.032 1280 Dihedral : 5.131 20.328 970 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer Outliers : 2.09 % 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: -2.60 (0.27), residues: 910 helix: -2.10 (0.44), residues: 129 sheet: -1.93 (0.32), residues: 255 loop : -1.47 (0.26), residues: 526 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 171 time to evaluate : 0.946 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 180 average time/residue: 0.2103 time to fit residues: 50.9189 Evaluate side-chains 178 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 0.968 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0735 time to fit residues: 2.7419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 86 ASN ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 650 ASN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 7638 Z= 0.229 Angle : 0.572 7.920 10358 Z= 0.289 Chirality : 0.046 0.278 1241 Planarity : 0.003 0.031 1280 Dihedral : 4.927 17.983 970 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer Outliers : 1.60 % 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: -2.56 (0.27), residues: 910 helix: -2.05 (0.45), residues: 127 sheet: -1.90 (0.32), residues: 254 loop : -1.46 (0.26), residues: 529 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 176 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 183 average time/residue: 0.2146 time to fit residues: 52.7308 Evaluate side-chains 178 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 171 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1166 time to fit residues: 2.4313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 0.0010 chunk 87 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 86 ASN C 422 HIS ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 7638 Z= 0.388 Angle : 0.669 12.815 10358 Z= 0.332 Chirality : 0.050 0.242 1241 Planarity : 0.004 0.037 1280 Dihedral : 5.251 20.539 970 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer Outliers : 1.85 % 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: -2.64 (0.27), residues: 910 helix: -2.09 (0.45), residues: 127 sheet: -1.88 (0.33), residues: 247 loop : -1.58 (0.26), residues: 536 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 175 time to evaluate : 0.929 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 184 average time/residue: 0.2183 time to fit residues: 53.4678 Evaluate side-chains 180 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 172 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0773 time to fit residues: 2.3253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 0.0770 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 86 ASN C 422 HIS ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7638 Z= 0.215 Angle : 0.594 9.262 10358 Z= 0.298 Chirality : 0.046 0.215 1241 Planarity : 0.003 0.036 1280 Dihedral : 5.018 18.265 970 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer Outliers : 0.74 % 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: -2.57 (0.27), residues: 910 helix: -2.06 (0.45), residues: 127 sheet: -1.93 (0.32), residues: 257 loop : -1.45 (0.26), residues: 526 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 182 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 184 average time/residue: 0.2111 time to fit residues: 52.2126 Evaluate side-chains 173 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0762 time to fit residues: 1.3575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 0.0670 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 overall best weight: 1.5124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 86 ASN C 422 HIS ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 650 ASN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.061 7638 Z= 0.428 Angle : 0.696 12.479 10358 Z= 0.345 Chirality : 0.051 0.235 1241 Planarity : 0.004 0.042 1280 Dihedral : 5.434 20.995 970 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer Outliers : 0.86 % 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: -2.72 (0.27), residues: 910 helix: -2.10 (0.44), residues: 127 sheet: -1.83 (0.35), residues: 223 loop : -1.74 (0.25), residues: 560 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 170 time to evaluate : 0.961 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 170 average time/residue: 0.2150 time to fit residues: 48.7612 Evaluate side-chains 175 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 170 time to evaluate : 0.860 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0751 time to fit residues: 1.8905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 86 ASN C 422 HIS ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7638 Z= 0.240 Angle : 0.616 10.092 10358 Z= 0.307 Chirality : 0.048 0.313 1241 Planarity : 0.003 0.038 1280 Dihedral : 5.137 18.853 970 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer Outliers : 0.37 % 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: -2.65 (0.27), residues: 910 helix: -2.06 (0.45), residues: 127 sheet: -1.87 (0.34), residues: 223 loop : -1.65 (0.25), residues: 560 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 179 time to evaluate : 0.997 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 180 average time/residue: 0.2177 time to fit residues: 52.3477 Evaluate side-chains 177 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 0.894 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3702 time to fit residues: 1.5743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 0.0020 chunk 30 optimal weight: 0.7980 chunk 74 optimal weight: 0.0040 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 86 ASN C 351 ASN C 422 HIS ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.100769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.091021 restraints weight = 11476.367| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.93 r_work: 0.3100 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7638 Z= 0.194 Angle : 0.598 10.113 10358 Z= 0.298 Chirality : 0.047 0.399 1241 Planarity : 0.003 0.039 1280 Dihedral : 4.869 17.114 970 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer Outliers : 0.49 % 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: -2.54 (0.27), residues: 910 helix: -2.06 (0.45), residues: 127 sheet: -1.90 (0.32), residues: 256 loop : -1.43 (0.27), residues: 527 =============================================================================== Job complete usr+sys time: 2021.99 seconds wall clock time: 37 minutes 16.13 seconds (2236.13 seconds total)