Starting phenix.real_space_refine on Tue Feb 20 07:55:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8w_15242/02_2024/8a8w_15242_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8w_15242/02_2024/8a8w_15242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8w_15242/02_2024/8a8w_15242.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8w_15242/02_2024/8a8w_15242.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8w_15242/02_2024/8a8w_15242_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8w_15242/02_2024/8a8w_15242_updated.pdb" } resolution = 4.29 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= 0.118 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 66 5.16 5 C 17060 2.51 5 N 4842 2.21 5 O 5199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 349": "OE1" <-> "OE2" Residue "A GLU 643": "OE1" <-> "OE2" Residue "A PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B GLU 367": "OE1" <-> "OE2" Residue "B GLU 511": "OE1" <-> "OE2" Residue "B GLU 626": "OE1" <-> "OE2" Residue "B GLU 643": "OE1" <-> "OE2" Residue "C GLU 275": "OE1" <-> "OE2" Residue "C GLU 605": "OE1" <-> "OE2" Residue "C GLU 708": "OE1" <-> "OE2" Residue "D GLU 522": "OE1" <-> "OE2" Residue "D GLU 584": "OE1" <-> "OE2" Residue "D GLU 726": "OE1" <-> "OE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "F TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27187 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4403 Classifications: {'peptide': 558} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 540} Chain breaks: 4 Chain: "B" Number of atoms: 4483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4483 Classifications: {'peptide': 568} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 548} Chain breaks: 3 Chain: "C" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4510 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 553} Chain breaks: 2 Chain: "D" Number of atoms: 4537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4537 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 556} Chain breaks: 2 Chain: "E" Number of atoms: 4490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4490 Classifications: {'peptide': 569} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 548} Chain breaks: 3 Chain: "F" Number of atoms: 4370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4370 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 531} Chain breaks: 5 Chain: "G" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 124 Classifications: {'peptide': 25} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 24} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 25} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.88, per 1000 atoms: 0.55 Number of scatterers: 27187 At special positions: 0 Unit cell: (123.12, 140.22, 152.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 20 15.00 O 5199 8.00 N 4842 7.00 C 17060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.70 Conformation dependent library (CDL) restraints added in 5.0 seconds 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 168 helices and 27 sheets defined 50.9% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.09 Creating SS restraints... Processing helix chain 'A' and resid 178 through 184 Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 222 through 235 removed outlier: 3.580A pdb=" N HIS A 235 " --> pdb=" O GLN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 289 through 294 removed outlier: 4.033A pdb=" N VAL A 293 " --> pdb=" O HIS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 Proline residue: A 310 - end of helix Processing helix chain 'A' and resid 325 through 334 removed outlier: 3.978A pdb=" N GLU A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LYS A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 352 through 370 removed outlier: 5.182A pdb=" N ASP A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ARG A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 386 Processing helix chain 'A' and resid 397 through 414 Processing helix chain 'A' and resid 481 through 492 Processing helix chain 'A' and resid 496 through 499 No H-bonds generated for 'chain 'A' and resid 496 through 499' Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 510 through 515 Processing helix chain 'A' and resid 522 through 536 Processing helix chain 'A' and resid 559 through 571 Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.899A pdb=" N ARG A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 616 Processing helix chain 'A' and resid 632 through 644 Processing helix chain 'A' and resid 690 through 704 Processing helix chain 'A' and resid 707 through 712 Processing helix chain 'A' and resid 724 through 745 removed outlier: 4.625A pdb=" N SER A 744 " --> pdb=" O GLY A 740 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LYS A 745 " --> pdb=" O GLN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 763 Processing helix chain 'A' and resid 769 through 790 Proline residue: A 772 - end of helix removed outlier: 4.234A pdb=" N ILE A 777 " --> pdb=" O ARG A 774 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 778 " --> pdb=" O ARG A 775 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU A 780 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLU A 782 " --> pdb=" O ARG A 779 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASP A 783 " --> pdb=" O GLU A 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 178 through 184 removed outlier: 3.736A pdb=" N GLU B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.559A pdb=" N VAL B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 264 through 279 Processing helix chain 'B' and resid 289 through 292 Processing helix chain 'B' and resid 304 through 314 Proline residue: B 310 - end of helix Processing helix chain 'B' and resid 325 through 331 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 352 through 370 removed outlier: 4.519A pdb=" N ASP B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ARG B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 389 Processing helix chain 'B' and resid 397 through 414 Processing helix chain 'B' and resid 481 through 492 Processing helix chain 'B' and resid 501 through 516 removed outlier: 5.222A pdb=" N GLU B 511 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N GLU B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 536 Processing helix chain 'B' and resid 561 through 571 Processing helix chain 'B' and resid 589 through 595 removed outlier: 3.750A pdb=" N PHE B 595 " --> pdb=" O SER B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 616 Processing helix chain 'B' and resid 627 through 629 No H-bonds generated for 'chain 'B' and resid 627 through 629' Processing helix chain 'B' and resid 633 through 643 removed outlier: 4.337A pdb=" N GLN B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL B 641 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 704 Processing helix chain 'B' and resid 707 through 712 removed outlier: 3.632A pdb=" N ARG B 712 " --> pdb=" O GLU B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 745 removed outlier: 3.852A pdb=" N ASP B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ARG B 737 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL B 738 " --> pdb=" O MET B 734 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER B 744 " --> pdb=" O GLY B 740 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS B 745 " --> pdb=" O GLN B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 762 Processing helix chain 'B' and resid 771 through 779 Processing helix chain 'B' and resid 782 through 790 Processing helix chain 'C' and resid 171 through 174 No H-bonds generated for 'chain 'C' and resid 171 through 174' Processing helix chain 'C' and resid 178 through 184 removed outlier: 3.714A pdb=" N GLU C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 222 through 235 removed outlier: 3.774A pdb=" N VAL C 226 " --> pdb=" O LYS C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 262 through 279 Processing helix chain 'C' and resid 289 through 292 Processing helix chain 'C' and resid 304 through 314 Proline residue: C 310 - end of helix Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 336 through 341 removed outlier: 3.642A pdb=" N ARG C 341 " --> pdb=" O ALA C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 370 removed outlier: 5.050A pdb=" N ASP C 364 " --> pdb=" O LYS C 360 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ARG C 365 " --> pdb=" O GLY C 361 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 388 Processing helix chain 'C' and resid 397 through 414 Processing helix chain 'C' and resid 481 through 492 Processing helix chain 'C' and resid 501 through 508 Processing helix chain 'C' and resid 510 through 517 removed outlier: 4.067A pdb=" N ARG C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 536 Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.590A pdb=" N SER C 563 " --> pdb=" O LYS C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 595 removed outlier: 3.672A pdb=" N ALA C 591 " --> pdb=" O ARG C 588 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER C 592 " --> pdb=" O PHE C 589 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU C 594 " --> pdb=" O ALA C 591 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE C 595 " --> pdb=" O SER C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 616 Processing helix chain 'C' and resid 632 through 643 removed outlier: 4.840A pdb=" N GLN C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N VAL C 641 " --> pdb=" O SER C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 704 Processing helix chain 'C' and resid 707 through 712 Processing helix chain 'C' and resid 724 through 745 removed outlier: 4.089A pdb=" N SER C 744 " --> pdb=" O GLY C 740 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS C 745 " --> pdb=" O GLN C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 761 Processing helix chain 'C' and resid 771 through 780 removed outlier: 3.894A pdb=" N ARG C 775 " --> pdb=" O ARG C 771 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N THR C 776 " --> pdb=" O PRO C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 790 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 222 through 235 removed outlier: 4.533A pdb=" N VAL D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLU D 227 " --> pdb=" O THR D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 264 through 279 Processing helix chain 'D' and resid 289 through 291 No H-bonds generated for 'chain 'D' and resid 289 through 291' Processing helix chain 'D' and resid 304 through 313 Proline residue: D 310 - end of helix Processing helix chain 'D' and resid 325 through 331 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 352 through 369 removed outlier: 4.591A pdb=" N ASP D 364 " --> pdb=" O LYS D 360 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ARG D 365 " --> pdb=" O GLY D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 389 removed outlier: 3.952A pdb=" N VAL D 380 " --> pdb=" O ASP D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 414 Processing helix chain 'D' and resid 481 through 492 Processing helix chain 'D' and resid 501 through 508 Processing helix chain 'D' and resid 510 through 517 removed outlier: 4.101A pdb=" N ARG D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 536 Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.880A pdb=" N SER D 563 " --> pdb=" O LYS D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 584 No H-bonds generated for 'chain 'D' and resid 582 through 584' Processing helix chain 'D' and resid 588 through 595 removed outlier: 3.690A pdb=" N ALA D 591 " --> pdb=" O ARG D 588 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER D 592 " --> pdb=" O PHE D 589 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE D 595 " --> pdb=" O SER D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 616 Processing helix chain 'D' and resid 634 through 641 removed outlier: 3.517A pdb=" N SER D 637 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN D 640 " --> pdb=" O SER D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 704 Processing helix chain 'D' and resid 707 through 712 removed outlier: 4.580A pdb=" N ARG D 712 " --> pdb=" O GLU D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 745 removed outlier: 3.937A pdb=" N ASP D 732 " --> pdb=" O ILE D 728 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG D 737 " --> pdb=" O LEU D 733 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL D 738 " --> pdb=" O MET D 734 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER D 744 " --> pdb=" O GLY D 740 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS D 745 " --> pdb=" O GLN D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 753 through 762 Processing helix chain 'D' and resid 771 through 780 Processing helix chain 'D' and resid 782 through 790 Processing helix chain 'E' and resid 169 through 173 Processing helix chain 'E' and resid 179 through 184 Processing helix chain 'E' and resid 194 through 205 Processing helix chain 'E' and resid 222 through 235 removed outlier: 3.853A pdb=" N VAL E 226 " --> pdb=" O LYS E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 256 Processing helix chain 'E' and resid 264 through 279 Processing helix chain 'E' and resid 289 through 291 No H-bonds generated for 'chain 'E' and resid 289 through 291' Processing helix chain 'E' and resid 304 through 314 Proline residue: E 310 - end of helix Processing helix chain 'E' and resid 325 through 331 removed outlier: 3.612A pdb=" N ARG E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 339 No H-bonds generated for 'chain 'E' and resid 336 through 339' Processing helix chain 'E' and resid 352 through 361 Processing helix chain 'E' and resid 363 through 370 Processing helix chain 'E' and resid 376 through 389 removed outlier: 3.716A pdb=" N THR E 384 " --> pdb=" O VAL E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 414 Processing helix chain 'E' and resid 481 through 492 Processing helix chain 'E' and resid 501 through 508 Processing helix chain 'E' and resid 510 through 517 removed outlier: 3.817A pdb=" N ARG E 517 " --> pdb=" O GLU E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 536 Processing helix chain 'E' and resid 559 through 571 removed outlier: 3.868A pdb=" N SER E 563 " --> pdb=" O LYS E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 582 through 584 No H-bonds generated for 'chain 'E' and resid 582 through 584' Processing helix chain 'E' and resid 590 through 595 Processing helix chain 'E' and resid 611 through 616 Processing helix chain 'E' and resid 627 through 629 No H-bonds generated for 'chain 'E' and resid 627 through 629' Processing helix chain 'E' and resid 632 through 644 removed outlier: 4.350A pdb=" N GLN E 640 " --> pdb=" O ASN E 636 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL E 641 " --> pdb=" O SER E 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 691 through 704 Processing helix chain 'E' and resid 707 through 711 Processing helix chain 'E' and resid 724 through 745 removed outlier: 3.795A pdb=" N ARG E 737 " --> pdb=" O LEU E 733 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL E 738 " --> pdb=" O MET E 734 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER E 744 " --> pdb=" O GLY E 740 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LYS E 745 " --> pdb=" O GLN E 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 753 through 762 Processing helix chain 'E' and resid 771 through 780 Processing helix chain 'E' and resid 782 through 790 removed outlier: 3.641A pdb=" N LEU E 790 " --> pdb=" O SER E 786 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 184 Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 222 through 235 Processing helix chain 'F' and resid 240 through 242 No H-bonds generated for 'chain 'F' and resid 240 through 242' Processing helix chain 'F' and resid 264 through 279 Processing helix chain 'F' and resid 289 through 291 No H-bonds generated for 'chain 'F' and resid 289 through 291' Processing helix chain 'F' and resid 305 through 313 removed outlier: 3.739A pdb=" N LYS F 309 " --> pdb=" O ALA F 305 " (cutoff:3.500A) Proline residue: F 310 - end of helix Processing helix chain 'F' and resid 325 through 331 Processing helix chain 'F' and resid 336 through 339 No H-bonds generated for 'chain 'F' and resid 336 through 339' Processing helix chain 'F' and resid 352 through 370 removed outlier: 4.341A pdb=" N ASP F 364 " --> pdb=" O LYS F 360 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG F 365 " --> pdb=" O GLY F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 389 Processing helix chain 'F' and resid 397 through 415 Processing helix chain 'F' and resid 481 through 492 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 510 through 515 Processing helix chain 'F' and resid 522 through 536 Processing helix chain 'F' and resid 559 through 570 Processing helix chain 'F' and resid 588 through 591 No H-bonds generated for 'chain 'F' and resid 588 through 591' Processing helix chain 'F' and resid 610 through 615 Processing helix chain 'F' and resid 627 through 629 No H-bonds generated for 'chain 'F' and resid 627 through 629' Processing helix chain 'F' and resid 632 through 644 Processing helix chain 'F' and resid 688 through 703 Processing helix chain 'F' and resid 707 through 711 Processing helix chain 'F' and resid 724 through 745 removed outlier: 4.285A pdb=" N LEU F 733 " --> pdb=" O ARG F 729 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG F 737 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL F 738 " --> pdb=" O MET F 734 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS F 745 " --> pdb=" O GLN F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 753 through 762 Processing helix chain 'F' and resid 771 through 791 removed outlier: 3.934A pdb=" N ARG F 775 " --> pdb=" O ARG F 771 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU F 782 " --> pdb=" O GLN F 778 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASP F 783 " --> pdb=" O ARG F 779 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN F 784 " --> pdb=" O GLU F 780 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 343 through 346 removed outlier: 4.637A pdb=" N GLN A 318 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A 322 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN A 246 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N PHE A 285 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR A 248 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASP A 287 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 250 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 715 through 719 removed outlier: 3.553A pdb=" N ASP A 715 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY A 553 " --> pdb=" O SER A 666 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 578 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASP A 625 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE A 580 " --> pdb=" O ASP A 625 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 646 through 648 Processing sheet with id= D, first strand: chain 'A' and resid 748 through 751 Processing sheet with id= E, first strand: chain 'B' and resid 175 through 177 removed outlier: 4.354A pdb=" N ASP B 287 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA B 322 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 372 through 374 removed outlier: 6.853A pdb=" N ALA B 477 " --> pdb=" O SER B 373 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 715 through 719 removed outlier: 3.867A pdb=" N ASP B 715 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE B 550 " --> pdb=" O ASP B 715 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 717 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B 553 " --> pdb=" O SER B 666 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE B 578 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ASP B 625 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE B 580 " --> pdb=" O ASP B 625 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 646 through 648 Processing sheet with id= I, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.504A pdb=" N VAL B 817 " --> pdb=" O ASP B 805 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 175 through 177 removed outlier: 4.855A pdb=" N ASP C 287 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLN C 343 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 215 " --> pdb=" O GLN C 343 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL C 345 " --> pdb=" O ILE C 215 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 372 through 374 removed outlier: 6.560A pdb=" N ALA C 477 " --> pdb=" O SER C 373 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 715 through 719 removed outlier: 3.582A pdb=" N ASP C 715 " --> pdb=" O SER C 548 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE C 578 " --> pdb=" O LEU C 623 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ASP C 625 " --> pdb=" O ILE C 578 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE C 580 " --> pdb=" O ASP C 625 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 646 through 648 Processing sheet with id= N, first strand: chain 'C' and resid 748 through 751 Processing sheet with id= O, first strand: chain 'D' and resid 343 through 346 removed outlier: 8.423A pdb=" N ILE D 320 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU D 284 " --> pdb=" O ILE D 320 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ALA D 322 " --> pdb=" O LEU D 284 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ILE D 286 " --> pdb=" O ALA D 322 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N THR D 324 " --> pdb=" O ILE D 286 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLN D 246 " --> pdb=" O ILE D 283 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE D 285 " --> pdb=" O GLN D 246 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N TYR D 248 " --> pdb=" O PHE D 285 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 715 through 718 removed outlier: 6.741A pdb=" N ILE D 578 " --> pdb=" O LEU D 623 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASP D 625 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE D 580 " --> pdb=" O ASP D 625 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 646 through 648 Processing sheet with id= R, first strand: chain 'D' and resid 748 through 751 Processing sheet with id= S, first strand: chain 'E' and resid 175 through 177 Processing sheet with id= T, first strand: chain 'E' and resid 342 through 346 removed outlier: 6.637A pdb=" N ASN E 211 " --> pdb=" O GLN E 343 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL E 345 " --> pdb=" O ASN E 211 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL E 213 " --> pdb=" O VAL E 345 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLY E 321 " --> pdb=" O LEU E 214 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 715 through 718 removed outlier: 3.896A pdb=" N GLY E 547 " --> pdb=" O THR E 660 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER E 620 " --> pdb=" O VAL E 661 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE E 663 " --> pdb=" O SER E 620 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL E 622 " --> pdb=" O ILE E 663 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N THR E 665 " --> pdb=" O VAL E 622 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N PHE E 624 " --> pdb=" O THR E 665 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE E 578 " --> pdb=" O LEU E 623 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP E 625 " --> pdb=" O ILE E 578 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE E 580 " --> pdb=" O ASP E 625 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 646 through 648 Processing sheet with id= W, first strand: chain 'E' and resid 749 through 751 removed outlier: 6.607A pdb=" N VAL E 800 " --> pdb=" O VAL E 750 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 175 through 177 removed outlier: 5.697A pdb=" N ASP F 287 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN F 318 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ILE F 286 " --> pdb=" O GLN F 318 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE F 320 " --> pdb=" O ILE F 286 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL F 213 " --> pdb=" O GLN F 343 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 715 through 718 removed outlier: 3.738A pdb=" N ASP F 715 " --> pdb=" O SER F 548 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL F 622 " --> pdb=" O ILE F 663 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR F 665 " --> pdb=" O VAL F 622 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N PHE F 624 " --> pdb=" O THR F 665 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 749 through 751 removed outlier: 6.387A pdb=" N VAL F 800 " --> pdb=" O VAL F 750 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'F' and resid 803 through 805 removed outlier: 3.577A pdb=" N ASP F 805 " --> pdb=" O VAL F 817 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL F 817 " --> pdb=" O ASP F 805 " (cutoff:3.500A) 1142 hydrogen bonds defined for protein. 3321 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: 9.72 Time building geometry restraints manager: 10.62 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: 8746 1.34 - 1.46: 3830 1.46 - 1.58: 14840 1.58 - 1.70: 30 1.70 - 1.82: 132 Bond restraints: 27578 Sorted by residual: bond pdb=" N LYS C 330 " pdb=" CA LYS C 330 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.22e-02 6.72e+03 4.89e+00 bond pdb=" CA ASP D 335 " pdb=" CB ASP D 335 " ideal model delta sigma weight residual 1.526 1.563 -0.037 1.70e-02 3.46e+03 4.78e+00 bond pdb=" N THR F 416 " pdb=" CA THR F 416 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.23e-02 6.61e+03 4.56e+00 bond pdb=" C LYS C 330 " pdb=" N TYR C 331 " ideal model delta sigma weight residual 1.332 1.303 0.029 1.40e-02 5.10e+03 4.29e+00 bond pdb=" CA LYS C 330 " pdb=" C LYS C 330 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.34e-02 5.57e+03 3.44e+00 ... (remaining 27573 not shown) Histogram of bond angle deviations from ideal: 97.19 - 105.04: 424 105.04 - 112.89: 14817 112.89 - 120.73: 13084 120.73 - 128.58: 8756 128.58 - 136.43: 126 Bond angle restraints: 37207 Sorted by residual: angle pdb=" N VAL A 170 " pdb=" CA VAL A 170 " pdb=" C VAL A 170 " ideal model delta sigma weight residual 113.71 107.87 5.84 9.50e-01 1.11e+00 3.78e+01 angle pdb=" C LYS C 330 " pdb=" N TYR C 331 " pdb=" CA TYR C 331 " ideal model delta sigma weight residual 121.54 112.64 8.90 1.91e+00 2.74e-01 2.17e+01 angle pdb=" C LYS C 330 " pdb=" CA LYS C 330 " pdb=" CB LYS C 330 " ideal model delta sigma weight residual 110.72 102.97 7.75 1.69e+00 3.50e-01 2.10e+01 angle pdb=" C PHE F 497 " pdb=" N LYS F 498 " pdb=" CA LYS F 498 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.97e+01 angle pdb=" CA TYR C 328 " pdb=" C TYR C 328 " pdb=" N ARG C 329 " ideal model delta sigma weight residual 118.08 112.55 5.53 1.30e+00 5.92e-01 1.81e+01 ... (remaining 37202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 16502 34.84 - 69.68: 324 69.68 - 104.52: 39 104.52 - 139.36: 10 139.36 - 174.20: 3 Dihedral angle restraints: 16878 sinusoidal: 7107 harmonic: 9771 Sorted by residual: dihedral pdb=" C5' ADP A 901 " pdb=" O5' ADP A 901 " pdb=" PA ADP A 901 " pdb=" O2A ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 114.20 -174.20 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP D 902 " pdb=" O5' ADP D 902 " pdb=" PA ADP D 902 " pdb=" O2A ADP D 902 " ideal model delta sinusoidal sigma weight residual -60.00 89.08 -149.08 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O2A ADP D 902 " pdb=" O3A ADP D 902 " pdb=" PA ADP D 902 " pdb=" PB ADP D 902 " ideal model delta sinusoidal sigma weight residual -60.00 79.50 -139.50 1 2.00e+01 2.50e-03 4.23e+01 ... (remaining 16875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3174 0.051 - 0.102: 902 0.102 - 0.154: 144 0.154 - 0.205: 19 0.205 - 0.256: 6 Chirality restraints: 4245 Sorted by residual: chirality pdb=" CB ILE C 550 " pdb=" CA ILE C 550 " pdb=" CG1 ILE C 550 " pdb=" CG2 ILE C 550 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB ILE A 286 " pdb=" CA ILE A 286 " pdb=" CG1 ILE A 286 " pdb=" CG2 ILE A 286 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB THR A 665 " pdb=" CA THR A 665 " pdb=" OG1 THR A 665 " pdb=" CG2 THR A 665 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 4242 not shown) Planarity restraints: 4825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET F 415 " 0.028 2.00e-02 2.50e+03 5.44e-02 2.95e+01 pdb=" C MET F 415 " -0.094 2.00e-02 2.50e+03 pdb=" O MET F 415 " 0.035 2.00e-02 2.50e+03 pdb=" N THR F 416 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 328 " -0.026 2.00e-02 2.50e+03 5.43e-02 2.95e+01 pdb=" C TYR C 328 " 0.094 2.00e-02 2.50e+03 pdb=" O TYR C 328 " -0.036 2.00e-02 2.50e+03 pdb=" N ARG C 329 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 494 " -0.055 5.00e-02 4.00e+02 8.43e-02 1.14e+01 pdb=" N PRO C 495 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO C 495 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 495 " -0.046 5.00e-02 4.00e+02 ... (remaining 4822 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1414 2.73 - 3.27: 28663 3.27 - 3.81: 47123 3.81 - 4.36: 55950 4.36 - 4.90: 92454 Nonbonded interactions: 225604 Sorted by model distance: nonbonded pdb=" O ILE C 627 " pdb=" OH TYR C 635 " model vdw 2.183 2.440 nonbonded pdb=" O THR B 560 " pdb=" OG SER B 563 " model vdw 2.188 2.440 nonbonded pdb=" O ILE E 627 " pdb=" OH TYR E 635 " model vdw 2.231 2.440 nonbonded pdb=" OE2 GLU C 288 " pdb=" NE2 HIS C 290 " model vdw 2.239 2.520 nonbonded pdb=" OD1 ASN D 177 " pdb=" OG1 THR D 179 " model vdw 2.262 2.440 ... (remaining 225599 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 594 or resid 609 through 668 or resid 691 through 808 or resid 815 through 8 \ 21 or resid 901)) selection = (chain 'B' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 821 or resid 901)) selection = (chain 'C' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 821 or resid 901)) selection = (chain 'D' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 821 or resid 901)) selection = (chain 'E' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 821 or resid 901)) selection = (chain 'F' and (resid 170 through 415 or resid 477 through 668 or resid 691 thro \ ugh 808 or resid 815 through 821 or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.020 Extract box with map and model: 5.150 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 73.000 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.130 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 : 0.003 0.045 27578 Z= 0.207 Angle : 0.813 12.435 37207 Z= 0.416 Chirality : 0.047 0.256 4245 Planarity : 0.006 0.084 4825 Dihedral : 15.186 174.199 10558 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -0.24 (0.14), residues: 3348 helix: -0.13 (0.12), residues: 1770 sheet: 0.01 (0.25), residues: 404 loop : 0.07 (0.20), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 491 HIS 0.007 0.001 HIS C 290 PHE 0.034 0.002 PHE B 551 TYR 0.026 0.002 TYR A 389 ARG 0.011 0.000 ARG E 646 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 3.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9633 (mp) cc_final: 0.9409 (mp) REVERT: A 250 LEU cc_start: 0.9013 (tt) cc_final: 0.8332 (mt) REVERT: A 379 MET cc_start: 0.9127 (mpp) cc_final: 0.8624 (mpp) REVERT: B 198 GLU cc_start: 0.8982 (pt0) cc_final: 0.8773 (tp30) REVERT: B 622 VAL cc_start: 0.9256 (t) cc_final: 0.9038 (t) REVERT: B 815 ASP cc_start: 0.9005 (m-30) cc_final: 0.8687 (t0) REVERT: C 227 GLU cc_start: 0.9245 (mp0) cc_final: 0.9021 (mp0) REVERT: C 274 LYS cc_start: 0.9293 (ttpt) cc_final: 0.8972 (tppt) REVERT: C 288 GLU cc_start: 0.7324 (tp30) cc_final: 0.6940 (tp30) REVERT: C 410 MET cc_start: 0.9329 (mmt) cc_final: 0.9111 (mmp) REVERT: C 579 GLN cc_start: 0.8253 (tm130) cc_final: 0.7996 (tm-30) REVERT: C 586 HIS cc_start: 0.8550 (p-80) cc_final: 0.8305 (p-80) REVERT: C 730 MET cc_start: 0.9117 (mmp) cc_final: 0.8840 (mmp) REVERT: D 201 MET cc_start: 0.8901 (mtp) cc_final: 0.8331 (mtm) REVERT: D 272 VAL cc_start: 0.8923 (t) cc_final: 0.8721 (p) REVERT: D 303 ASP cc_start: 0.8153 (p0) cc_final: 0.7935 (p0) REVERT: D 346 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8596 (mm110) REVERT: D 581 ASP cc_start: 0.9053 (m-30) cc_final: 0.8849 (m-30) REVERT: D 582 MET cc_start: 0.9029 (mmm) cc_final: 0.8577 (mmm) REVERT: D 627 ILE cc_start: 0.9348 (tp) cc_final: 0.9143 (tp) REVERT: D 638 LEU cc_start: 0.9491 (mp) cc_final: 0.9264 (mp) REVERT: D 656 ASP cc_start: 0.8968 (p0) cc_final: 0.8744 (p0) REVERT: E 183 MET cc_start: 0.9422 (ptp) cc_final: 0.8775 (ptp) REVERT: E 342 PHE cc_start: 0.9067 (m-80) cc_final: 0.8683 (m-80) REVERT: E 582 MET cc_start: 0.9438 (mmp) cc_final: 0.9129 (mmp) REVERT: E 616 ARG cc_start: 0.8927 (ptm160) cc_final: 0.8232 (tmm-80) REVERT: E 747 MET cc_start: 0.8419 (mtp) cc_final: 0.8093 (mtp) REVERT: F 201 MET cc_start: 0.8871 (mpp) cc_final: 0.8249 (mpp) REVERT: F 379 MET cc_start: 0.8720 (mpp) cc_final: 0.8421 (mpp) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.3666 time to fit residues: 196.9554 Evaluate side-chains 243 residues out of total 2851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 20.0000 chunk 256 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 264 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 306 optimal weight: 0.0010 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 GLN D 343 GLN D 636 ASN E 490 ASN E 568 ASN ** E 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 720 HIS F 290 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27578 Z= 0.166 Angle : 0.579 7.351 37207 Z= 0.280 Chirality : 0.041 0.212 4245 Planarity : 0.004 0.064 4825 Dihedral : 8.778 173.772 3835 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.11 % Allowed : 3.93 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.39 (0.15), residues: 3348 helix: 0.48 (0.12), residues: 1786 sheet: -0.05 (0.25), residues: 428 loop : 0.32 (0.20), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 491 HIS 0.005 0.001 HIS C 290 PHE 0.031 0.001 PHE F 497 TYR 0.021 0.001 TYR A 331 ARG 0.005 0.000 ARG F 329 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 300 time to evaluate : 3.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9672 (mp) cc_final: 0.9436 (mp) REVERT: A 250 LEU cc_start: 0.9165 (tt) cc_final: 0.8875 (tt) REVERT: A 379 MET cc_start: 0.9223 (mpp) cc_final: 0.8644 (mpp) REVERT: A 389 TYR cc_start: 0.8104 (m-10) cc_final: 0.7507 (m-10) REVERT: A 662 LEU cc_start: 0.9474 (mt) cc_final: 0.9263 (mt) REVERT: B 287 ASP cc_start: 0.9345 (m-30) cc_final: 0.9097 (m-30) REVERT: C 379 MET cc_start: 0.9109 (pmm) cc_final: 0.8879 (pmm) REVERT: C 410 MET cc_start: 0.9370 (mmt) cc_final: 0.9144 (mmp) REVERT: C 579 GLN cc_start: 0.8013 (tm-30) cc_final: 0.7762 (tm-30) REVERT: C 730 MET cc_start: 0.9176 (mmp) cc_final: 0.8890 (mmp) REVERT: C 768 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6689 (mm) REVERT: D 201 MET cc_start: 0.8874 (mtp) cc_final: 0.8522 (mtm) REVERT: D 244 ASP cc_start: 0.8404 (m-30) cc_final: 0.8040 (m-30) REVERT: D 272 VAL cc_start: 0.8949 (t) cc_final: 0.8743 (p) REVERT: D 303 ASP cc_start: 0.8144 (p0) cc_final: 0.7814 (p0) REVERT: D 346 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8578 (mm-40) REVERT: D 379 MET cc_start: 0.9273 (mpp) cc_final: 0.8781 (mpp) REVERT: D 582 MET cc_start: 0.8701 (mmm) cc_final: 0.8455 (mmm) REVERT: D 627 ILE cc_start: 0.9388 (tp) cc_final: 0.9153 (tp) REVERT: E 332 ILE cc_start: 0.8961 (mt) cc_final: 0.8697 (mt) REVERT: E 342 PHE cc_start: 0.9090 (m-80) cc_final: 0.8660 (m-80) REVERT: E 616 ARG cc_start: 0.8982 (ptm160) cc_final: 0.8184 (tmm-80) REVERT: E 623 LEU cc_start: 0.9668 (tt) cc_final: 0.9348 (tt) REVERT: F 201 MET cc_start: 0.8879 (mpp) cc_final: 0.8401 (mpp) REVERT: F 329 ARG cc_start: 0.9016 (ttp80) cc_final: 0.8806 (ptm-80) REVERT: F 510 MET cc_start: 0.8870 (tmm) cc_final: 0.8335 (tmm) REVERT: F 551 PHE cc_start: 0.9384 (m-80) cc_final: 0.9129 (m-10) REVERT: F 582 MET cc_start: 0.7411 (mpp) cc_final: 0.7090 (mpp) outliers start: 3 outliers final: 1 residues processed: 303 average time/residue: 0.3642 time to fit residues: 180.3384 Evaluate side-chains 230 residues out of total 2851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 228 time to evaluate : 3.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 170 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 307 optimal weight: 2.9990 chunk 332 optimal weight: 6.9990 chunk 273 optimal weight: 0.9980 chunk 304 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 246 optimal weight: 0.8980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 483 GLN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 632 GLN ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN E 568 ASN E 667 ASN F 290 HIS ** F 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27578 Z= 0.239 Angle : 0.625 8.594 37207 Z= 0.306 Chirality : 0.042 0.226 4245 Planarity : 0.004 0.056 4825 Dihedral : 8.482 173.692 3835 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.66 (0.15), residues: 3348 helix: 0.69 (0.13), residues: 1776 sheet: -0.20 (0.24), residues: 442 loop : 0.59 (0.21), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 491 HIS 0.005 0.001 HIS C 290 PHE 0.028 0.002 PHE C 791 TYR 0.028 0.002 TYR A 331 ARG 0.007 0.000 ARG D 692 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 276 time to evaluate : 4.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 MET cc_start: 0.9318 (mpp) cc_final: 0.8622 (mpp) REVERT: A 389 TYR cc_start: 0.8118 (m-10) cc_final: 0.7510 (m-10) REVERT: B 287 ASP cc_start: 0.9416 (m-30) cc_final: 0.9204 (m-30) REVERT: B 582 MET cc_start: 0.8380 (mmp) cc_final: 0.8175 (mmm) REVERT: C 227 GLU cc_start: 0.9221 (mp0) cc_final: 0.8963 (mp0) REVERT: C 287 ASP cc_start: 0.8518 (t0) cc_final: 0.8240 (t70) REVERT: C 379 MET cc_start: 0.9002 (pmm) cc_final: 0.8746 (pmm) REVERT: C 395 LEU cc_start: 0.9440 (mt) cc_final: 0.9228 (mt) REVERT: C 410 MET cc_start: 0.9419 (mmt) cc_final: 0.9189 (mmp) REVERT: C 540 LYS cc_start: 0.9479 (pptt) cc_final: 0.9157 (pptt) REVERT: C 579 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7812 (tm-30) REVERT: C 730 MET cc_start: 0.9207 (mmp) cc_final: 0.8855 (mmp) REVERT: D 201 MET cc_start: 0.8929 (mtp) cc_final: 0.8614 (mtp) REVERT: D 244 ASP cc_start: 0.8482 (m-30) cc_final: 0.8128 (m-30) REVERT: D 379 MET cc_start: 0.9449 (mpp) cc_final: 0.9248 (mpp) REVERT: D 582 MET cc_start: 0.9271 (mmm) cc_final: 0.8913 (mmm) REVERT: D 627 ILE cc_start: 0.9376 (tp) cc_final: 0.9077 (tp) REVERT: E 291 THR cc_start: 0.9658 (p) cc_final: 0.8744 (p) REVERT: E 342 PHE cc_start: 0.9085 (m-10) cc_final: 0.8774 (m-80) REVERT: E 594 LEU cc_start: 0.9011 (tp) cc_final: 0.8740 (tp) REVERT: E 616 ARG cc_start: 0.9086 (ptm160) cc_final: 0.8327 (tmm-80) REVERT: E 623 LEU cc_start: 0.9725 (tt) cc_final: 0.9280 (tt) REVERT: E 747 MET cc_start: 0.8943 (mtt) cc_final: 0.8580 (mmm) REVERT: F 200 VAL cc_start: 0.9485 (p) cc_final: 0.9263 (p) REVERT: F 201 MET cc_start: 0.9149 (mpp) cc_final: 0.8700 (mpp) REVERT: F 289 LEU cc_start: 0.9612 (mm) cc_final: 0.9387 (mm) REVERT: F 329 ARG cc_start: 0.9065 (ttp80) cc_final: 0.8843 (ptm-80) REVERT: F 379 MET cc_start: 0.8811 (mpp) cc_final: 0.8370 (mpp) REVERT: F 510 MET cc_start: 0.8952 (tmm) cc_final: 0.8447 (tmm) REVERT: F 551 PHE cc_start: 0.9398 (m-80) cc_final: 0.9182 (m-10) REVERT: F 582 MET cc_start: 0.7503 (mpp) cc_final: 0.7052 (mpp) outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.3739 time to fit residues: 168.8990 Evaluate side-chains 216 residues out of total 2851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 3.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 303 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 146 optimal weight: 0.0010 chunk 206 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 326 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 292 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 ASN E 631 HIS F 290 HIS ** F 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 741 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27578 Z= 0.176 Angle : 0.582 7.542 37207 Z= 0.278 Chirality : 0.041 0.215 4245 Planarity : 0.004 0.057 4825 Dihedral : 8.188 169.043 3835 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.76 (0.15), residues: 3348 helix: 0.77 (0.13), residues: 1787 sheet: -0.22 (0.24), residues: 437 loop : 0.69 (0.21), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 491 HIS 0.003 0.001 HIS D 515 PHE 0.028 0.001 PHE F 497 TYR 0.013 0.001 TYR D 331 ARG 0.005 0.000 ARG F 544 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 3.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 MET cc_start: 0.9343 (mpp) cc_final: 0.8643 (mpp) REVERT: A 389 TYR cc_start: 0.8137 (m-10) cc_final: 0.7475 (m-10) REVERT: A 510 MET cc_start: 0.9180 (ptp) cc_final: 0.8850 (mtm) REVERT: A 622 VAL cc_start: 0.8571 (t) cc_final: 0.8333 (p) REVERT: B 287 ASP cc_start: 0.9319 (m-30) cc_final: 0.9030 (m-30) REVERT: B 582 MET cc_start: 0.8441 (mmp) cc_final: 0.7952 (mmm) REVERT: C 290 HIS cc_start: 0.8275 (p90) cc_final: 0.7555 (p-80) REVERT: C 333 GLU cc_start: 0.8652 (tp30) cc_final: 0.7669 (tp30) REVERT: C 410 MET cc_start: 0.9410 (mmt) cc_final: 0.9156 (mmp) REVERT: C 510 MET cc_start: 0.9354 (ppp) cc_final: 0.9108 (ppp) REVERT: C 540 LYS cc_start: 0.9410 (pptt) cc_final: 0.9152 (pptt) REVERT: C 579 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7749 (tm-30) REVERT: C 730 MET cc_start: 0.9174 (mmp) cc_final: 0.8845 (mmp) REVERT: C 747 MET cc_start: 0.8269 (mtt) cc_final: 0.8010 (mtt) REVERT: D 201 MET cc_start: 0.8884 (mtp) cc_final: 0.8589 (mtp) REVERT: D 244 ASP cc_start: 0.8462 (m-30) cc_final: 0.8094 (m-30) REVERT: D 272 VAL cc_start: 0.8965 (t) cc_final: 0.8765 (p) REVERT: D 288 GLU cc_start: 0.8212 (pp20) cc_final: 0.7849 (pp20) REVERT: D 291 THR cc_start: 0.9029 (p) cc_final: 0.8604 (p) REVERT: D 303 ASP cc_start: 0.8170 (p0) cc_final: 0.7888 (p0) REVERT: D 582 MET cc_start: 0.9226 (mmm) cc_final: 0.8872 (mmm) REVERT: D 627 ILE cc_start: 0.9379 (tp) cc_final: 0.9153 (tp) REVERT: E 183 MET cc_start: 0.9304 (ptp) cc_final: 0.8667 (ptp) REVERT: E 291 THR cc_start: 0.9503 (p) cc_final: 0.9060 (p) REVERT: E 342 PHE cc_start: 0.9029 (m-10) cc_final: 0.8713 (m-80) REVERT: E 582 MET cc_start: 0.9561 (mmp) cc_final: 0.9360 (mmm) REVERT: E 594 LEU cc_start: 0.9031 (tp) cc_final: 0.8748 (tp) REVERT: E 616 ARG cc_start: 0.9089 (ptm160) cc_final: 0.8292 (tmm-80) REVERT: E 623 LEU cc_start: 0.9710 (tt) cc_final: 0.9248 (tt) REVERT: E 747 MET cc_start: 0.9022 (mtt) cc_final: 0.8585 (mmm) REVERT: F 201 MET cc_start: 0.9036 (mpp) cc_final: 0.8596 (mpp) REVERT: F 289 LEU cc_start: 0.9612 (mm) cc_final: 0.9339 (mm) REVERT: F 329 ARG cc_start: 0.9020 (ttp80) cc_final: 0.8801 (ptm-80) REVERT: F 379 MET cc_start: 0.8835 (mpp) cc_final: 0.8326 (mpp) REVERT: F 510 MET cc_start: 0.9004 (tmm) cc_final: 0.8457 (tmm) REVERT: F 551 PHE cc_start: 0.9310 (m-80) cc_final: 0.9091 (m-10) REVERT: F 582 MET cc_start: 0.7673 (mpp) cc_final: 0.7198 (mpp) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.3744 time to fit residues: 171.5045 Evaluate side-chains 222 residues out of total 2851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 3.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 272 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 243 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 225 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 293 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 343 GLN ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 ASN E 631 HIS ** E 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27578 Z= 0.193 Angle : 0.595 9.404 37207 Z= 0.285 Chirality : 0.041 0.217 4245 Planarity : 0.004 0.056 4825 Dihedral : 7.988 161.200 3835 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.84 (0.15), residues: 3348 helix: 0.86 (0.13), residues: 1774 sheet: -0.20 (0.24), residues: 448 loop : 0.68 (0.21), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 491 HIS 0.003 0.001 HIS C 290 PHE 0.035 0.001 PHE C 791 TYR 0.018 0.001 TYR D 331 ARG 0.006 0.000 ARG F 268 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 3.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9675 (mp) cc_final: 0.9465 (mp) REVERT: A 379 MET cc_start: 0.9359 (mpp) cc_final: 0.8633 (mpp) REVERT: A 389 TYR cc_start: 0.8154 (m-10) cc_final: 0.7488 (m-10) REVERT: A 510 MET cc_start: 0.9184 (ptp) cc_final: 0.8830 (mtm) REVERT: A 622 VAL cc_start: 0.8433 (t) cc_final: 0.8135 (p) REVERT: B 287 ASP cc_start: 0.9339 (m-30) cc_final: 0.9034 (m-30) REVERT: B 582 MET cc_start: 0.8480 (mmp) cc_final: 0.7775 (mmm) REVERT: C 227 GLU cc_start: 0.9256 (mp0) cc_final: 0.9020 (mp0) REVERT: C 287 ASP cc_start: 0.8692 (p0) cc_final: 0.8484 (t0) REVERT: C 333 GLU cc_start: 0.8759 (tp30) cc_final: 0.7863 (tp30) REVERT: C 540 LYS cc_start: 0.9423 (pptt) cc_final: 0.9172 (pptt) REVERT: C 579 GLN cc_start: 0.7988 (tm-30) cc_final: 0.7735 (tm-30) REVERT: C 730 MET cc_start: 0.9182 (mmp) cc_final: 0.8868 (mmp) REVERT: C 747 MET cc_start: 0.8279 (mtt) cc_final: 0.8001 (mtt) REVERT: D 201 MET cc_start: 0.8947 (mtp) cc_final: 0.8615 (mtp) REVERT: D 244 ASP cc_start: 0.8462 (m-30) cc_final: 0.8099 (m-30) REVERT: D 272 VAL cc_start: 0.8979 (t) cc_final: 0.8775 (p) REVERT: D 303 ASP cc_start: 0.8192 (p0) cc_final: 0.7918 (p0) REVERT: D 379 MET cc_start: 0.9357 (mpp) cc_final: 0.9060 (mpp) REVERT: D 582 MET cc_start: 0.9262 (mmm) cc_final: 0.8895 (mmm) REVERT: D 627 ILE cc_start: 0.9365 (tp) cc_final: 0.9128 (tp) REVERT: E 183 MET cc_start: 0.9311 (ptp) cc_final: 0.8659 (ptp) REVERT: E 291 THR cc_start: 0.9587 (p) cc_final: 0.9163 (p) REVERT: E 342 PHE cc_start: 0.8966 (m-10) cc_final: 0.8479 (m-80) REVERT: E 582 MET cc_start: 0.9611 (mmp) cc_final: 0.9350 (mmm) REVERT: E 594 LEU cc_start: 0.9083 (tp) cc_final: 0.8786 (tp) REVERT: E 616 ARG cc_start: 0.9103 (ptm160) cc_final: 0.8287 (tmm-80) REVERT: E 623 LEU cc_start: 0.9724 (tt) cc_final: 0.9235 (tt) REVERT: E 747 MET cc_start: 0.9042 (mtt) cc_final: 0.8617 (mmm) REVERT: F 201 MET cc_start: 0.9050 (mpp) cc_final: 0.8550 (mpp) REVERT: F 284 LEU cc_start: 0.9389 (tp) cc_final: 0.9178 (tp) REVERT: F 289 LEU cc_start: 0.9619 (mm) cc_final: 0.9307 (mm) REVERT: F 379 MET cc_start: 0.8792 (mpp) cc_final: 0.8389 (mpp) REVERT: F 510 MET cc_start: 0.9031 (tmm) cc_final: 0.8478 (tmm) REVERT: F 582 MET cc_start: 0.7691 (mpp) cc_final: 0.7327 (mpp) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.3570 time to fit residues: 159.7926 Evaluate side-chains 214 residues out of total 2851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 109 optimal weight: 6.9990 chunk 294 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 327 optimal weight: 0.6980 chunk 271 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 108 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS C 290 HIS ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 806 ASN ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 ASN E 631 HIS ** E 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27578 Z= 0.215 Angle : 0.610 8.375 37207 Z= 0.295 Chirality : 0.042 0.291 4245 Planarity : 0.004 0.053 4825 Dihedral : 7.888 152.746 3835 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.83 (0.15), residues: 3348 helix: 0.84 (0.13), residues: 1782 sheet: -0.18 (0.24), residues: 446 loop : 0.69 (0.21), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 491 HIS 0.005 0.001 HIS C 290 PHE 0.030 0.001 PHE C 791 TYR 0.022 0.001 TYR D 331 ARG 0.005 0.000 ARG E 646 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 3.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 TYR cc_start: 0.9085 (m-10) cc_final: 0.8774 (m-10) REVERT: A 379 MET cc_start: 0.9381 (mpp) cc_final: 0.8677 (mpp) REVERT: A 389 TYR cc_start: 0.8227 (m-10) cc_final: 0.7618 (m-10) REVERT: A 510 MET cc_start: 0.9206 (ptp) cc_final: 0.8833 (mtm) REVERT: A 622 VAL cc_start: 0.8640 (t) cc_final: 0.8371 (p) REVERT: B 582 MET cc_start: 0.8540 (mmp) cc_final: 0.8226 (mmm) REVERT: B 693 MET cc_start: 0.7837 (pmm) cc_final: 0.7614 (pmm) REVERT: C 227 GLU cc_start: 0.9137 (mp0) cc_final: 0.8820 (mp0) REVERT: C 333 GLU cc_start: 0.8836 (tp30) cc_final: 0.7923 (tp30) REVERT: C 540 LYS cc_start: 0.9401 (pptt) cc_final: 0.9135 (pptt) REVERT: C 579 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7696 (tm-30) REVERT: C 730 MET cc_start: 0.9191 (mmp) cc_final: 0.8890 (mmp) REVERT: C 747 MET cc_start: 0.8233 (mtt) cc_final: 0.7882 (mtt) REVERT: D 201 MET cc_start: 0.8931 (mtp) cc_final: 0.8646 (mtp) REVERT: D 244 ASP cc_start: 0.8485 (m-30) cc_final: 0.8123 (m-30) REVERT: D 272 VAL cc_start: 0.8980 (t) cc_final: 0.8778 (p) REVERT: D 392 ASP cc_start: 0.7960 (t0) cc_final: 0.7737 (t0) REVERT: D 582 MET cc_start: 0.9324 (mmm) cc_final: 0.9010 (mmm) REVERT: D 627 ILE cc_start: 0.9363 (tp) cc_final: 0.9144 (tp) REVERT: D 726 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8366 (mt-10) REVERT: E 183 MET cc_start: 0.9319 (ptp) cc_final: 0.8656 (ptp) REVERT: E 291 THR cc_start: 0.9578 (p) cc_final: 0.9134 (p) REVERT: E 342 PHE cc_start: 0.9047 (m-10) cc_final: 0.8588 (m-80) REVERT: E 582 MET cc_start: 0.9626 (mmp) cc_final: 0.9354 (mmm) REVERT: E 594 LEU cc_start: 0.9207 (tp) cc_final: 0.8897 (tp) REVERT: E 616 ARG cc_start: 0.9121 (ptm160) cc_final: 0.8286 (tmm-80) REVERT: E 623 LEU cc_start: 0.9743 (tt) cc_final: 0.9254 (tt) REVERT: E 747 MET cc_start: 0.9075 (mtt) cc_final: 0.8630 (mmm) REVERT: F 201 MET cc_start: 0.9055 (mpp) cc_final: 0.8539 (mpp) REVERT: F 284 LEU cc_start: 0.9392 (tp) cc_final: 0.9188 (tp) REVERT: F 289 LEU cc_start: 0.9619 (mm) cc_final: 0.9270 (mm) REVERT: F 379 MET cc_start: 0.8802 (mpp) cc_final: 0.8435 (mpp) REVERT: F 510 MET cc_start: 0.8991 (tmm) cc_final: 0.8555 (tmm) REVERT: F 582 MET cc_start: 0.7758 (mpp) cc_final: 0.7362 (mpp) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.3648 time to fit residues: 163.3854 Evaluate side-chains 210 residues out of total 2851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 315 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 275 optimal weight: 0.7980 chunk 182 optimal weight: 0.0870 chunk 325 optimal weight: 7.9990 chunk 203 optimal weight: 0.8980 chunk 198 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 ASN E 631 HIS E 711 ASN ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27578 Z= 0.152 Angle : 0.599 8.289 37207 Z= 0.283 Chirality : 0.042 0.226 4245 Planarity : 0.004 0.055 4825 Dihedral : 7.690 143.538 3835 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.88 (0.15), residues: 3348 helix: 0.86 (0.13), residues: 1783 sheet: -0.13 (0.24), residues: 447 loop : 0.73 (0.21), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 491 HIS 0.003 0.000 HIS C 290 PHE 0.028 0.001 PHE C 791 TYR 0.019 0.001 TYR E 604 ARG 0.006 0.000 ARG D 593 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 3.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9688 (mp) cc_final: 0.9482 (mp) REVERT: A 251 ASP cc_start: 0.8309 (t70) cc_final: 0.8053 (t0) REVERT: A 379 MET cc_start: 0.9376 (mpp) cc_final: 0.8694 (mpp) REVERT: A 389 TYR cc_start: 0.8219 (m-10) cc_final: 0.7574 (m-10) REVERT: A 510 MET cc_start: 0.9212 (ptp) cc_final: 0.8794 (mtm) REVERT: A 622 VAL cc_start: 0.8611 (t) cc_final: 0.8373 (p) REVERT: A 625 ASP cc_start: 0.8605 (t70) cc_final: 0.8360 (t70) REVERT: B 287 ASP cc_start: 0.9421 (m-30) cc_final: 0.9202 (m-30) REVERT: B 582 MET cc_start: 0.8440 (mmp) cc_final: 0.8166 (mmm) REVERT: B 693 MET cc_start: 0.7695 (pmm) cc_final: 0.7483 (pmm) REVERT: C 227 GLU cc_start: 0.9267 (mp0) cc_final: 0.8990 (mp0) REVERT: C 333 GLU cc_start: 0.8742 (tp30) cc_final: 0.7825 (tp30) REVERT: C 410 MET cc_start: 0.9278 (mmp) cc_final: 0.8946 (mmt) REVERT: C 540 LYS cc_start: 0.9402 (pptt) cc_final: 0.9123 (pptt) REVERT: C 579 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7656 (tm-30) REVERT: D 201 MET cc_start: 0.8875 (mtp) cc_final: 0.8389 (ptm) REVERT: D 244 ASP cc_start: 0.8601 (m-30) cc_final: 0.8344 (m-30) REVERT: D 303 ASP cc_start: 0.8313 (p0) cc_final: 0.8059 (p0) REVERT: D 392 ASP cc_start: 0.7861 (t0) cc_final: 0.7641 (t0) REVERT: D 582 MET cc_start: 0.8972 (mmm) cc_final: 0.8671 (mmm) REVERT: D 627 ILE cc_start: 0.9365 (tp) cc_final: 0.9143 (tp) REVERT: E 183 MET cc_start: 0.9328 (ptp) cc_final: 0.8603 (ptp) REVERT: E 291 THR cc_start: 0.9554 (p) cc_final: 0.9097 (p) REVERT: E 342 PHE cc_start: 0.8933 (m-10) cc_final: 0.8405 (m-80) REVERT: E 582 MET cc_start: 0.9555 (mmp) cc_final: 0.9331 (mmm) REVERT: E 594 LEU cc_start: 0.9214 (tp) cc_final: 0.8903 (tp) REVERT: E 616 ARG cc_start: 0.9111 (ptm160) cc_final: 0.8270 (tmm-80) REVERT: E 623 LEU cc_start: 0.9732 (tt) cc_final: 0.9192 (tt) REVERT: E 747 MET cc_start: 0.9012 (mtt) cc_final: 0.8639 (mmm) REVERT: F 201 MET cc_start: 0.8990 (mpp) cc_final: 0.8456 (mpp) REVERT: F 289 LEU cc_start: 0.9575 (mm) cc_final: 0.9326 (mm) REVERT: F 379 MET cc_start: 0.8781 (mpp) cc_final: 0.8381 (mpp) REVERT: F 510 MET cc_start: 0.9007 (tmm) cc_final: 0.8541 (tmm) REVERT: F 551 PHE cc_start: 0.9315 (m-80) cc_final: 0.9093 (m-10) REVERT: F 582 MET cc_start: 0.7721 (mpp) cc_final: 0.7315 (mpp) REVERT: F 734 MET cc_start: 0.9113 (mpp) cc_final: 0.8726 (mpp) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.3612 time to fit residues: 168.9836 Evaluate side-chains 222 residues out of total 2851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 3.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 201 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 194 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 221 optimal weight: 0.9980 chunk 161 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 256 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 GLN ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 ASN E 631 HIS ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27578 Z= 0.157 Angle : 0.599 7.713 37207 Z= 0.285 Chirality : 0.042 0.197 4245 Planarity : 0.003 0.055 4825 Dihedral : 7.539 137.950 3835 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.94 (0.15), residues: 3348 helix: 0.91 (0.13), residues: 1768 sheet: -0.06 (0.24), residues: 447 loop : 0.76 (0.21), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 491 HIS 0.004 0.000 HIS C 290 PHE 0.029 0.001 PHE C 791 TYR 0.021 0.001 TYR A 331 ARG 0.004 0.000 ARG F 371 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 3.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7799 (ttp80) REVERT: A 178 LEU cc_start: 0.9700 (mp) cc_final: 0.9480 (mp) REVERT: A 251 ASP cc_start: 0.8316 (t70) cc_final: 0.7971 (t0) REVERT: A 331 TYR cc_start: 0.8917 (m-10) cc_final: 0.8713 (m-10) REVERT: A 379 MET cc_start: 0.9378 (mpp) cc_final: 0.8665 (mpp) REVERT: A 389 TYR cc_start: 0.8239 (m-10) cc_final: 0.7577 (m-10) REVERT: B 198 GLU cc_start: 0.9023 (pt0) cc_final: 0.8822 (tp30) REVERT: B 287 ASP cc_start: 0.9432 (m-30) cc_final: 0.9214 (m-30) REVERT: B 582 MET cc_start: 0.8383 (mmp) cc_final: 0.8126 (mmm) REVERT: B 693 MET cc_start: 0.7739 (pmm) cc_final: 0.7506 (pmm) REVERT: C 227 GLU cc_start: 0.9240 (mp0) cc_final: 0.9018 (mp0) REVERT: C 410 MET cc_start: 0.9299 (mmp) cc_final: 0.8337 (ttm) REVERT: C 540 LYS cc_start: 0.9400 (pptt) cc_final: 0.9128 (pptt) REVERT: C 730 MET cc_start: 0.9156 (mmp) cc_final: 0.8939 (mmp) REVERT: C 747 MET cc_start: 0.8179 (mtt) cc_final: 0.7924 (mtt) REVERT: D 201 MET cc_start: 0.8847 (mtp) cc_final: 0.8356 (ptm) REVERT: D 244 ASP cc_start: 0.8612 (m-30) cc_final: 0.8328 (m-30) REVERT: D 303 ASP cc_start: 0.8276 (p0) cc_final: 0.8031 (p0) REVERT: D 392 ASP cc_start: 0.7916 (t0) cc_final: 0.7603 (t0) REVERT: D 582 MET cc_start: 0.8998 (mmm) cc_final: 0.8739 (mmm) REVERT: D 627 ILE cc_start: 0.9361 (tp) cc_final: 0.9148 (tp) REVERT: E 183 MET cc_start: 0.9336 (ptp) cc_final: 0.8616 (ptp) REVERT: E 291 THR cc_start: 0.9560 (p) cc_final: 0.9106 (p) REVERT: E 342 PHE cc_start: 0.8928 (m-10) cc_final: 0.8352 (m-80) REVERT: E 582 MET cc_start: 0.9561 (mmp) cc_final: 0.9306 (mmm) REVERT: E 616 ARG cc_start: 0.9109 (ptm160) cc_final: 0.8278 (tmm-80) REVERT: E 623 LEU cc_start: 0.9735 (tt) cc_final: 0.9244 (tt) REVERT: E 747 MET cc_start: 0.9017 (mtt) cc_final: 0.8644 (mmm) REVERT: F 201 MET cc_start: 0.8980 (mpp) cc_final: 0.8516 (mpp) REVERT: F 289 LEU cc_start: 0.9591 (mm) cc_final: 0.9322 (mm) REVERT: F 379 MET cc_start: 0.8780 (mpp) cc_final: 0.8363 (mpp) REVERT: F 510 MET cc_start: 0.9107 (tmm) cc_final: 0.8684 (tmm) REVERT: F 582 MET cc_start: 0.7394 (mpp) cc_final: 0.7045 (mpp) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.3761 time to fit residues: 172.5756 Evaluate side-chains 229 residues out of total 2851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 7.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 296 optimal weight: 5.9990 chunk 312 optimal weight: 10.0000 chunk 284 optimal weight: 0.8980 chunk 303 optimal weight: 0.8980 chunk 182 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 238 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 274 optimal weight: 0.6980 chunk 287 optimal weight: 0.9990 chunk 302 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 579 GLN ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 ASN E 631 HIS ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 27578 Z= 0.155 Angle : 0.605 10.796 37207 Z= 0.286 Chirality : 0.042 0.189 4245 Planarity : 0.003 0.058 4825 Dihedral : 7.391 137.118 3835 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.92 (0.15), residues: 3348 helix: 0.87 (0.13), residues: 1777 sheet: -0.02 (0.24), residues: 447 loop : 0.77 (0.21), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 491 HIS 0.003 0.000 HIS C 290 PHE 0.027 0.001 PHE C 791 TYR 0.020 0.001 TYR D 331 ARG 0.005 0.000 ARG E 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 3.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ARG cc_start: 0.8111 (ttp80) cc_final: 0.7886 (ttp80) REVERT: A 251 ASP cc_start: 0.8337 (t70) cc_final: 0.8077 (t0) REVERT: A 330 LYS cc_start: 0.9338 (tmmt) cc_final: 0.9053 (tmmt) REVERT: A 331 TYR cc_start: 0.8949 (m-10) cc_final: 0.8665 (m-10) REVERT: A 379 MET cc_start: 0.9374 (mpp) cc_final: 0.8659 (mpp) REVERT: A 389 TYR cc_start: 0.8267 (m-10) cc_final: 0.7585 (m-10) REVERT: A 625 ASP cc_start: 0.8526 (t70) cc_final: 0.8235 (t70) REVERT: B 287 ASP cc_start: 0.9412 (m-30) cc_final: 0.9208 (m-30) REVERT: B 582 MET cc_start: 0.8338 (mmp) cc_final: 0.8074 (mmm) REVERT: B 693 MET cc_start: 0.7767 (pmm) cc_final: 0.7529 (pmm) REVERT: C 227 GLU cc_start: 0.9231 (mp0) cc_final: 0.9018 (mp0) REVERT: C 333 GLU cc_start: 0.8741 (tp30) cc_final: 0.7847 (tp30) REVERT: C 410 MET cc_start: 0.9300 (mmp) cc_final: 0.8238 (ttm) REVERT: C 540 LYS cc_start: 0.9392 (pptt) cc_final: 0.9132 (pptt) REVERT: C 579 GLN cc_start: 0.7842 (tm130) cc_final: 0.7605 (tm-30) REVERT: C 747 MET cc_start: 0.8190 (mtt) cc_final: 0.7928 (mtt) REVERT: D 201 MET cc_start: 0.8832 (mtp) cc_final: 0.8347 (ptm) REVERT: D 244 ASP cc_start: 0.8669 (m-30) cc_final: 0.8391 (m-30) REVERT: D 288 GLU cc_start: 0.8140 (pp20) cc_final: 0.7930 (pp20) REVERT: D 566 LEU cc_start: 0.9411 (tt) cc_final: 0.9137 (mm) REVERT: D 582 MET cc_start: 0.9007 (mmm) cc_final: 0.8677 (mmm) REVERT: D 627 ILE cc_start: 0.9360 (tp) cc_final: 0.9154 (tp) REVERT: E 183 MET cc_start: 0.9341 (ptp) cc_final: 0.8611 (ptp) REVERT: E 291 THR cc_start: 0.9565 (p) cc_final: 0.9116 (p) REVERT: E 342 PHE cc_start: 0.8959 (m-10) cc_final: 0.8717 (m-80) REVERT: E 582 MET cc_start: 0.9518 (mmp) cc_final: 0.9277 (mmm) REVERT: E 616 ARG cc_start: 0.9110 (ptm160) cc_final: 0.8283 (tmm-80) REVERT: E 623 LEU cc_start: 0.9696 (tt) cc_final: 0.9134 (tt) REVERT: E 747 MET cc_start: 0.9016 (mtt) cc_final: 0.8648 (mmm) REVERT: F 201 MET cc_start: 0.8963 (mpp) cc_final: 0.8489 (mpp) REVERT: F 289 LEU cc_start: 0.9590 (mm) cc_final: 0.9310 (mm) REVERT: F 330 LYS cc_start: 0.9126 (ptmm) cc_final: 0.8895 (ptmm) REVERT: F 331 TYR cc_start: 0.8371 (m-80) cc_final: 0.7504 (m-80) REVERT: F 379 MET cc_start: 0.8773 (mpp) cc_final: 0.8349 (mpp) REVERT: F 510 MET cc_start: 0.9126 (tmm) cc_final: 0.8692 (tmm) REVERT: F 582 MET cc_start: 0.7391 (mpp) cc_final: 0.6964 (mpp) REVERT: F 730 MET cc_start: 0.8556 (mmp) cc_final: 0.8128 (mmt) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.3757 time to fit residues: 169.8303 Evaluate side-chains 224 residues out of total 2851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 199 optimal weight: 0.9990 chunk 321 optimal weight: 0.6980 chunk 195 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 223 optimal weight: 9.9990 chunk 336 optimal weight: 20.0000 chunk 309 optimal weight: 7.9990 chunk 268 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 207 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 GLN ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 579 GLN ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 ASN E 631 HIS F 290 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27578 Z= 0.156 Angle : 0.614 10.122 37207 Z= 0.290 Chirality : 0.042 0.324 4245 Planarity : 0.004 0.107 4825 Dihedral : 7.274 136.456 3835 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.93 (0.15), residues: 3348 helix: 0.89 (0.13), residues: 1775 sheet: -0.06 (0.24), residues: 439 loop : 0.75 (0.21), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 491 HIS 0.007 0.001 HIS C 631 PHE 0.028 0.001 PHE C 791 TYR 0.021 0.001 TYR D 331 ARG 0.019 0.000 ARG C 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 3.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8289 (t70) cc_final: 0.8064 (t0) REVERT: A 379 MET cc_start: 0.9372 (mpp) cc_final: 0.8660 (mpp) REVERT: A 389 TYR cc_start: 0.8289 (m-10) cc_final: 0.7591 (m-10) REVERT: A 625 ASP cc_start: 0.8514 (t70) cc_final: 0.8273 (t70) REVERT: A 747 MET cc_start: 0.7636 (tpt) cc_final: 0.7367 (mmm) REVERT: B 582 MET cc_start: 0.8300 (mmp) cc_final: 0.8047 (mmm) REVERT: B 693 MET cc_start: 0.7789 (pmm) cc_final: 0.7548 (pmm) REVERT: C 227 GLU cc_start: 0.9230 (mp0) cc_final: 0.9003 (mp0) REVERT: C 328 TYR cc_start: 0.8777 (t80) cc_final: 0.8573 (t80) REVERT: C 333 GLU cc_start: 0.8772 (tp30) cc_final: 0.7932 (tp30) REVERT: C 540 LYS cc_start: 0.9391 (pptt) cc_final: 0.9140 (pptt) REVERT: C 747 MET cc_start: 0.8193 (mtt) cc_final: 0.7927 (mtt) REVERT: D 201 MET cc_start: 0.8850 (mtp) cc_final: 0.8337 (ptm) REVERT: D 244 ASP cc_start: 0.8662 (m-30) cc_final: 0.8377 (m-30) REVERT: D 582 MET cc_start: 0.9023 (mmm) cc_final: 0.8691 (mmm) REVERT: D 627 ILE cc_start: 0.9366 (tp) cc_final: 0.9156 (tp) REVERT: E 183 MET cc_start: 0.9342 (ptp) cc_final: 0.9122 (ptp) REVERT: E 291 THR cc_start: 0.9212 (p) cc_final: 0.8686 (p) REVERT: E 342 PHE cc_start: 0.8964 (m-10) cc_final: 0.8718 (m-80) REVERT: E 582 MET cc_start: 0.9508 (mmp) cc_final: 0.9276 (mmm) REVERT: E 616 ARG cc_start: 0.9109 (ptm160) cc_final: 0.8291 (tmm-80) REVERT: E 623 LEU cc_start: 0.9727 (tt) cc_final: 0.9148 (tt) REVERT: E 730 MET cc_start: 0.9273 (tpp) cc_final: 0.8806 (tpt) REVERT: E 747 MET cc_start: 0.9008 (mtt) cc_final: 0.8644 (mmm) REVERT: F 201 MET cc_start: 0.9044 (mpp) cc_final: 0.8433 (mpp) REVERT: F 289 LEU cc_start: 0.9604 (mm) cc_final: 0.9348 (mm) REVERT: F 379 MET cc_start: 0.8761 (mpp) cc_final: 0.8335 (mpp) REVERT: F 510 MET cc_start: 0.9142 (tmm) cc_final: 0.8706 (tmm) REVERT: F 582 MET cc_start: 0.7393 (mpp) cc_final: 0.6955 (mpp) REVERT: F 730 MET cc_start: 0.8554 (mmp) cc_final: 0.8185 (mmt) REVERT: F 734 MET cc_start: 0.9070 (mpp) cc_final: 0.8821 (mmt) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.3779 time to fit residues: 169.6470 Evaluate side-chains 221 residues out of total 2851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 212 optimal weight: 0.9980 chunk 285 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 247 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 268 optimal weight: 3.9990 chunk 112 optimal weight: 0.4980 chunk 275 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 GLN ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 579 GLN ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN E 568 ASN E 631 HIS F 290 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.066808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.053741 restraints weight = 160458.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.055302 restraints weight = 100264.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.056428 restraints weight = 70328.052| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27578 Z= 0.156 Angle : 0.610 11.332 37207 Z= 0.290 Chirality : 0.042 0.305 4245 Planarity : 0.004 0.098 4825 Dihedral : 7.097 135.445 3835 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.95 (0.15), residues: 3348 helix: 0.90 (0.13), residues: 1780 sheet: -0.05 (0.24), residues: 439 loop : 0.77 (0.21), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 491 HIS 0.007 0.001 HIS C 631 PHE 0.028 0.001 PHE C 791 TYR 0.019 0.001 TYR D 331 ARG 0.014 0.000 ARG C 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4651.05 seconds wall clock time: 86 minutes 38.72 seconds (5198.72 seconds total)