Starting phenix.real_space_refine on Wed Mar 20 11:11:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8u_15240/03_2024/8a8u_15240_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8u_15240/03_2024/8a8u_15240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8u_15240/03_2024/8a8u_15240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8u_15240/03_2024/8a8u_15240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8u_15240/03_2024/8a8u_15240_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8u_15240/03_2024/8a8u_15240_updated.pdb" } resolution = 3.62 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= -0.001 sd= 0.058 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 17023 2.51 5 N 4833 2.21 5 O 5187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 196": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B GLU 349": "OE1" <-> "OE2" Residue "B GLU 367": "OE1" <-> "OE2" Residue "B GLU 522": "OE1" <-> "OE2" Residue "B GLU 626": "OE1" <-> "OE2" Residue "B GLU 792": "OE1" <-> "OE2" Residue "C GLU 217": "OE1" <-> "OE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C GLU 333": "OE1" <-> "OE2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "C GLU 478": "OE1" <-> "OE2" Residue "C GLU 486": "OE1" <-> "OE2" Residue "C GLU 501": "OE1" <-> "OE2" Residue "C GLU 511": "OE1" <-> "OE2" Residue "C GLU 512": "OE1" <-> "OE2" Residue "C GLU 513": "OE1" <-> "OE2" Residue "C GLU 561": "OE1" <-> "OE2" Residue "C GLU 612": "OE1" <-> "OE2" Residue "C GLU 628": "OE1" <-> "OE2" Residue "C GLU 691": "OE1" <-> "OE2" Residue "C GLU 708": "OE1" <-> "OE2" Residue "C GLU 787": "OE1" <-> "OE2" Residue "C GLU 792": "OE1" <-> "OE2" Residue "D GLU 194": "OE1" <-> "OE2" Residue "D GLU 217": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D GLU 288": "OE1" <-> "OE2" Residue "D GLU 349": "OE1" <-> "OE2" Residue "D GLU 503": "OE1" <-> "OE2" Residue "D GLU 512": "OE1" <-> "OE2" Residue "D GLU 522": "OE1" <-> "OE2" Residue "D GLU 606": "OE1" <-> "OE2" Residue "D GLU 814": "OE1" <-> "OE2" Residue "E GLU 275": "OE1" <-> "OE2" Residue "E GLU 357": "OE1" <-> "OE2" Residue "E GLU 478": "OE1" <-> "OE2" Residue "E GLU 503": "OE1" <-> "OE2" Residue "E GLU 612": "OE1" <-> "OE2" Residue "E GLU 700": "OE1" <-> "OE2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F GLU 266": "OE1" <-> "OE2" Residue "F GLU 353": "OE1" <-> "OE2" Residue "F GLU 522": "OE1" <-> "OE2" Residue "F GLU 633": "OE1" <-> "OE2" Residue "F GLU 810": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27129 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: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4530 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 555} 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: 4329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4329 Classifications: {'peptide': 546} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 527} Chain breaks: 5 Chain: "G" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 114 Classifications: {'peptide': 23} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 22} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 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: 13.42, per 1000 atoms: 0.49 Number of scatterers: 27129 At special positions: 0 Unit cell: (119.7, 135.09, 150.48, 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 5187 8.00 N 4833 7.00 C 17023 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: 11.30 Conformation dependent library (CDL) restraints added in 5.0 seconds 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6302 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 25 sheets defined 50.7% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.41 Creating SS restraints... Processing helix chain 'A' and resid 178 through 184 Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 222 through 235 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 256 removed outlier: 4.006A pdb=" N VAL A 256 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 289 through 292 Processing helix chain 'A' and resid 304 through 312 Proline residue: A 310 - end of helix Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 336 through 341 removed outlier: 3.723A pdb=" N ARG A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 370 removed outlier: 4.608A pdb=" N ASP A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ARG A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 389 removed outlier: 4.053A pdb=" N ARG A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) 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 588 through 594 removed outlier: 3.512A 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: 4.981A pdb=" N SER A 744 " --> pdb=" O GLY A 740 " (cutoff:3.500A) removed outlier: 5.834A 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 771 through 790 removed outlier: 4.062A pdb=" N ARG A 774 " --> pdb=" O ARG A 771 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A 777 " --> pdb=" O ARG A 774 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN A 778 " --> pdb=" O ARG A 775 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 780 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLU A 782 " --> pdb=" O ARG A 779 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASP A 783 " --> pdb=" O GLU A 780 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 790 " --> pdb=" O GLU A 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 174 No H-bonds generated for 'chain 'B' and resid 171 through 174' Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.672A 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 255 No H-bonds generated for 'chain 'B' and resid 252 through 255' 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 340 Processing helix chain 'B' and resid 352 through 370 removed outlier: 4.890A pdb=" N ASP B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 5.069A 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 508 Processing helix chain 'B' and resid 510 through 515 Processing helix chain 'B' and resid 522 through 536 Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.730A pdb=" N SER B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 576 No H-bonds generated for 'chain 'B' and resid 574 through 576' Processing helix chain 'B' and resid 589 through 595 removed outlier: 3.566A pdb=" N ARG B 593 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 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 632 through 644 removed outlier: 3.780A pdb=" N ASN B 636 " --> pdb=" O GLN B 632 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL B 641 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 704 Processing helix chain 'B' and resid 707 through 711 Processing helix chain 'B' and resid 724 through 745 removed outlier: 3.993A pdb=" N ASP B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG B 737 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 738 " --> pdb=" O MET B 734 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER B 744 " --> pdb=" O GLY B 740 " (cutoff:3.500A) removed outlier: 4.689A 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 791 Processing helix chain 'C' and resid 169 through 174 removed outlier: 4.022A pdb=" N GLN C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE C 174 " --> pdb=" O VAL C 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 174' Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 222 through 235 removed outlier: 3.725A 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 removed outlier: 3.772A pdb=" N ARG C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 336 through 340 Processing helix chain 'C' and resid 352 through 361 Processing helix chain 'C' and resid 363 through 370 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 515 Processing helix chain 'C' and resid 522 through 536 Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.879A pdb=" N SER C 563 " --> pdb=" O LYS C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 595 removed outlier: 3.732A pdb=" N LEU C 594 " --> pdb=" O ALA C 591 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE C 595 " --> pdb=" O SER C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 616 Processing helix chain 'C' and resid 627 through 629 No H-bonds generated for 'chain 'C' and resid 627 through 629' Processing helix chain 'C' and resid 632 through 643 removed outlier: 4.798A pdb=" N GLN C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) removed outlier: 4.756A 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: 4.369A pdb=" N SER C 744 " --> pdb=" O GLY C 740 " (cutoff:3.500A) removed outlier: 4.747A 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 775 through 780 Processing helix chain 'C' and resid 782 through 790 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: 3.957A pdb=" N VAL D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU D 227 " --> pdb=" O THR D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' 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 370 removed outlier: 4.774A pdb=" N ASP D 364 " --> pdb=" O LYS D 360 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG D 365 " --> pdb=" O GLY D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 389 removed outlier: 3.806A 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 516 Processing helix chain 'D' and resid 522 through 536 Processing helix chain 'D' and resid 559 through 570 removed outlier: 3.539A pdb=" N SER D 563 " --> pdb=" O LYS D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 576 No H-bonds generated for 'chain 'D' and resid 574 through 576' 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: 3.646A pdb=" N ALA D 591 " --> pdb=" O ARG D 588 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER D 592 " --> pdb=" O PHE D 589 " (cutoff:3.500A) removed outlier: 3.890A 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 627 through 629 No H-bonds generated for 'chain 'D' and resid 627 through 629' Processing helix chain 'D' and resid 634 through 641 removed outlier: 3.510A pdb=" N LEU D 639 " --> pdb=" O ASN D 636 " (cutoff:3.500A) removed outlier: 4.025A 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 710 No H-bonds generated for 'chain 'D' and resid 707 through 710' Processing helix chain 'D' and resid 724 through 745 removed outlier: 4.004A pdb=" N ASP D 732 " --> pdb=" O ILE D 728 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG D 737 " --> pdb=" O LEU D 733 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL D 738 " --> pdb=" O MET D 734 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER D 744 " --> pdb=" O GLY D 740 " (cutoff:3.500A) removed outlier: 4.292A 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 removed outlier: 4.087A pdb=" N SER E 205 " --> pdb=" O MET E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 235 removed outlier: 4.213A 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 292 Processing helix chain 'E' and resid 304 through 314 Proline residue: E 310 - end of helix Processing helix chain 'E' and resid 325 through 328 No H-bonds generated for 'chain 'E' and resid 325 through 328' Processing helix chain 'E' and resid 352 through 370 removed outlier: 5.659A pdb=" N ASP E 364 " --> pdb=" O LYS E 360 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG E 365 " --> pdb=" O GLY E 361 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR E 366 " --> pdb=" O LEU E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 389 removed outlier: 3.963A pdb=" N THR E 384 " --> pdb=" O VAL E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 414 removed outlier: 3.874A pdb=" N LEU E 402 " --> pdb=" O LYS E 398 " (cutoff:3.500A) 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: 4.197A 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: 3.651A pdb=" N SER E 563 " --> pdb=" O LYS E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 576 No H-bonds generated for 'chain 'E' and resid 574 through 576' Processing helix chain 'E' and resid 590 through 595 removed outlier: 3.707A pdb=" N ARG E 593 " --> pdb=" O THR E 590 " (cutoff:3.500A) 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 643 removed outlier: 3.627A pdb=" N ASN E 636 " --> pdb=" O GLN E 632 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER E 637 " --> pdb=" O GLU E 633 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN E 640 " --> pdb=" O ASN E 636 " (cutoff:3.500A) removed outlier: 3.548A 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: 4.023A pdb=" N SER E 744 " --> pdb=" O GLY E 740 " (cutoff:3.500A) removed outlier: 5.017A 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: 3.764A pdb=" N LEU E 790 " --> pdb=" O SER E 786 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 174 No H-bonds generated for 'chain 'F' and resid 171 through 174' Processing helix chain 'F' and resid 181 through 183 No H-bonds generated for 'chain 'F' and resid 181 through 183' Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 224 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 292 No H-bonds generated for 'chain 'F' and resid 289 through 292' Processing helix chain 'F' and resid 304 through 313 removed outlier: 4.139A pdb=" N LEU F 308 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS F 309 " --> pdb=" O SER F 306 " (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 352 through 370 removed outlier: 4.580A pdb=" N ASP F 364 " --> pdb=" O LYS F 360 " (cutoff:3.500A) removed outlier: 4.837A 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 414 removed outlier: 3.998A pdb=" N LEU F 402 " --> pdb=" O LYS F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 481 through 492 Processing helix chain 'F' and resid 503 through 507 Processing helix chain 'F' and resid 510 through 517 removed outlier: 3.821A pdb=" N ARG F 517 " --> pdb=" O GLU F 513 " (cutoff:3.500A) 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 616 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: 4.174A pdb=" N LEU F 733 " --> pdb=" O ARG F 729 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG F 737 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL F 738 " --> pdb=" O MET F 734 " (cutoff:3.500A) Processing helix chain 'F' and resid 753 through 762 Processing helix chain 'F' and resid 771 through 780 removed outlier: 3.652A pdb=" N ARG F 775 " --> pdb=" O ARG F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 782 through 791 removed outlier: 3.624A pdb=" N LEU F 790 " --> pdb=" O SER F 786 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 343 through 346 removed outlier: 6.822A pdb=" N GLY A 321 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 246 through 251 Processing sheet with id= C, first strand: chain 'A' and resid 372 through 374 removed outlier: 5.990A pdb=" N ALA A 477 " --> pdb=" O SER A 373 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 715 through 718 removed outlier: 3.803A pdb=" N ASP A 715 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR A 665 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE A 578 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASP A 625 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE A 580 " --> pdb=" O ASP A 625 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 646 through 648 removed outlier: 3.852A pdb=" N LEU A 647 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 655 " --> pdb=" O LEU A 647 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 748 through 751 Processing sheet with id= G, first strand: chain 'B' and resid 175 through 177 removed outlier: 4.610A pdb=" N ASP B 287 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 322 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 715 through 718 removed outlier: 3.517A pdb=" N THR B 665 " --> pdb=" O PHE B 624 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE B 578 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ASP B 625 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE B 580 " --> pdb=" O ASP B 625 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 646 through 648 Processing sheet with id= J, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.785A pdb=" N ASP B 805 " --> pdb=" O VAL B 817 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 817 " --> pdb=" O ASP B 805 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 175 through 177 removed outlier: 5.043A pdb=" N ASP C 287 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 322 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLN C 343 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE C 215 " --> pdb=" O GLN C 343 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL C 345 " --> pdb=" O ILE C 215 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 372 through 374 removed outlier: 6.732A pdb=" N ALA C 477 " --> pdb=" O SER C 373 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 715 through 718 removed outlier: 3.510A pdb=" N ASP C 715 " --> pdb=" O SER C 548 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE C 578 " --> pdb=" O LEU C 623 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ASP C 625 " --> pdb=" O ILE C 578 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE C 580 " --> pdb=" O ASP C 625 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 646 through 648 removed outlier: 3.718A pdb=" N LEU C 647 " --> pdb=" O VAL C 655 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 748 through 751 removed outlier: 3.680A pdb=" N ASP C 805 " --> pdb=" O VAL C 817 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 817 " --> pdb=" O ASP C 805 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 175 through 177 removed outlier: 8.357A pdb=" N THR D 323 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU D 214 " --> pdb=" O THR D 323 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLN D 343 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE D 215 " --> pdb=" O GLN D 343 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL D 345 " --> pdb=" O ILE D 215 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 715 through 718 removed outlier: 6.746A pdb=" N ILE D 578 " --> pdb=" O LEU D 623 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASP D 625 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE D 580 " --> pdb=" O ASP D 625 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 646 through 648 removed outlier: 3.575A pdb=" N LEU D 647 " --> pdb=" O VAL D 655 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 748 through 751 removed outlier: 3.759A pdb=" N VAL D 817 " --> pdb=" O ASP D 805 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 175 through 177 removed outlier: 5.443A pdb=" N ASP E 287 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA E 322 " --> pdb=" O ILE E 286 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 715 through 718 removed outlier: 3.777A pdb=" N ASP E 715 " --> pdb=" O SER E 548 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE E 550 " --> pdb=" O ASP E 715 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY E 547 " --> pdb=" O THR E 660 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER E 620 " --> pdb=" O VAL E 661 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILE E 663 " --> pdb=" O SER E 620 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL E 622 " --> pdb=" O ILE E 663 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N THR E 665 " --> pdb=" O VAL E 622 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE E 624 " --> pdb=" O THR E 665 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE E 578 " --> pdb=" O LEU E 623 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASP E 625 " --> pdb=" O ILE E 578 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE E 580 " --> pdb=" O ASP E 625 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 749 through 751 removed outlier: 6.037A pdb=" N VAL E 800 " --> pdb=" O VAL E 750 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP E 805 " --> pdb=" O VAL E 817 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL E 817 " --> pdb=" O ASP E 805 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 175 through 177 removed outlier: 3.961A pdb=" N LEU F 250 " --> pdb=" O PHE F 285 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP F 287 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN F 318 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE F 286 " --> pdb=" O GLN F 318 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE F 320 " --> pdb=" O ILE F 286 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY F 216 " --> pdb=" O THR F 323 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 715 through 718 removed outlier: 3.643A pdb=" N ASP F 715 " --> pdb=" O SER F 548 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 550 " --> pdb=" O ASP F 715 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA F 552 " --> pdb=" O ILE F 717 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL F 622 " --> pdb=" O ILE F 663 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N THR F 665 " --> pdb=" O VAL F 622 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE F 624 " --> pdb=" O THR F 665 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE F 578 " --> pdb=" O LEU F 623 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASP F 625 " --> pdb=" O ILE F 578 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE F 580 " --> pdb=" O ASP F 625 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 801 through 805 removed outlier: 3.778A pdb=" N ASP F 805 " --> pdb=" O VAL F 817 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL F 817 " --> pdb=" O ASP F 805 " (cutoff:3.500A) 1120 hydrogen bonds defined for protein. 3267 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: 8.88 Time building geometry restraints manager: 12.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7740 1.33 - 1.46: 4469 1.46 - 1.58: 15146 1.58 - 1.70: 31 1.70 - 1.82: 132 Bond restraints: 27518 Sorted by residual: bond pdb=" C GLY A 553 " pdb=" N PRO A 554 " ideal model delta sigma weight residual 1.330 1.358 -0.028 1.22e-02 6.72e+03 5.42e+00 bond pdb=" CB PRO F 218 " pdb=" CG PRO F 218 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.67e+00 bond pdb=" C PRO A 554 " pdb=" O PRO A 554 " ideal model delta sigma weight residual 1.233 1.212 0.021 1.18e-02 7.18e+03 3.18e+00 bond pdb=" CA ASP B 815 " pdb=" C ASP B 815 " ideal model delta sigma weight residual 1.524 1.549 -0.025 1.66e-02 3.63e+03 2.18e+00 bond pdb=" C ARG B 544 " pdb=" N PRO B 545 " ideal model delta sigma weight residual 1.331 1.349 -0.018 1.21e-02 6.83e+03 2.17e+00 ... (remaining 27513 not shown) Histogram of bond angle deviations from ideal: 98.78 - 106.29: 614 106.29 - 113.81: 15650 113.81 - 121.32: 14074 121.32 - 128.83: 6661 128.83 - 136.34: 122 Bond angle restraints: 37121 Sorted by residual: angle pdb=" N VAL D 557 " pdb=" CA VAL D 557 " pdb=" C VAL D 557 " ideal model delta sigma weight residual 112.17 105.11 7.06 9.50e-01 1.11e+00 5.53e+01 angle pdb=" CA PRO F 218 " pdb=" N PRO F 218 " pdb=" CD PRO F 218 " ideal model delta sigma weight residual 112.00 104.10 7.90 1.40e+00 5.10e-01 3.18e+01 angle pdb=" CB MET B 415 " pdb=" CG MET B 415 " pdb=" SD MET B 415 " ideal model delta sigma weight residual 112.70 126.63 -13.93 3.00e+00 1.11e-01 2.15e+01 angle pdb=" N GLY C 769 " pdb=" CA GLY C 769 " pdb=" C GLY C 769 " ideal model delta sigma weight residual 110.29 104.48 5.81 1.28e+00 6.10e-01 2.06e+01 angle pdb=" N VAL A 170 " pdb=" CA VAL A 170 " pdb=" C VAL A 170 " ideal model delta sigma weight residual 113.53 109.09 4.44 9.80e-01 1.04e+00 2.05e+01 ... (remaining 37116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.75: 16209 30.75 - 61.51: 573 61.51 - 92.26: 43 92.26 - 123.01: 9 123.01 - 153.76: 6 Dihedral angle restraints: 16840 sinusoidal: 7096 harmonic: 9744 Sorted by residual: 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 93.77 -153.76 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" O1B ADP D 902 " pdb=" O3A ADP D 902 " pdb=" PB ADP D 902 " pdb=" PA ADP D 902 " ideal model delta sinusoidal sigma weight residual -60.00 80.48 -140.48 1 2.00e+01 2.50e-03 4.25e+01 dihedral pdb=" C5' ADP E 901 " pdb=" O5' ADP E 901 " pdb=" PA ADP E 901 " pdb=" O2A ADP E 901 " ideal model delta sinusoidal sigma weight residual -60.00 79.49 -139.48 1 2.00e+01 2.50e-03 4.22e+01 ... (remaining 16837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3624 0.068 - 0.136: 580 0.136 - 0.205: 24 0.205 - 0.273: 3 0.273 - 0.341: 2 Chirality restraints: 4233 Sorted by residual: chirality pdb=" CB VAL B 256 " pdb=" CA VAL B 256 " pdb=" CG1 VAL B 256 " pdb=" CG2 VAL B 256 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB ILE B 716 " pdb=" CA ILE B 716 " pdb=" CG1 ILE B 716 " pdb=" CG2 ILE B 716 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CB ILE C 716 " pdb=" CA ILE C 716 " pdb=" CG1 ILE C 716 " pdb=" CG2 ILE C 716 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 4230 not shown) Planarity restraints: 4813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 217 " 0.096 5.00e-02 4.00e+02 1.40e-01 3.15e+01 pdb=" N PRO F 218 " -0.243 5.00e-02 4.00e+02 pdb=" CA PRO F 218 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO F 218 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 597 " -0.061 5.00e-02 4.00e+02 9.20e-02 1.36e+01 pdb=" N PRO E 598 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO E 598 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 598 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 771 " -0.049 5.00e-02 4.00e+02 7.35e-02 8.65e+00 pdb=" N PRO E 772 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO E 772 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 772 " -0.041 5.00e-02 4.00e+02 ... (remaining 4810 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1971 2.74 - 3.28: 27957 3.28 - 3.82: 45491 3.82 - 4.36: 53890 4.36 - 4.90: 90996 Nonbonded interactions: 220305 Sorted by model distance: nonbonded pdb=" O ILE C 627 " pdb=" OH TYR C 635 " model vdw 2.196 2.440 nonbonded pdb=" OE2 GLU A 628 " pdb=" OG SER A 666 " model vdw 2.242 2.440 nonbonded pdb=" O LEU D 733 " pdb=" OG SER D 736 " model vdw 2.252 2.440 nonbonded pdb=" O LEU A 733 " pdb=" OG SER A 736 " model vdw 2.264 2.440 nonbonded pdb=" OG1 THR D 500 " pdb=" OE1 GLU D 503 " model vdw 2.266 2.440 ... (remaining 220300 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: 0.010 Normalize map: mean=0, sd=1: 6.610 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: 26.780 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 68.950 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 27518 Z= 0.249 Angle : 0.834 13.925 37121 Z= 0.428 Chirality : 0.048 0.341 4233 Planarity : 0.006 0.140 4813 Dihedral : 15.490 153.765 10538 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.04 % Allowed : 0.46 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.14), residues: 3341 helix: -0.17 (0.12), residues: 1781 sheet: -0.35 (0.25), residues: 400 loop : -0.03 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 807 HIS 0.012 0.001 HIS B 631 PHE 0.025 0.002 PHE F 394 TYR 0.032 0.002 TYR A 389 ARG 0.019 0.001 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 420 time to evaluate : 3.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 653 ARG cc_start: 0.6700 (mtt90) cc_final: 0.5772 (tpt170) REVERT: A 690 TYR cc_start: 0.7134 (p90) cc_final: 0.6855 (m-80) REVERT: A 727 ILE cc_start: 0.6169 (mt) cc_final: 0.5767 (mt) REVERT: A 747 MET cc_start: 0.5193 (mmp) cc_final: 0.4947 (mmm) REVERT: B 325 LEU cc_start: 0.7696 (mt) cc_final: 0.7191 (mp) REVERT: B 587 ASP cc_start: 0.6259 (m-30) cc_final: 0.5472 (p0) REVERT: B 747 MET cc_start: 0.6789 (mtp) cc_final: 0.6570 (mtp) REVERT: C 638 LEU cc_start: 0.8836 (mt) cc_final: 0.8589 (mp) REVERT: D 815 ASP cc_start: 0.6748 (p0) cc_final: 0.5929 (p0) REVERT: E 510 MET cc_start: 0.6444 (ttp) cc_final: 0.6077 (ttp) REVERT: E 730 MET cc_start: 0.7815 (mmm) cc_final: 0.7583 (mmm) REVERT: F 323 THR cc_start: 0.7035 (m) cc_final: 0.6804 (m) REVERT: F 571 PHE cc_start: 0.6059 (m-80) cc_final: 0.5572 (m-80) REVERT: F 573 ASP cc_start: 0.5473 (p0) cc_final: 0.5220 (p0) REVERT: F 587 ASP cc_start: 0.5962 (m-30) cc_final: 0.5537 (t0) REVERT: F 634 ILE cc_start: 0.7688 (mm) cc_final: 0.7420 (mm) REVERT: F 693 MET cc_start: 0.5982 (mmm) cc_final: 0.5763 (ptm) outliers start: 1 outliers final: 0 residues processed: 420 average time/residue: 0.3783 time to fit residues: 254.2721 Evaluate side-chains 317 residues out of total 2845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 2.9990 chunk 255 optimal weight: 0.6980 chunk 141 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 196 optimal weight: 0.5980 chunk 306 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 HIS C 631 HIS ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 659 ASN D 806 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27518 Z= 0.230 Angle : 0.627 8.132 37121 Z= 0.298 Chirality : 0.043 0.229 4233 Planarity : 0.004 0.079 4813 Dihedral : 8.823 170.441 3826 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.27 % Allowed : 9.24 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.17 (0.15), residues: 3341 helix: 0.38 (0.12), residues: 1790 sheet: -0.55 (0.25), residues: 415 loop : 0.26 (0.20), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 807 HIS 0.007 0.001 HIS A 290 PHE 0.027 0.001 PHE C 791 TYR 0.010 0.001 TYR B 328 ARG 0.006 0.000 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 344 time to evaluate : 3.412 Fit side-chains revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6974 (tp30) cc_final: 0.6610 (tp30) REVERT: B 325 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7615 (mt) REVERT: B 701 LEU cc_start: 0.8003 (pp) cc_final: 0.7348 (tt) REVERT: B 747 MET cc_start: 0.6741 (mtp) cc_final: 0.6465 (mtp) REVERT: C 494 ILE cc_start: 0.8030 (mm) cc_final: 0.7686 (mm) REVERT: C 714 ASP cc_start: 0.8010 (t70) cc_final: 0.7789 (t0) REVERT: D 815 ASP cc_start: 0.6857 (p0) cc_final: 0.6185 (p0) REVERT: E 183 MET cc_start: 0.8826 (mpp) cc_final: 0.7990 (mpp) REVERT: E 324 THR cc_start: 0.9048 (m) cc_final: 0.8838 (p) REVERT: E 510 MET cc_start: 0.6767 (ttp) cc_final: 0.6457 (ttp) REVERT: F 571 PHE cc_start: 0.6022 (m-80) cc_final: 0.5503 (m-80) REVERT: F 573 ASP cc_start: 0.5594 (p0) cc_final: 0.5228 (p0) REVERT: F 587 ASP cc_start: 0.5868 (m-30) cc_final: 0.5409 (t0) REVERT: F 634 ILE cc_start: 0.7687 (mm) cc_final: 0.7480 (mm) REVERT: F 693 MET cc_start: 0.6121 (mmm) cc_final: 0.5811 (ptm) outliers start: 36 outliers final: 25 residues processed: 357 average time/residue: 0.3708 time to fit residues: 212.0453 Evaluate side-chains 324 residues out of total 2845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 298 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 571 PHE Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain C residue 753 ASP Chi-restraints excluded: chain D residue 732 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 636 ASN Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 746 ASP Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 665 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 170 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 254 optimal weight: 0.5980 chunk 208 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 306 optimal weight: 0.0870 chunk 331 optimal weight: 0.3980 chunk 273 optimal weight: 0.9980 chunk 304 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 245 optimal weight: 2.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN C 586 HIS C 631 HIS ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 711 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27518 Z= 0.151 Angle : 0.577 8.390 37121 Z= 0.267 Chirality : 0.042 0.227 4233 Planarity : 0.004 0.068 4813 Dihedral : 8.237 168.181 3826 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.37 % Allowed : 12.34 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.54 (0.15), residues: 3341 helix: 0.69 (0.12), residues: 1782 sheet: -0.52 (0.26), residues: 397 loop : 0.44 (0.20), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 807 HIS 0.008 0.001 HIS A 290 PHE 0.021 0.001 PHE D 589 TYR 0.014 0.001 TYR D 331 ARG 0.007 0.000 ARG F 329 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 337 time to evaluate : 3.366 Fit side-chains revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6929 (tp30) cc_final: 0.6621 (tp30) REVERT: A 389 TYR cc_start: 0.7682 (m-10) cc_final: 0.7353 (m-80) REVERT: A 747 MET cc_start: 0.5330 (mmm) cc_final: 0.5035 (mmm) REVERT: B 501 GLU cc_start: 0.7672 (mp0) cc_final: 0.7381 (pm20) REVERT: B 625 ASP cc_start: 0.7837 (m-30) cc_final: 0.7381 (m-30) REVERT: B 639 LEU cc_start: 0.8092 (mt) cc_final: 0.7474 (mt) REVERT: B 643 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7222 (mp0) REVERT: B 701 LEU cc_start: 0.7966 (pp) cc_final: 0.7404 (tt) REVERT: B 747 MET cc_start: 0.6763 (mtp) cc_final: 0.6463 (mtp) REVERT: C 494 ILE cc_start: 0.7971 (mm) cc_final: 0.7646 (mm) REVERT: C 588 ARG cc_start: 0.6591 (mmp-170) cc_final: 0.5878 (mmm-85) REVERT: C 714 ASP cc_start: 0.7887 (t70) cc_final: 0.7645 (t0) REVERT: D 415 MET cc_start: 0.5567 (mpp) cc_final: 0.5305 (mpp) REVERT: D 815 ASP cc_start: 0.6858 (p0) cc_final: 0.6135 (p0) REVERT: E 183 MET cc_start: 0.8764 (mpp) cc_final: 0.7936 (mpp) REVERT: E 324 THR cc_start: 0.9051 (m) cc_final: 0.8838 (p) REVERT: E 696 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7310 (mmtm) REVERT: F 571 PHE cc_start: 0.6024 (m-80) cc_final: 0.5550 (m-80) REVERT: F 573 ASP cc_start: 0.5543 (p0) cc_final: 0.5157 (p0) REVERT: F 587 ASP cc_start: 0.5905 (m-30) cc_final: 0.5468 (t0) REVERT: F 693 MET cc_start: 0.6103 (mmm) cc_final: 0.5818 (ptm) outliers start: 39 outliers final: 21 residues processed: 356 average time/residue: 0.3490 time to fit residues: 202.8005 Evaluate side-chains 330 residues out of total 2845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 308 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 732 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 636 ASN Chi-restraints excluded: chain E residue 696 LYS Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain E residue 746 ASP Chi-restraints excluded: chain F residue 213 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 302 optimal weight: 0.6980 chunk 230 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 chunk 205 optimal weight: 0.1980 chunk 307 optimal weight: 6.9990 chunk 325 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 291 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS E 711 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27518 Z= 0.171 Angle : 0.580 8.417 37121 Z= 0.269 Chirality : 0.042 0.278 4233 Planarity : 0.004 0.067 4813 Dihedral : 7.933 168.302 3826 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.76 % Allowed : 13.81 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.69 (0.15), residues: 3341 helix: 0.83 (0.13), residues: 1768 sheet: -0.50 (0.25), residues: 415 loop : 0.52 (0.20), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 807 HIS 0.007 0.001 HIS A 290 PHE 0.042 0.001 PHE C 791 TYR 0.012 0.001 TYR D 604 ARG 0.005 0.000 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 327 time to evaluate : 3.298 Fit side-chains revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6909 (tp30) cc_final: 0.6596 (tp30) REVERT: A 410 MET cc_start: 0.8111 (mmp) cc_final: 0.7909 (mtt) REVERT: B 625 ASP cc_start: 0.7875 (m-30) cc_final: 0.7308 (m-30) REVERT: B 643 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7057 (mp0) REVERT: B 701 LEU cc_start: 0.8008 (pp) cc_final: 0.7450 (tt) REVERT: B 747 MET cc_start: 0.6731 (mtp) cc_final: 0.6463 (mtp) REVERT: C 494 ILE cc_start: 0.7982 (mm) cc_final: 0.7639 (mm) REVERT: D 815 ASP cc_start: 0.6881 (p0) cc_final: 0.6148 (p0) REVERT: E 183 MET cc_start: 0.8856 (mpp) cc_final: 0.7968 (mpp) REVERT: E 324 THR cc_start: 0.9072 (m) cc_final: 0.8822 (p) REVERT: E 696 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7340 (mmtm) REVERT: F 571 PHE cc_start: 0.5987 (m-80) cc_final: 0.5481 (m-80) REVERT: F 573 ASP cc_start: 0.5552 (p0) cc_final: 0.5148 (p0) REVERT: F 587 ASP cc_start: 0.6016 (m-30) cc_final: 0.5591 (t0) REVERT: F 693 MET cc_start: 0.6109 (mmm) cc_final: 0.5869 (ptm) REVERT: F 730 MET cc_start: 0.6696 (mmt) cc_final: 0.6464 (mtt) outliers start: 50 outliers final: 25 residues processed: 349 average time/residue: 0.3544 time to fit residues: 201.9927 Evaluate side-chains 332 residues out of total 2845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 306 time to evaluate : 3.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 571 PHE Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 636 ASN Chi-restraints excluded: chain E residue 696 LYS Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain E residue 746 ASP Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 665 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 271 optimal weight: 0.8980 chunk 184 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 225 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 0.0070 chunk 292 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27518 Z= 0.179 Angle : 0.582 9.540 37121 Z= 0.270 Chirality : 0.042 0.287 4233 Planarity : 0.004 0.066 4813 Dihedral : 7.671 167.777 3826 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.32 % Allowed : 14.41 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.15), residues: 3341 helix: 0.87 (0.13), residues: 1771 sheet: -0.47 (0.25), residues: 405 loop : 0.53 (0.20), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 807 HIS 0.007 0.001 HIS A 290 PHE 0.025 0.001 PHE D 589 TYR 0.011 0.001 TYR D 604 ARG 0.005 0.000 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 323 time to evaluate : 3.510 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: A 275 GLU cc_start: 0.6893 (tp30) cc_final: 0.6602 (tp30) REVERT: A 310 PRO cc_start: 0.8637 (Cg_endo) cc_final: 0.8423 (Cg_exo) REVERT: A 389 TYR cc_start: 0.7655 (m-10) cc_final: 0.7398 (m-10) REVERT: A 410 MET cc_start: 0.8087 (mmp) cc_final: 0.7859 (mtt) REVERT: A 655 VAL cc_start: 0.6203 (OUTLIER) cc_final: 0.5935 (t) REVERT: A 747 MET cc_start: 0.5443 (mmm) cc_final: 0.5070 (mmm) REVERT: B 501 GLU cc_start: 0.7699 (mp0) cc_final: 0.7451 (pm20) REVERT: B 701 LEU cc_start: 0.8051 (pp) cc_final: 0.7469 (tt) REVERT: B 747 MET cc_start: 0.6648 (mtp) cc_final: 0.6413 (mtp) REVERT: C 217 GLU cc_start: 0.6570 (tt0) cc_final: 0.6325 (tt0) REVERT: C 494 ILE cc_start: 0.7971 (mm) cc_final: 0.7669 (mm) REVERT: D 282 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7645 (mp) REVERT: D 815 ASP cc_start: 0.6891 (p0) cc_final: 0.6127 (p0) REVERT: E 183 MET cc_start: 0.8852 (mpp) cc_final: 0.8570 (mmt) REVERT: E 324 THR cc_start: 0.9103 (m) cc_final: 0.8866 (p) REVERT: E 340 ARG cc_start: 0.7599 (tmm-80) cc_final: 0.7264 (tpp-160) REVERT: E 696 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7376 (mmtm) REVERT: F 571 PHE cc_start: 0.5962 (m-80) cc_final: 0.5463 (m-80) REVERT: F 573 ASP cc_start: 0.5537 (p0) cc_final: 0.5135 (p0) REVERT: F 617 LYS cc_start: 0.7214 (tppt) cc_final: 0.6519 (mmtm) REVERT: F 693 MET cc_start: 0.6110 (mmm) cc_final: 0.5871 (ptm) REVERT: F 747 MET cc_start: 0.7064 (mmp) cc_final: 0.6634 (mmp) outliers start: 66 outliers final: 38 residues processed: 364 average time/residue: 0.3428 time to fit residues: 204.5692 Evaluate side-chains 348 residues out of total 2845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 307 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 571 PHE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain C residue 753 ASP Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 631 HIS Chi-restraints excluded: chain E residue 636 ASN Chi-restraints excluded: chain E residue 696 LYS Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain E residue 746 ASP Chi-restraints excluded: chain F residue 213 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 109 optimal weight: 0.8980 chunk 293 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 326 optimal weight: 0.9980 chunk 270 optimal weight: 0.0470 chunk 150 optimal weight: 0.6980 chunk 27 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27518 Z= 0.169 Angle : 0.585 10.346 37121 Z= 0.271 Chirality : 0.042 0.297 4233 Planarity : 0.004 0.066 4813 Dihedral : 7.422 165.217 3826 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.18 % Allowed : 15.64 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.79 (0.15), residues: 3341 helix: 0.90 (0.13), residues: 1779 sheet: -0.45 (0.25), residues: 419 loop : 0.60 (0.21), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 807 HIS 0.007 0.001 HIS A 290 PHE 0.025 0.001 PHE C 791 TYR 0.010 0.001 TYR E 248 ARG 0.007 0.000 ARG F 544 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 326 time to evaluate : 3.048 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: A 275 GLU cc_start: 0.6927 (tp30) cc_final: 0.6622 (tp30) REVERT: A 329 ARG cc_start: 0.9010 (ttm110) cc_final: 0.8673 (ttm-80) REVERT: A 389 TYR cc_start: 0.7664 (m-10) cc_final: 0.7271 (m-10) REVERT: A 410 MET cc_start: 0.8129 (mmp) cc_final: 0.7898 (mtt) REVERT: B 501 GLU cc_start: 0.7681 (mp0) cc_final: 0.7462 (pm20) REVERT: B 625 ASP cc_start: 0.7912 (m-30) cc_final: 0.7288 (m-30) REVERT: B 701 LEU cc_start: 0.8014 (pp) cc_final: 0.7452 (tt) REVERT: B 747 MET cc_start: 0.6632 (mtp) cc_final: 0.6370 (mtp) REVERT: C 494 ILE cc_start: 0.7945 (mm) cc_final: 0.7639 (mm) REVERT: D 282 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7653 (mp) REVERT: D 815 ASP cc_start: 0.6868 (p0) cc_final: 0.6104 (p0) REVERT: E 183 MET cc_start: 0.8887 (mpp) cc_final: 0.8138 (mpp) REVERT: E 247 LEU cc_start: 0.8660 (tt) cc_final: 0.8396 (tt) REVERT: E 324 THR cc_start: 0.9118 (m) cc_final: 0.8855 (p) REVERT: E 644 ASP cc_start: 0.8040 (t70) cc_final: 0.7783 (t0) REVERT: E 696 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7439 (mmtm) REVERT: F 571 PHE cc_start: 0.5930 (m-80) cc_final: 0.5422 (m-80) REVERT: F 573 ASP cc_start: 0.5534 (p0) cc_final: 0.5165 (p0) REVERT: F 617 LYS cc_start: 0.7223 (tppt) cc_final: 0.6529 (mmtm) REVERT: F 693 MET cc_start: 0.6023 (mmm) cc_final: 0.5785 (ptm) REVERT: F 747 MET cc_start: 0.7076 (mmp) cc_final: 0.6656 (mmp) outliers start: 62 outliers final: 43 residues processed: 362 average time/residue: 0.3666 time to fit residues: 214.2237 Evaluate side-chains 356 residues out of total 2845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 311 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 571 PHE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 715 ASP Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 631 HIS Chi-restraints excluded: chain E residue 636 ASN Chi-restraints excluded: chain E residue 696 LYS Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain E residue 746 ASP Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 768 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 314 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 274 optimal weight: 0.0370 chunk 182 optimal weight: 3.9990 chunk 324 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 198 optimal weight: 0.6980 chunk 149 optimal weight: 0.1980 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 ASN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN F 640 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27518 Z= 0.224 Angle : 0.609 9.138 37121 Z= 0.286 Chirality : 0.043 0.290 4233 Planarity : 0.004 0.065 4813 Dihedral : 7.413 162.614 3826 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.28 % Allowed : 16.38 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.79 (0.15), residues: 3341 helix: 0.92 (0.13), residues: 1755 sheet: -0.34 (0.25), residues: 429 loop : 0.54 (0.21), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 491 HIS 0.006 0.001 HIS A 290 PHE 0.024 0.001 PHE D 589 TYR 0.011 0.001 TYR B 389 ARG 0.006 0.000 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 320 time to evaluate : 3.222 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: A 275 GLU cc_start: 0.6914 (tp30) cc_final: 0.6628 (tp30) REVERT: A 389 TYR cc_start: 0.7698 (m-10) cc_final: 0.7269 (m-10) REVERT: A 655 VAL cc_start: 0.6305 (OUTLIER) cc_final: 0.6018 (t) REVERT: A 734 MET cc_start: 0.7381 (ppp) cc_final: 0.6497 (ppp) REVERT: B 210 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.8034 (p0) REVERT: B 501 GLU cc_start: 0.7695 (mp0) cc_final: 0.7477 (pm20) REVERT: B 634 ILE cc_start: 0.7911 (mm) cc_final: 0.7646 (tp) REVERT: B 701 LEU cc_start: 0.8076 (pp) cc_final: 0.7445 (tt) REVERT: B 747 MET cc_start: 0.6633 (mtp) cc_final: 0.6397 (mtp) REVERT: C 494 ILE cc_start: 0.7985 (mm) cc_final: 0.7642 (mm) REVERT: D 282 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7678 (mp) REVERT: D 693 MET cc_start: 0.7913 (ttt) cc_final: 0.7621 (ttt) REVERT: D 815 ASP cc_start: 0.6851 (p0) cc_final: 0.6087 (p0) REVERT: E 324 THR cc_start: 0.9129 (m) cc_final: 0.8901 (p) REVERT: E 696 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7486 (mmtm) REVERT: F 561 GLU cc_start: 0.5302 (mt-10) cc_final: 0.5093 (mp0) REVERT: F 571 PHE cc_start: 0.5955 (m-80) cc_final: 0.5462 (m-80) REVERT: F 573 ASP cc_start: 0.5487 (p0) cc_final: 0.5091 (p0) REVERT: F 617 LYS cc_start: 0.7234 (tppt) cc_final: 0.6516 (mmtm) REVERT: F 693 MET cc_start: 0.6050 (mmm) cc_final: 0.5763 (ptm) REVERT: F 730 MET cc_start: 0.6633 (mtt) cc_final: 0.6413 (mtt) REVERT: F 747 MET cc_start: 0.7081 (mmp) cc_final: 0.6726 (mmp) outliers start: 65 outliers final: 50 residues processed: 357 average time/residue: 0.3576 time to fit residues: 206.7909 Evaluate side-chains 361 residues out of total 2845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 307 time to evaluate : 3.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 715 ASP Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 575 ASP Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain C residue 753 ASP Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 604 TYR Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 631 HIS Chi-restraints excluded: chain E residue 636 ASN Chi-restraints excluded: chain E residue 696 LYS Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain E residue 746 ASP Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 768 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 200 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 193 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 206 optimal weight: 0.9990 chunk 221 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 255 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 609 GLN D 806 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27518 Z= 0.188 Angle : 0.601 10.217 37121 Z= 0.280 Chirality : 0.043 0.297 4233 Planarity : 0.004 0.064 4813 Dihedral : 7.267 162.149 3826 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.28 % Allowed : 17.19 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.81 (0.15), residues: 3341 helix: 0.92 (0.13), residues: 1762 sheet: -0.35 (0.25), residues: 435 loop : 0.56 (0.21), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 807 HIS 0.006 0.001 HIS A 290 PHE 0.023 0.001 PHE D 589 TYR 0.012 0.001 TYR B 389 ARG 0.006 0.000 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 326 time to evaluate : 3.311 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 275 GLU cc_start: 0.6922 (tp30) cc_final: 0.6611 (tp30) REVERT: A 389 TYR cc_start: 0.7718 (m-10) cc_final: 0.7280 (m-10) REVERT: A 410 MET cc_start: 0.8138 (mmp) cc_final: 0.7930 (mmm) REVERT: A 539 LEU cc_start: 0.5854 (mp) cc_final: 0.4951 (tt) REVERT: A 655 VAL cc_start: 0.6330 (OUTLIER) cc_final: 0.6027 (t) REVERT: B 210 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8044 (p0) REVERT: B 501 GLU cc_start: 0.7681 (mp0) cc_final: 0.7470 (pm20) REVERT: B 625 ASP cc_start: 0.7973 (m-30) cc_final: 0.7404 (m-30) REVERT: B 634 ILE cc_start: 0.7938 (mm) cc_final: 0.7641 (tp) REVERT: B 643 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6755 (mp0) REVERT: B 701 LEU cc_start: 0.8021 (pp) cc_final: 0.7413 (tt) REVERT: B 747 MET cc_start: 0.6630 (mtp) cc_final: 0.6402 (mtp) REVERT: C 494 ILE cc_start: 0.7976 (mm) cc_final: 0.7672 (mm) REVERT: D 282 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7682 (mp) REVERT: D 325 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7321 (tp) REVERT: D 690 TYR cc_start: 0.4812 (t80) cc_final: 0.4115 (t80) REVERT: D 815 ASP cc_start: 0.6884 (p0) cc_final: 0.5907 (p0) REVERT: E 183 MET cc_start: 0.8889 (mpp) cc_final: 0.8621 (mmt) REVERT: E 324 THR cc_start: 0.9117 (m) cc_final: 0.8866 (p) REVERT: E 696 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7492 (mmtm) REVERT: F 561 GLU cc_start: 0.5229 (mt-10) cc_final: 0.5009 (mp0) REVERT: F 571 PHE cc_start: 0.5922 (m-80) cc_final: 0.5412 (m-80) REVERT: F 573 ASP cc_start: 0.5445 (p0) cc_final: 0.5098 (p0) REVERT: F 617 LYS cc_start: 0.7295 (tppt) cc_final: 0.6582 (mmtm) REVERT: F 693 MET cc_start: 0.6026 (mmm) cc_final: 0.5769 (ptm) REVERT: F 730 MET cc_start: 0.6718 (mtt) cc_final: 0.6457 (mtt) outliers start: 65 outliers final: 48 residues processed: 366 average time/residue: 0.3691 time to fit residues: 218.5784 Evaluate side-chains 373 residues out of total 2845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 320 time to evaluate : 3.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 715 ASP Chi-restraints excluded: chain B residue 741 GLN Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 604 TYR Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 631 HIS Chi-restraints excluded: chain E residue 636 ASN Chi-restraints excluded: chain E residue 696 LYS Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain E residue 746 ASP Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 768 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 295 optimal weight: 2.9990 chunk 311 optimal weight: 10.0000 chunk 283 optimal weight: 1.9990 chunk 302 optimal weight: 7.9990 chunk 182 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 237 optimal weight: 0.9990 chunk 92 optimal weight: 0.0070 chunk 273 optimal weight: 0.6980 chunk 286 optimal weight: 6.9990 chunk 301 optimal weight: 1.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 ASN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 632 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27518 Z= 0.197 Angle : 0.614 10.987 37121 Z= 0.287 Chirality : 0.043 0.280 4233 Planarity : 0.004 0.064 4813 Dihedral : 7.197 161.212 3826 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.21 % Allowed : 17.68 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.80 (0.15), residues: 3341 helix: 0.93 (0.13), residues: 1748 sheet: -0.39 (0.25), residues: 430 loop : 0.54 (0.21), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 491 HIS 0.006 0.001 HIS A 290 PHE 0.022 0.001 PHE D 589 TYR 0.014 0.001 TYR E 248 ARG 0.007 0.000 ARG D 616 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 327 time to evaluate : 3.339 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: A 275 GLU cc_start: 0.6918 (tp30) cc_final: 0.6609 (tp30) REVERT: A 389 TYR cc_start: 0.7766 (m-10) cc_final: 0.7328 (m-10) REVERT: A 539 LEU cc_start: 0.5804 (mp) cc_final: 0.4926 (tt) REVERT: A 655 VAL cc_start: 0.6387 (OUTLIER) cc_final: 0.6116 (t) REVERT: A 693 MET cc_start: 0.2689 (tpt) cc_final: 0.2477 (mtm) REVERT: B 210 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8060 (p0) REVERT: B 501 GLU cc_start: 0.7687 (mp0) cc_final: 0.7470 (pm20) REVERT: B 625 ASP cc_start: 0.8017 (m-30) cc_final: 0.7406 (m-30) REVERT: B 634 ILE cc_start: 0.7949 (mm) cc_final: 0.7652 (tp) REVERT: B 643 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6748 (mp0) REVERT: B 701 LEU cc_start: 0.8007 (pp) cc_final: 0.7387 (tt) REVERT: B 747 MET cc_start: 0.6636 (mtp) cc_final: 0.6423 (mtp) REVERT: C 217 GLU cc_start: 0.6382 (tt0) cc_final: 0.6134 (tt0) REVERT: C 494 ILE cc_start: 0.7993 (mm) cc_final: 0.7648 (mm) REVERT: D 282 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7668 (mp) REVERT: D 815 ASP cc_start: 0.6957 (p0) cc_final: 0.6165 (p0) REVERT: E 183 MET cc_start: 0.8913 (mpp) cc_final: 0.8665 (mmt) REVERT: E 324 THR cc_start: 0.9117 (m) cc_final: 0.8871 (p) REVERT: E 696 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7562 (mmtm) REVERT: F 561 GLU cc_start: 0.5300 (mt-10) cc_final: 0.5088 (mp0) REVERT: F 571 PHE cc_start: 0.5880 (m-80) cc_final: 0.5378 (m-80) REVERT: F 573 ASP cc_start: 0.5523 (p0) cc_final: 0.5219 (p0) REVERT: F 617 LYS cc_start: 0.7339 (tppt) cc_final: 0.6611 (mmtm) REVERT: F 693 MET cc_start: 0.6030 (mmm) cc_final: 0.5771 (ptm) outliers start: 63 outliers final: 54 residues processed: 364 average time/residue: 0.3554 time to fit residues: 210.4437 Evaluate side-chains 368 residues out of total 2845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 310 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 715 ASP Chi-restraints excluded: chain B residue 741 GLN Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 575 ASP Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 604 TYR Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 631 HIS Chi-restraints excluded: chain E residue 636 ASN Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 649 ASP Chi-restraints excluded: chain E residue 696 LYS Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain E residue 746 ASP Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 768 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 198 optimal weight: 0.0020 chunk 320 optimal weight: 9.9990 chunk 195 optimal weight: 0.0040 chunk 151 optimal weight: 0.8980 chunk 222 optimal weight: 0.9980 chunk 335 optimal weight: 7.9990 chunk 309 optimal weight: 7.9990 chunk 267 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 206 optimal weight: 6.9990 chunk 163 optimal weight: 0.0770 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 27518 Z= 0.147 Angle : 0.607 11.775 37121 Z= 0.282 Chirality : 0.043 0.280 4233 Planarity : 0.004 0.064 4813 Dihedral : 6.967 159.072 3826 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.90 % Allowed : 18.45 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 3341 helix: 1.00 (0.13), residues: 1741 sheet: -0.27 (0.25), residues: 427 loop : 0.61 (0.21), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP F 807 HIS 0.005 0.000 HIS A 290 PHE 0.023 0.001 PHE D 589 TYR 0.015 0.001 TYR F 328 ARG 0.008 0.000 ARG C 724 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 340 time to evaluate : 3.392 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: A 275 GLU cc_start: 0.6897 (tp30) cc_final: 0.6539 (tp30) REVERT: A 389 TYR cc_start: 0.7725 (m-10) cc_final: 0.7285 (m-10) REVERT: A 539 LEU cc_start: 0.5899 (mp) cc_final: 0.5031 (tt) REVERT: A 693 MET cc_start: 0.2758 (tpt) cc_final: 0.2504 (mtm) REVERT: B 501 GLU cc_start: 0.7666 (mp0) cc_final: 0.7455 (pm20) REVERT: B 625 ASP cc_start: 0.7860 (m-30) cc_final: 0.7230 (m-30) REVERT: B 634 ILE cc_start: 0.7937 (mm) cc_final: 0.7622 (tp) REVERT: B 643 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6716 (mp0) REVERT: B 701 LEU cc_start: 0.8018 (pp) cc_final: 0.7406 (tt) REVERT: B 747 MET cc_start: 0.6638 (mtp) cc_final: 0.6421 (mtp) REVERT: C 217 GLU cc_start: 0.6388 (tt0) cc_final: 0.6122 (tt0) REVERT: C 494 ILE cc_start: 0.7909 (mm) cc_final: 0.7627 (mm) REVERT: D 282 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7692 (mp) REVERT: D 783 ASP cc_start: 0.7953 (m-30) cc_final: 0.7636 (m-30) REVERT: D 815 ASP cc_start: 0.6936 (p0) cc_final: 0.6198 (p0) REVERT: E 247 LEU cc_start: 0.8629 (tt) cc_final: 0.8417 (tt) REVERT: E 324 THR cc_start: 0.9107 (m) cc_final: 0.8839 (p) REVERT: E 696 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7570 (mmtm) REVERT: F 571 PHE cc_start: 0.5837 (m-80) cc_final: 0.5424 (m-80) REVERT: F 573 ASP cc_start: 0.5519 (p0) cc_final: 0.5219 (p0) REVERT: F 617 LYS cc_start: 0.7318 (tppt) cc_final: 0.6607 (mmtm) REVERT: F 730 MET cc_start: 0.6671 (mtt) cc_final: 0.6417 (mtt) outliers start: 54 outliers final: 46 residues processed: 376 average time/residue: 0.3507 time to fit residues: 214.8225 Evaluate side-chains 363 residues out of total 2845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 315 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 715 ASP Chi-restraints excluded: chain B residue 741 GLN Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 631 HIS Chi-restraints excluded: chain E residue 636 ASN Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 649 ASP Chi-restraints excluded: chain E residue 696 LYS Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain E residue 746 ASP Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 768 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 212 optimal weight: 0.7980 chunk 284 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 246 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 267 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 274 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 GLN C 290 HIS ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS F 318 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.151671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.117665 restraints weight = 56585.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.117552 restraints weight = 36069.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.118325 restraints weight = 22660.828| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27518 Z= 0.199 Angle : 0.623 11.877 37121 Z= 0.289 Chirality : 0.043 0.205 4233 Planarity : 0.004 0.064 4813 Dihedral : 6.977 157.093 3826 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.86 % Allowed : 18.95 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.86 (0.15), residues: 3341 helix: 0.95 (0.13), residues: 1753 sheet: -0.33 (0.25), residues: 422 loop : 0.61 (0.21), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 491 HIS 0.006 0.001 HIS A 290 PHE 0.023 0.001 PHE D 589 TYR 0.012 0.001 TYR D 331 ARG 0.009 0.000 ARG C 724 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5269.49 seconds wall clock time: 96 minutes 38.56 seconds (5798.56 seconds total)