Starting phenix.real_space_refine on Tue Dec 31 06:48:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m1y_30049/12_2024/6m1y_30049.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m1y_30049/12_2024/6m1y_30049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m1y_30049/12_2024/6m1y_30049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m1y_30049/12_2024/6m1y_30049.map" model { file = "/net/cci-nas-00/data/ceres_data/6m1y_30049/12_2024/6m1y_30049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m1y_30049/12_2024/6m1y_30049.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 S 108 5.16 5 Cl 4 4.86 5 C 9594 2.51 5 N 2472 2.21 5 O 2674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14858 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 7313 Classifications: {'peptide': 938} Link IDs: {'PTRANS': 32, 'TRANS': 905} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 7313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 7313 Classifications: {'peptide': 938} Link IDs: {'PTRANS': 32, 'TRANS': 905} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "C" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {' K': 1, ' CL': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {' K': 1, ' CL': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.92, per 1000 atoms: 0.60 Number of scatterers: 14858 At special positions: 0 Unit cell: (95.656, 116.309, 156.528, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 Cl 4 17.00 S 108 16.00 P 4 15.00 O 2674 8.00 N 2472 7.00 C 9594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.02 Simple disulfide: pdb=" SG CYS A 359 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 339 " distance=2.02 Simple disulfide: pdb=" SG CYS B 359 " - pdb=" SG CYS B 369 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1110 " - " ASN A 347 " " NAG A1111 " - " ASN A 360 " " NAG B1110 " - " ASN B 347 " " NAG B1111 " - " ASN B 360 " " NAG C 1 " - " ASN A 328 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 377 " " NAG F 1 " - " ASN B 328 " " NAG G 1 " - " ASN B 366 " " NAG H 1 " - " ASN B 377 " Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 2.0 seconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3468 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 4 sheets defined 54.3% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.701A pdb=" N ASN A 120 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.563A pdb=" N VAL A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 147 removed outlier: 3.583A pdb=" N ASN A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 164 through 192 removed outlier: 3.697A pdb=" N GLN A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 180 " --> pdb=" O CYS A 176 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 183 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 191 " --> pdb=" O MET A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.523A pdb=" N MET A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 207 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 208 " --> pdb=" O MET A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 242 removed outlier: 3.537A pdb=" N ILE A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 292 removed outlier: 3.725A pdb=" N ASN A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ARG A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 292 " --> pdb=" O TYR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 314 removed outlier: 3.566A pdb=" N CYS A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 303 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 312 " --> pdb=" O TYR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 removed outlier: 3.519A pdb=" N GLY A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 removed outlier: 3.534A pdb=" N VAL A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N HIS A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 375' Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.781A pdb=" N THR A 393 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 3.915A pdb=" N LEU A 437 " --> pdb=" O SER A 433 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 447 through 452 removed outlier: 3.593A pdb=" N GLY A 451 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER A 452 " --> pdb=" O MET A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 489 removed outlier: 3.637A pdb=" N LEU A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 497 Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'A' and resid 523 through 540 removed outlier: 4.006A pdb=" N PHE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.695A pdb=" N ALA A 546 " --> pdb=" O ARG A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 569 through 579 removed outlier: 3.617A pdb=" N LEU A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.729A pdb=" N ILE A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 614 removed outlier: 3.618A pdb=" N VAL A 591 " --> pdb=" O SER A 587 " (cutoff:3.500A) Proline residue: A 593 - end of helix removed outlier: 3.648A pdb=" N MET A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 598 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 605 " --> pdb=" O MET A 601 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 614 " --> pdb=" O CYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 646 removed outlier: 3.907A pdb=" N SER A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 639 " --> pdb=" O MET A 635 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS A 640 " --> pdb=" O GLY A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 676 removed outlier: 3.782A pdb=" N ILE A 658 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 660 " --> pdb=" O MET A 656 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 666 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 673 " --> pdb=" O GLN A 669 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU A 674 " --> pdb=" O GLY A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 694 removed outlier: 3.911A pdb=" N SER A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 734 removed outlier: 3.920A pdb=" N THR A 727 " --> pdb=" O PRO A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 770 removed outlier: 3.625A pdb=" N LEU A 757 " --> pdb=" O TYR A 753 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 758 " --> pdb=" O GLY A 754 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 761 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 762 " --> pdb=" O ALA A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 794 removed outlier: 3.821A pdb=" N GLN A 793 " --> pdb=" O SER A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 835 removed outlier: 4.191A pdb=" N PHE A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 870 through 881 Proline residue: A 876 - end of helix removed outlier: 3.741A pdb=" N GLN A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 915 removed outlier: 3.510A pdb=" N THR A 911 " --> pdb=" O LYS A 907 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS A 915 " --> pdb=" O THR A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 937 removed outlier: 3.536A pdb=" N TYR A 937 " --> pdb=" O SER A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 951 removed outlier: 3.509A pdb=" N MET A 949 " --> pdb=" O GLN A 945 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 969 Processing helix chain 'A' and resid 1036 through 1044 removed outlier: 3.977A pdb=" N GLU A1041 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL A1042 " --> pdb=" O LYS A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1078 removed outlier: 3.771A pdb=" N THR A1078 " --> pdb=" O LEU A1074 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.701A pdb=" N ASN B 120 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 removed outlier: 3.563A pdb=" N VAL B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 147 removed outlier: 3.583A pdb=" N ASN B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 156 through 163 Processing helix chain 'B' and resid 164 through 192 removed outlier: 3.697A pdb=" N GLN B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 180 " --> pdb=" O CYS B 176 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR B 183 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 191 " --> pdb=" O MET B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.523A pdb=" N MET B 204 " --> pdb=" O GLY B 200 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG B 207 " --> pdb=" O PHE B 203 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 208 " --> pdb=" O MET B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 242 removed outlier: 3.537A pdb=" N ILE B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 292 removed outlier: 3.725A pdb=" N ASN B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 273 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ARG B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 292 " --> pdb=" O TYR B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 314 removed outlier: 3.566A pdb=" N CYS B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 300 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER B 303 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE B 312 " --> pdb=" O TYR B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 359 removed outlier: 3.519A pdb=" N GLY B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.534A pdb=" N VAL B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N HIS B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 370 through 375' Processing helix chain 'B' and resid 390 through 395 removed outlier: 3.781A pdb=" N THR B 393 " --> pdb=" O GLY B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 removed outlier: 3.915A pdb=" N LEU B 437 " --> pdb=" O SER B 433 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 438 " --> pdb=" O PHE B 434 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 445 No H-bonds generated for 'chain 'B' and resid 443 through 445' Processing helix chain 'B' and resid 447 through 452 removed outlier: 3.593A pdb=" N GLY B 451 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 452 " --> pdb=" O MET B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 489 removed outlier: 3.637A pdb=" N LEU B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 497 Processing helix chain 'B' and resid 518 through 523 Processing helix chain 'B' and resid 523 through 540 removed outlier: 4.006A pdb=" N PHE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 529 " --> pdb=" O SER B 525 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 549 removed outlier: 3.695A pdb=" N ALA B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 553 through 557 Processing helix chain 'B' and resid 569 through 579 removed outlier: 3.617A pdb=" N LEU B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 585 removed outlier: 3.729A pdb=" N ILE B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 614 removed outlier: 3.618A pdb=" N VAL B 591 " --> pdb=" O SER B 587 " (cutoff:3.500A) Proline residue: B 593 - end of helix removed outlier: 3.648A pdb=" N MET B 597 " --> pdb=" O PRO B 593 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 598 " --> pdb=" O ILE B 594 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 605 " --> pdb=" O MET B 601 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR B 614 " --> pdb=" O CYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 646 removed outlier: 3.907A pdb=" N SER B 633 " --> pdb=" O HIS B 629 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 639 " --> pdb=" O MET B 635 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS B 640 " --> pdb=" O GLY B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 676 removed outlier: 3.782A pdb=" N ILE B 658 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA B 659 " --> pdb=" O ALA B 655 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 660 " --> pdb=" O MET B 656 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 666 " --> pdb=" O ILE B 662 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 673 " --> pdb=" O GLN B 669 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU B 674 " --> pdb=" O GLY B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 694 removed outlier: 3.911A pdb=" N SER B 683 " --> pdb=" O ILE B 679 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 734 removed outlier: 3.920A pdb=" N THR B 727 " --> pdb=" O PRO B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 770 removed outlier: 3.625A pdb=" N LEU B 757 " --> pdb=" O TYR B 753 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 758 " --> pdb=" O GLY B 754 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN B 761 " --> pdb=" O LEU B 757 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 762 " --> pdb=" O ALA B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 794 removed outlier: 3.821A pdb=" N GLN B 793 " --> pdb=" O SER B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 835 removed outlier: 4.191A pdb=" N PHE B 825 " --> pdb=" O ALA B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 Processing helix chain 'B' and resid 870 through 881 Proline residue: B 876 - end of helix removed outlier: 3.741A pdb=" N GLN B 881 " --> pdb=" O PHE B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 915 removed outlier: 3.510A pdb=" N THR B 911 " --> pdb=" O LYS B 907 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS B 915 " --> pdb=" O THR B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 937 removed outlier: 3.536A pdb=" N TYR B 937 " --> pdb=" O SER B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 951 removed outlier: 3.509A pdb=" N MET B 949 " --> pdb=" O GLN B 945 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B 951 " --> pdb=" O SER B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 969 Processing helix chain 'B' and resid 1036 through 1044 removed outlier: 3.977A pdb=" N GLU B1041 " --> pdb=" O VAL B1037 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL B1042 " --> pdb=" O LYS B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1078 removed outlier: 3.771A pdb=" N THR B1078 " --> pdb=" O LEU B1074 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 322 through 325 Processing sheet with id=AA2, first strand: chain 'A' and resid 775 through 781 removed outlier: 6.147A pdb=" N VAL A 710 " --> pdb=" O GLY A 742 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N VAL A 744 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU A 709 " --> pdb=" O VAL A 806 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N GLY A 808 " --> pdb=" O LEU A 709 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N LEU A 711 " --> pdb=" O GLY A 808 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A1084 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A1053 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL A1087 " --> pdb=" O VAL A1053 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU A1055 " --> pdb=" O VAL A1087 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN A1056 " --> pdb=" O TRP A 863 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE A 865 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY A 858 " --> pdb=" O SER A 889 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ARG A 891 " --> pdb=" O GLY A 858 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE A 860 " --> pdb=" O ARG A 891 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE A 893 " --> pdb=" O ILE A 860 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL A 862 " --> pdb=" O PHE A 893 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL A 895 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N TRP A 864 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 322 through 325 Processing sheet with id=AA4, first strand: chain 'B' and resid 775 through 781 removed outlier: 6.147A pdb=" N VAL B 710 " --> pdb=" O GLY B 742 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N VAL B 744 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU B 709 " --> pdb=" O VAL B 806 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N GLY B 808 " --> pdb=" O LEU B 709 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N LEU B 711 " --> pdb=" O GLY B 808 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B1084 " --> pdb=" O LYS B 843 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL B1053 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL B1087 " --> pdb=" O VAL B1053 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B1055 " --> pdb=" O VAL B1087 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN B1056 " --> pdb=" O TRP B 863 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE B 865 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY B 858 " --> pdb=" O SER B 889 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ARG B 891 " --> pdb=" O GLY B 858 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE B 860 " --> pdb=" O ARG B 891 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE B 893 " --> pdb=" O ILE B 860 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL B 862 " --> pdb=" O PHE B 893 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL B 895 " --> pdb=" O VAL B 862 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N TRP B 864 " --> pdb=" O VAL B 895 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1674 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: 4.67 Time building geometry restraints manager: 4.14 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: 4614 1.34 - 1.46: 3246 1.46 - 1.58: 7126 1.58 - 1.69: 12 1.69 - 1.81: 178 Bond restraints: 15176 Sorted by residual: bond pdb=" OG1 TPO B 997 " pdb=" P TPO B 997 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" OG1 TPO A 997 " pdb=" P TPO A 997 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" OG1 TPO A 940 " pdb=" P TPO A 940 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" OG1 TPO B 940 " pdb=" P TPO B 940 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C GLY A 697 " pdb=" N PRO A 698 " ideal model delta sigma weight residual 1.329 1.390 -0.061 1.18e-02 7.18e+03 2.66e+01 ... (remaining 15171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 20128 2.71 - 5.42: 362 5.42 - 8.13: 72 8.13 - 10.84: 14 10.84 - 13.55: 8 Bond angle restraints: 20584 Sorted by residual: angle pdb=" C GLY A 697 " pdb=" N PRO A 698 " pdb=" CA PRO A 698 " ideal model delta sigma weight residual 120.38 114.00 6.38 1.03e+00 9.43e-01 3.84e+01 angle pdb=" C GLY B 697 " pdb=" N PRO B 698 " pdb=" CA PRO B 698 " ideal model delta sigma weight residual 120.38 114.00 6.38 1.03e+00 9.43e-01 3.84e+01 angle pdb=" C ARG A 705 " pdb=" N PRO A 706 " pdb=" CA PRO A 706 " ideal model delta sigma weight residual 119.76 114.23 5.53 1.00e+00 1.00e+00 3.06e+01 angle pdb=" C ARG B 705 " pdb=" N PRO B 706 " pdb=" CA PRO B 706 " ideal model delta sigma weight residual 119.76 114.23 5.53 1.00e+00 1.00e+00 3.06e+01 angle pdb=" C ALA A 112 " pdb=" N LYS A 113 " pdb=" CA LYS A 113 " ideal model delta sigma weight residual 121.54 130.78 -9.24 1.91e+00 2.74e-01 2.34e+01 ... (remaining 20579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 8152 17.08 - 34.15: 784 34.15 - 51.23: 174 51.23 - 68.30: 30 68.30 - 85.38: 18 Dihedral angle restraints: 9158 sinusoidal: 3768 harmonic: 5390 Sorted by residual: dihedral pdb=" CB CYS A 324 " pdb=" SG CYS A 324 " pdb=" SG CYS A 339 " pdb=" CB CYS A 339 " ideal model delta sinusoidal sigma weight residual -86.00 -166.84 80.84 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS B 324 " pdb=" SG CYS B 324 " pdb=" SG CYS B 339 " pdb=" CB CYS B 339 " ideal model delta sinusoidal sigma weight residual -86.00 -166.84 80.84 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CA LEU B 584 " pdb=" C LEU B 584 " pdb=" N ILE B 585 " pdb=" CA ILE B 585 " ideal model delta harmonic sigma weight residual 180.00 157.85 22.15 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 9155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 2408 0.224 - 0.449: 10 0.449 - 0.673: 0 0.673 - 0.898: 0 0.898 - 1.122: 2 Chirality restraints: 2420 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 377 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.28 -1.12 2.00e-01 2.50e+01 3.15e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 377 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.28 -1.12 2.00e-01 2.50e+01 3.15e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 366 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 2417 not shown) Planarity restraints: 2550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 347 " 0.008 2.00e-02 2.50e+03 5.07e-02 3.21e+01 pdb=" CG ASN B 347 " -0.071 2.00e-02 2.50e+03 pdb=" OD1 ASN B 347 " 0.061 2.00e-02 2.50e+03 pdb=" ND2 ASN B 347 " -0.044 2.00e-02 2.50e+03 pdb=" C1 NAG B1110 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 347 " 0.008 2.00e-02 2.50e+03 5.07e-02 3.21e+01 pdb=" CG ASN A 347 " -0.071 2.00e-02 2.50e+03 pdb=" OD1 ASN A 347 " 0.061 2.00e-02 2.50e+03 pdb=" ND2 ASN A 347 " -0.044 2.00e-02 2.50e+03 pdb=" C1 NAG A1110 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 347 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" CG ASN A 347 " -0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN A 347 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN A 347 " 0.020 2.00e-02 2.50e+03 ... (remaining 2547 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 4662 2.82 - 3.40: 14424 3.40 - 3.98: 25263 3.98 - 4.56: 36580 4.56 - 5.14: 53645 Nonbonded interactions: 134574 Sorted by model distance: nonbonded pdb=" O ARG A 951 " pdb=" N MET A 953 " model vdw 2.245 3.120 nonbonded pdb=" O ARG B 951 " pdb=" N MET B 953 " model vdw 2.245 3.120 nonbonded pdb=" O GLN A 707 " pdb=" O LEU A 738 " model vdw 2.248 3.040 nonbonded pdb=" O GLN B 707 " pdb=" O LEU B 738 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR B 308 " pdb=" OG SER B 482 " model vdw 2.256 3.040 ... (remaining 134569 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 33.680 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.090 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.006 0.111 15176 Z= 0.381 Angle : 0.950 13.553 20584 Z= 0.497 Chirality : 0.064 1.122 2420 Planarity : 0.006 0.068 2540 Dihedral : 14.122 85.376 5678 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 1.41 % Allowed : 9.63 % Favored : 88.96 % Rotamer: Outliers : 1.65 % Allowed : 6.36 % Favored : 91.98 % 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: -6.04 (0.13), residues: 1848 helix: -4.94 (0.04), residues: 898 sheet: -0.94 (0.37), residues: 168 loop : -3.38 (0.19), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 649 HIS 0.003 0.001 HIS A 252 PHE 0.022 0.002 PHE B 555 TYR 0.014 0.002 TYR B 243 ARG 0.007 0.000 ARG A1088 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 274 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.7650 (tp) cc_final: 0.7340 (tp) REVERT: A 343 LYS cc_start: 0.9001 (tttp) cc_final: 0.8644 (tptp) REVERT: A 783 LYS cc_start: 0.8960 (mttt) cc_final: 0.8759 (mttp) REVERT: A 995 HIS cc_start: 0.7342 (t-90) cc_final: 0.7025 (t-170) REVERT: A 1071 MET cc_start: 0.9347 (mmm) cc_final: 0.9090 (tpp) REVERT: B 326 LEU cc_start: 0.7648 (tp) cc_final: 0.7340 (tp) REVERT: B 343 LYS cc_start: 0.9004 (tttp) cc_final: 0.8646 (tptp) REVERT: B 783 LYS cc_start: 0.8962 (mttt) cc_final: 0.8762 (mttp) REVERT: B 995 HIS cc_start: 0.7343 (t-90) cc_final: 0.7025 (t-170) REVERT: B 1071 MET cc_start: 0.9346 (mmm) cc_final: 0.9088 (tpp) outliers start: 26 outliers final: 6 residues processed: 296 average time/residue: 0.3003 time to fit residues: 126.4761 Evaluate side-chains 148 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain B residue 700 HIS Chi-restraints excluded: chain B residue 815 GLN Chi-restraints excluded: chain B residue 866 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 0.0040 chunk 75 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 507 ASN A 607 ASN A 613 GLN A 700 HIS A 707 GLN A 882 HIS A 952 HIS A 965 GLN B 290 ASN B 399 ASN B 507 ASN B 607 ASN B 613 GLN B 700 HIS B 707 GLN B 882 HIS B 952 HIS B 965 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15176 Z= 0.200 Angle : 0.706 12.379 20584 Z= 0.362 Chirality : 0.047 0.643 2420 Planarity : 0.005 0.048 2540 Dihedral : 7.251 56.978 2354 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.23 % Favored : 91.34 % Rotamer: Outliers : 2.29 % Allowed : 10.43 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.16), residues: 1848 helix: -2.47 (0.13), residues: 906 sheet: -0.70 (0.37), residues: 168 loop : -2.93 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 515 HIS 0.004 0.001 HIS A 700 PHE 0.012 0.001 PHE B 689 TYR 0.008 0.001 TYR A 663 ARG 0.009 0.001 ARG B1032 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 SER cc_start: 0.8766 (m) cc_final: 0.8504 (p) REVERT: A 343 LYS cc_start: 0.8996 (tttp) cc_final: 0.8699 (tptp) REVERT: A 939 ARG cc_start: 0.8084 (mtp180) cc_final: 0.7830 (mtp180) REVERT: A 943 MET cc_start: 0.8261 (tmm) cc_final: 0.8002 (tmm) REVERT: B 315 SER cc_start: 0.8764 (m) cc_final: 0.8503 (p) REVERT: B 343 LYS cc_start: 0.8994 (tttp) cc_final: 0.8700 (tptp) REVERT: B 939 ARG cc_start: 0.8083 (mtp180) cc_final: 0.7830 (mtp180) REVERT: B 943 MET cc_start: 0.8261 (tmm) cc_final: 0.8003 (tmm) outliers start: 36 outliers final: 8 residues processed: 186 average time/residue: 0.2635 time to fit residues: 74.3756 Evaluate side-chains 126 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 700 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 169 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 150 optimal weight: 0.7980 chunk 167 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 15176 Z= 0.173 Angle : 0.620 9.388 20584 Z= 0.312 Chirality : 0.046 0.614 2420 Planarity : 0.004 0.064 2540 Dihedral : 6.591 50.649 2346 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.98 % Favored : 90.80 % Rotamer: Outliers : 1.27 % Allowed : 12.72 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.18), residues: 1848 helix: -1.09 (0.16), residues: 918 sheet: -0.70 (0.38), residues: 168 loop : -2.62 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 515 HIS 0.009 0.001 HIS A 995 PHE 0.011 0.001 PHE A 555 TYR 0.009 0.001 TYR A 243 ARG 0.004 0.000 ARG A 622 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 PHE cc_start: 0.8266 (t80) cc_final: 0.7716 (t80) REVERT: A 315 SER cc_start: 0.8756 (m) cc_final: 0.8497 (p) REVERT: A 343 LYS cc_start: 0.8998 (tttp) cc_final: 0.8683 (tptp) REVERT: A 943 MET cc_start: 0.8296 (tmm) cc_final: 0.7987 (tmm) REVERT: B 274 PHE cc_start: 0.8265 (t80) cc_final: 0.7715 (t80) REVERT: B 315 SER cc_start: 0.8758 (m) cc_final: 0.8496 (p) REVERT: B 343 LYS cc_start: 0.8996 (tttp) cc_final: 0.8681 (tptp) REVERT: B 943 MET cc_start: 0.8295 (tmm) cc_final: 0.7987 (tmm) outliers start: 20 outliers final: 12 residues processed: 152 average time/residue: 0.2478 time to fit residues: 58.6956 Evaluate side-chains 128 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 700 HIS Chi-restraints excluded: chain B residue 866 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 169 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 HIS A 752 ASN A 854 GLN B 629 HIS B 752 ASN B 854 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 15176 Z= 0.474 Angle : 0.786 11.603 20584 Z= 0.396 Chirality : 0.052 0.645 2420 Planarity : 0.005 0.069 2540 Dihedral : 6.553 52.585 2346 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.39 % Favored : 89.39 % Rotamer: Outliers : 2.16 % Allowed : 13.36 % Favored : 84.48 % 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: -1.97 (0.19), residues: 1848 helix: -0.39 (0.17), residues: 940 sheet: -0.61 (0.38), residues: 164 loop : -2.69 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 515 HIS 0.007 0.001 HIS A 995 PHE 0.016 0.002 PHE B 749 TYR 0.021 0.002 TYR A 243 ARG 0.003 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8201 (mmm) cc_final: 0.7978 (mmm) REVERT: A 343 LYS cc_start: 0.9052 (tttp) cc_final: 0.8619 (tptp) REVERT: A 943 MET cc_start: 0.8281 (tmm) cc_final: 0.7939 (tmm) REVERT: B 138 MET cc_start: 0.8202 (mmm) cc_final: 0.7977 (mmm) REVERT: B 343 LYS cc_start: 0.9051 (tttp) cc_final: 0.8620 (tptp) REVERT: B 943 MET cc_start: 0.8280 (tmm) cc_final: 0.7937 (tmm) outliers start: 34 outliers final: 18 residues processed: 150 average time/residue: 0.2246 time to fit residues: 53.7249 Evaluate side-chains 122 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 700 HIS Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 925 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.0010 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 161 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 854 GLN B 854 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15176 Z= 0.181 Angle : 0.616 9.221 20584 Z= 0.308 Chirality : 0.046 0.581 2420 Planarity : 0.004 0.063 2540 Dihedral : 6.136 50.539 2346 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.66 % Favored : 91.13 % Rotamer: Outliers : 1.53 % Allowed : 14.63 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.20), residues: 1848 helix: 0.13 (0.18), residues: 936 sheet: -0.55 (0.39), residues: 162 loop : -2.49 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 515 HIS 0.004 0.001 HIS B 995 PHE 0.011 0.001 PHE A 555 TYR 0.010 0.001 TYR B 663 ARG 0.003 0.000 ARG A 622 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8577 (mmm) cc_final: 0.8144 (mmm) REVERT: A 343 LYS cc_start: 0.9032 (tttp) cc_final: 0.8662 (tptp) REVERT: A 943 MET cc_start: 0.8364 (tmm) cc_final: 0.7986 (tmm) REVERT: A 995 HIS cc_start: 0.6746 (t-170) cc_final: 0.6280 (t-170) REVERT: B 325 MET cc_start: 0.8576 (mmm) cc_final: 0.8142 (mmm) REVERT: B 343 LYS cc_start: 0.9032 (tttp) cc_final: 0.8662 (tptp) REVERT: B 943 MET cc_start: 0.8362 (tmm) cc_final: 0.7985 (tmm) REVERT: B 995 HIS cc_start: 0.6741 (t-170) cc_final: 0.6275 (t-170) outliers start: 24 outliers final: 18 residues processed: 136 average time/residue: 0.2217 time to fit residues: 49.3752 Evaluate side-chains 130 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 700 HIS Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 1057 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 0.0770 chunk 161 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 179 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 59 optimal weight: 0.3980 chunk 94 optimal weight: 4.9990 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 HIS ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15176 Z= 0.244 Angle : 0.634 12.430 20584 Z= 0.315 Chirality : 0.047 0.581 2420 Planarity : 0.004 0.059 2540 Dihedral : 5.937 51.066 2346 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.42 % Favored : 90.15 % Rotamer: Outliers : 2.04 % Allowed : 15.01 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.20), residues: 1848 helix: 0.43 (0.18), residues: 938 sheet: -0.46 (0.39), residues: 164 loop : -2.34 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 515 HIS 0.004 0.001 HIS B 719 PHE 0.010 0.001 PHE A 227 TYR 0.017 0.002 TYR B 937 ARG 0.002 0.000 ARG A 622 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.9052 (tttp) cc_final: 0.8689 (tptp) REVERT: A 943 MET cc_start: 0.8397 (tmm) cc_final: 0.7997 (tmm) REVERT: B 343 LYS cc_start: 0.9052 (tttp) cc_final: 0.8691 (tptp) REVERT: B 943 MET cc_start: 0.8394 (tmm) cc_final: 0.7996 (tmm) outliers start: 32 outliers final: 18 residues processed: 140 average time/residue: 0.2215 time to fit residues: 50.2115 Evaluate side-chains 128 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 767 MET Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 767 MET Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 909 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 151 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15176 Z= 0.186 Angle : 0.601 9.612 20584 Z= 0.300 Chirality : 0.045 0.560 2420 Planarity : 0.004 0.057 2540 Dihedral : 5.653 55.211 2342 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.71 % Favored : 90.85 % Rotamer: Outliers : 1.53 % Allowed : 15.20 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.20), residues: 1848 helix: 0.75 (0.18), residues: 940 sheet: -0.32 (0.40), residues: 164 loop : -2.22 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 515 HIS 0.003 0.001 HIS A 719 PHE 0.010 0.001 PHE A 555 TYR 0.010 0.001 TYR B 243 ARG 0.003 0.000 ARG A 622 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.9071 (tttp) cc_final: 0.8706 (tptp) REVERT: A 672 GLU cc_start: 0.8358 (tt0) cc_final: 0.8075 (tm-30) REVERT: A 943 MET cc_start: 0.8413 (tmm) cc_final: 0.7995 (tmm) REVERT: B 343 LYS cc_start: 0.9073 (tttp) cc_final: 0.8709 (tptp) REVERT: B 672 GLU cc_start: 0.8359 (tt0) cc_final: 0.8074 (tm-30) REVERT: B 943 MET cc_start: 0.8409 (tmm) cc_final: 0.7992 (tmm) outliers start: 24 outliers final: 20 residues processed: 134 average time/residue: 0.2212 time to fit residues: 48.8306 Evaluate side-chains 130 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 767 MET Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 767 MET Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 909 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 122 optimal weight: 0.2980 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 GLN ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 897 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15176 Z= 0.156 Angle : 0.603 12.718 20584 Z= 0.295 Chirality : 0.045 0.545 2420 Planarity : 0.004 0.055 2540 Dihedral : 5.461 52.782 2342 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.98 % Favored : 90.69 % Rotamer: Outliers : 1.78 % Allowed : 15.78 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.20), residues: 1848 helix: 0.93 (0.18), residues: 940 sheet: -0.24 (0.41), residues: 164 loop : -2.26 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 515 HIS 0.014 0.001 HIS A 995 PHE 0.010 0.001 PHE A 555 TYR 0.010 0.001 TYR B 663 ARG 0.002 0.000 ARG B 622 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.9104 (tttp) cc_final: 0.8741 (tptp) REVERT: A 672 GLU cc_start: 0.8333 (tt0) cc_final: 0.8079 (tm-30) REVERT: A 943 MET cc_start: 0.8441 (tmm) cc_final: 0.7999 (tmm) REVERT: A 1031 ARG cc_start: 0.7339 (mtp85) cc_final: 0.6801 (ptm160) REVERT: B 343 LYS cc_start: 0.9104 (tttp) cc_final: 0.8742 (tptp) REVERT: B 672 GLU cc_start: 0.8332 (tt0) cc_final: 0.8078 (tm-30) REVERT: B 943 MET cc_start: 0.8436 (tmm) cc_final: 0.7996 (tmm) REVERT: B 1031 ARG cc_start: 0.7341 (mtp85) cc_final: 0.6802 (ptm160) outliers start: 28 outliers final: 20 residues processed: 140 average time/residue: 0.2417 time to fit residues: 54.0510 Evaluate side-chains 134 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 649 TRP Chi-restraints excluded: chain A residue 767 MET Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 767 MET Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 909 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 51 optimal weight: 0.3980 chunk 150 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15176 Z= 0.169 Angle : 0.596 9.882 20584 Z= 0.294 Chirality : 0.045 0.543 2420 Planarity : 0.004 0.055 2540 Dihedral : 5.422 53.595 2342 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.77 % Favored : 90.91 % Rotamer: Outliers : 1.40 % Allowed : 15.52 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.21), residues: 1848 helix: 0.98 (0.18), residues: 946 sheet: -0.19 (0.41), residues: 164 loop : -2.22 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 515 HIS 0.012 0.001 HIS B 995 PHE 0.009 0.001 PHE A 555 TYR 0.010 0.001 TYR B 243 ARG 0.002 0.000 ARG B 622 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.9089 (tttp) cc_final: 0.8721 (tptp) REVERT: A 672 GLU cc_start: 0.8334 (tt0) cc_final: 0.8084 (tm-30) REVERT: A 943 MET cc_start: 0.8445 (tmm) cc_final: 0.7995 (tmm) REVERT: A 1031 ARG cc_start: 0.7449 (mtp85) cc_final: 0.6887 (ptm160) REVERT: B 343 LYS cc_start: 0.9090 (tttp) cc_final: 0.8723 (tptp) REVERT: B 672 GLU cc_start: 0.8333 (tt0) cc_final: 0.8084 (tm-30) REVERT: B 943 MET cc_start: 0.8442 (tmm) cc_final: 0.7993 (tmm) REVERT: B 1031 ARG cc_start: 0.7451 (mtp85) cc_final: 0.6888 (ptm160) outliers start: 22 outliers final: 22 residues processed: 134 average time/residue: 0.2394 time to fit residues: 51.4475 Evaluate side-chains 136 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 649 TRP Chi-restraints excluded: chain A residue 767 MET Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 767 MET Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 925 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.9980 chunk 176 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 185 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 113 optimal weight: 0.0870 chunk 90 optimal weight: 0.7980 overall best weight: 1.3160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 854 GLN ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 854 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15176 Z= 0.224 Angle : 0.639 12.324 20584 Z= 0.311 Chirality : 0.046 0.548 2420 Planarity : 0.004 0.054 2540 Dihedral : 5.489 54.604 2342 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.98 % Favored : 90.58 % Rotamer: Outliers : 1.40 % Allowed : 15.90 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.21), residues: 1848 helix: 1.09 (0.18), residues: 942 sheet: -0.19 (0.41), residues: 164 loop : -2.27 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 515 HIS 0.011 0.001 HIS B 995 PHE 0.009 0.001 PHE B 555 TYR 0.011 0.001 TYR A 243 ARG 0.002 0.000 ARG B 622 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.9102 (tttp) cc_final: 0.8722 (tptp) REVERT: A 672 GLU cc_start: 0.8365 (tt0) cc_final: 0.8105 (tm-30) REVERT: A 943 MET cc_start: 0.8460 (tmm) cc_final: 0.8000 (tmm) REVERT: A 1031 ARG cc_start: 0.7554 (mtp85) cc_final: 0.6918 (ptm160) REVERT: B 343 LYS cc_start: 0.9103 (tttp) cc_final: 0.8724 (tptp) REVERT: B 672 GLU cc_start: 0.8364 (tt0) cc_final: 0.8103 (tm-30) REVERT: B 943 MET cc_start: 0.8456 (tmm) cc_final: 0.7998 (tmm) REVERT: B 1031 ARG cc_start: 0.7555 (mtp85) cc_final: 0.6917 (ptm160) outliers start: 22 outliers final: 22 residues processed: 132 average time/residue: 0.2430 time to fit residues: 51.2725 Evaluate side-chains 134 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 649 TRP Chi-restraints excluded: chain A residue 767 MET Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 767 MET Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 925 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 45 optimal weight: 0.0050 chunk 136 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.094459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.069817 restraints weight = 31760.219| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.22 r_work: 0.2794 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15176 Z= 0.148 Angle : 0.611 13.696 20584 Z= 0.294 Chirality : 0.044 0.527 2420 Planarity : 0.004 0.054 2540 Dihedral : 5.354 53.243 2342 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.50 % Favored : 91.18 % Rotamer: Outliers : 1.40 % Allowed : 15.90 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1848 helix: 1.23 (0.18), residues: 944 sheet: -0.14 (0.41), residues: 164 loop : -2.25 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 515 HIS 0.011 0.001 HIS A 995 PHE 0.009 0.001 PHE A 555 TYR 0.010 0.001 TYR B 663 ARG 0.002 0.000 ARG B 622 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2624.84 seconds wall clock time: 49 minutes 26.18 seconds (2966.18 seconds total)