Starting phenix.real_space_refine on Sat Apr 13 04:46:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vya_8746/04_2024/5vya_8746_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vya_8746/04_2024/5vya_8746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vya_8746/04_2024/5vya_8746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vya_8746/04_2024/5vya_8746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vya_8746/04_2024/5vya_8746_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vya_8746/04_2024/5vya_8746_updated.pdb" } resolution = 4.0 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= 0.005 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 36 5.49 5 S 120 5.16 5 C 17303 2.51 5 N 4852 2.21 5 O 5380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 333": "NH1" <-> "NH2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "B GLU 875": "OE1" <-> "OE2" Residue "C ARG 333": "NH1" <-> "NH2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "E GLU 687": "OE1" <-> "OE2" Residue "E GLU 689": "OE1" <-> "OE2" Residue "F ARG 333": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 27691 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4530 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 17, 'TRANS': 561} Chain breaks: 2 Chain: "B" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4530 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 17, 'TRANS': 561} Chain breaks: 2 Chain: "C" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4530 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 17, 'TRANS': 561} Chain breaks: 2 Chain: "D" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4530 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 17, 'TRANS': 561} Chain breaks: 2 Chain: "E" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4530 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 17, 'TRANS': 561} Chain breaks: 2 Chain: "F" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4530 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 17, 'TRANS': 561} Chain breaks: 2 Chain: "P" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 139 Classifications: {'peptide': 28} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 27} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 28} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.92, per 1000 atoms: 0.50 Number of scatterers: 27691 At special positions: 0 Unit cell: (129, 144, 137, 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 120 16.00 P 36 15.00 O 5380 8.00 N 4852 7.00 C 17303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 721 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 721 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM27532 O5' AGS D1002 .*. O " rejected from bonding due to valence issues. Atom "HETATM27594 O5' AGS E1001 .*. O " rejected from bonding due to valence issues. Atom "HETATM27528 O3A AGS D1002 .*. O " rejected from bonding due to valence issues. Atom "HETATM27653 O3B AGS F1001 .*. O " rejected from bonding due to valence issues. Atom "HETATM27532 O5' AGS D1002 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.26 Conformation dependent library (CDL) restraints added in 4.9 seconds 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6546 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 195 helices and 17 sheets defined 51.2% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.96 Creating SS restraints... Processing helix chain 'A' and resid 166 through 170 Processing helix chain 'A' and resid 174 through 180 Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 218 through 230 removed outlier: 3.786A pdb=" N ILE A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 248 through 251 Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 318 through 328 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 345 through 363 Proline residue: A 357 - end of helix Processing helix chain 'A' and resid 369 through 382 Processing helix chain 'A' and resid 388 through 409 Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'A' and resid 557 through 559 No H-bonds generated for 'chain 'A' and resid 557 through 559' Processing helix chain 'A' and resid 571 through 579 Processing helix chain 'A' and resid 584 through 600 removed outlier: 5.041A pdb=" N SER A 599 " --> pdb=" O ARG A 595 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 632 Processing helix chain 'A' and resid 643 through 645 No H-bonds generated for 'chain 'A' and resid 643 through 645' Processing helix chain 'A' and resid 651 through 656 Processing helix chain 'A' and resid 672 through 675 No H-bonds generated for 'chain 'A' and resid 672 through 675' Processing helix chain 'A' and resid 688 through 690 No H-bonds generated for 'chain 'A' and resid 688 through 690' Processing helix chain 'A' and resid 693 through 703 removed outlier: 3.795A pdb=" N LEU A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN A 701 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N MET A 702 " --> pdb=" O VAL A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 736 removed outlier: 3.503A pdb=" N GLU A 732 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN A 735 " --> pdb=" O GLU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.528A pdb=" N HIS A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 765 removed outlier: 4.707A pdb=" N ARG A 765 " --> pdb=" O GLU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 794 Processing helix chain 'A' and resid 807 through 816 Processing helix chain 'A' and resid 826 through 834 Processing helix chain 'A' and resid 836 through 845 Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 174 through 179 Processing helix chain 'B' and resid 190 through 200 Processing helix chain 'B' and resid 218 through 230 Processing helix chain 'B' and resid 236 through 239 No H-bonds generated for 'chain 'B' and resid 236 through 239' Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 286 through 289 Processing helix chain 'B' and resid 300 through 307 removed outlier: 4.270A pdb=" N ALA B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 327 removed outlier: 4.056A pdb=" N LYS B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 345 through 363 Proline residue: B 357 - end of helix Processing helix chain 'B' and resid 369 through 382 Processing helix chain 'B' and resid 388 through 408 removed outlier: 3.751A pdb=" N LEU B 393 " --> pdb=" O PRO B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 557 through 560 Processing helix chain 'B' and resid 563 through 579 removed outlier: 4.163A pdb=" N GLU B 567 " --> pdb=" O SER B 564 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 570 " --> pdb=" O GLU B 567 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET B 572 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU B 573 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 576 " --> pdb=" O GLU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 599 Processing helix chain 'B' and resid 620 through 632 Processing helix chain 'B' and resid 635 through 637 No H-bonds generated for 'chain 'B' and resid 635 through 637' Processing helix chain 'B' and resid 643 through 645 No H-bonds generated for 'chain 'B' and resid 643 through 645' Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.783A pdb=" N LEU B 656 " --> pdb=" O SER B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 675 No H-bonds generated for 'chain 'B' and resid 672 through 675' Processing helix chain 'B' and resid 688 through 690 No H-bonds generated for 'chain 'B' and resid 688 through 690' Processing helix chain 'B' and resid 693 through 702 removed outlier: 3.572A pdb=" N LEU B 700 " --> pdb=" O LEU B 696 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN B 701 " --> pdb=" O THR B 697 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET B 702 " --> pdb=" O VAL B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 736 removed outlier: 3.691A pdb=" N ILE B 734 " --> pdb=" O ALA B 731 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN B 735 " --> pdb=" O GLU B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 760 through 765 removed outlier: 4.172A pdb=" N ARG B 765 " --> pdb=" O GLU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 794 Processing helix chain 'B' and resid 809 through 816 Processing helix chain 'B' and resid 826 through 835 Processing helix chain 'B' and resid 837 through 845 Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 190 through 200 Processing helix chain 'C' and resid 218 through 230 Processing helix chain 'C' and resid 248 through 252 Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 286 through 289 Processing helix chain 'C' and resid 295 through 297 No H-bonds generated for 'chain 'C' and resid 295 through 297' Processing helix chain 'C' and resid 302 through 307 removed outlier: 3.797A pdb=" N ARG C 307 " --> pdb=" O PRO C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 removed outlier: 4.529A pdb=" N LYS C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 Processing helix chain 'C' and resid 345 through 363 Proline residue: C 357 - end of helix Processing helix chain 'C' and resid 369 through 382 Processing helix chain 'C' and resid 388 through 409 Processing helix chain 'C' and resid 543 through 554 Processing helix chain 'C' and resid 557 through 560 Processing helix chain 'C' and resid 563 through 579 removed outlier: 4.264A pdb=" N GLU C 567 " --> pdb=" O SER C 564 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 570 " --> pdb=" O GLU C 567 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET C 572 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU C 573 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 599 Processing helix chain 'C' and resid 620 through 632 Processing helix chain 'C' and resid 635 through 637 No H-bonds generated for 'chain 'C' and resid 635 through 637' Processing helix chain 'C' and resid 648 through 656 removed outlier: 4.821A pdb=" N VAL C 652 " --> pdb=" O GLU C 648 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N SER C 653 " --> pdb=" O LYS C 649 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 655 " --> pdb=" O ALA C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 675 No H-bonds generated for 'chain 'C' and resid 672 through 675' Processing helix chain 'C' and resid 688 through 690 No H-bonds generated for 'chain 'C' and resid 688 through 690' Processing helix chain 'C' and resid 693 through 702 removed outlier: 4.152A pdb=" N GLN C 701 " --> pdb=" O THR C 697 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET C 702 " --> pdb=" O VAL C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 736 removed outlier: 4.838A pdb=" N ASN C 735 " --> pdb=" O GLU C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 760 through 765 removed outlier: 4.071A pdb=" N ARG C 765 " --> pdb=" O GLU C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 793 removed outlier: 3.539A pdb=" N LYS C 782 " --> pdb=" O LYS C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 817 Processing helix chain 'C' and resid 821 through 823 No H-bonds generated for 'chain 'C' and resid 821 through 823' Processing helix chain 'C' and resid 826 through 835 Processing helix chain 'C' and resid 837 through 845 Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.774A pdb=" N TYR D 170 " --> pdb=" O LEU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 190 through 200 Processing helix chain 'D' and resid 218 through 230 Processing helix chain 'D' and resid 236 through 239 No H-bonds generated for 'chain 'D' and resid 236 through 239' Processing helix chain 'D' and resid 248 through 252 Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 286 through 289 Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing helix chain 'D' and resid 302 through 307 Processing helix chain 'D' and resid 318 through 327 Processing helix chain 'D' and resid 330 through 334 Processing helix chain 'D' and resid 345 through 363 Proline residue: D 357 - end of helix Processing helix chain 'D' and resid 369 through 382 Processing helix chain 'D' and resid 388 through 409 Processing helix chain 'D' and resid 543 through 554 Processing helix chain 'D' and resid 557 through 559 No H-bonds generated for 'chain 'D' and resid 557 through 559' Processing helix chain 'D' and resid 563 through 578 removed outlier: 3.558A pdb=" N GLU D 567 " --> pdb=" O SER D 564 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET D 572 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU D 573 " --> pdb=" O ILE D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 598 Processing helix chain 'D' and resid 620 through 632 Processing helix chain 'D' and resid 635 through 637 No H-bonds generated for 'chain 'D' and resid 635 through 637' Processing helix chain 'D' and resid 643 through 645 No H-bonds generated for 'chain 'D' and resid 643 through 645' Processing helix chain 'D' and resid 651 through 656 Processing helix chain 'D' and resid 671 through 677 removed outlier: 3.836A pdb=" N TYR D 677 " --> pdb=" O ASN D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 702 Processing helix chain 'D' and resid 731 through 736 removed outlier: 3.974A pdb=" N SER D 736 " --> pdb=" O GLU D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 757 Processing helix chain 'D' and resid 760 through 765 removed outlier: 4.931A pdb=" N ARG D 765 " --> pdb=" O GLU D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 794 removed outlier: 3.598A pdb=" N LYS D 782 " --> pdb=" O LYS D 778 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP D 785 " --> pdb=" O HIS D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 817 Processing helix chain 'D' and resid 821 through 823 No H-bonds generated for 'chain 'D' and resid 821 through 823' Processing helix chain 'D' and resid 826 through 835 Processing helix chain 'D' and resid 837 through 845 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.672A pdb=" N TYR E 170 " --> pdb=" O LEU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'E' and resid 190 through 200 Processing helix chain 'E' and resid 218 through 230 Processing helix chain 'E' and resid 236 through 239 No H-bonds generated for 'chain 'E' and resid 236 through 239' Processing helix chain 'E' and resid 248 through 252 Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 295 through 297 No H-bonds generated for 'chain 'E' and resid 295 through 297' Processing helix chain 'E' and resid 302 through 307 Processing helix chain 'E' and resid 318 through 321 No H-bonds generated for 'chain 'E' and resid 318 through 321' Processing helix chain 'E' and resid 324 through 328 Processing helix chain 'E' and resid 330 through 334 Processing helix chain 'E' and resid 345 through 363 Proline residue: E 357 - end of helix Processing helix chain 'E' and resid 369 through 382 Processing helix chain 'E' and resid 388 through 409 Processing helix chain 'E' and resid 543 through 554 Processing helix chain 'E' and resid 557 through 560 Processing helix chain 'E' and resid 563 through 578 removed outlier: 4.559A pdb=" N GLU E 567 " --> pdb=" O SER E 564 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE E 570 " --> pdb=" O GLU E 567 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU E 573 " --> pdb=" O ILE E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 599 Processing helix chain 'E' and resid 620 through 632 Processing helix chain 'E' and resid 635 through 637 No H-bonds generated for 'chain 'E' and resid 635 through 637' Processing helix chain 'E' and resid 651 through 655 Processing helix chain 'E' and resid 671 through 675 Processing helix chain 'E' and resid 688 through 690 No H-bonds generated for 'chain 'E' and resid 688 through 690' Processing helix chain 'E' and resid 693 through 702 removed outlier: 4.024A pdb=" N GLN E 701 " --> pdb=" O THR E 697 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET E 702 " --> pdb=" O VAL E 698 " (cutoff:3.500A) Processing helix chain 'E' and resid 729 through 736 removed outlier: 4.369A pdb=" N GLU E 732 " --> pdb=" O LEU E 729 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN E 735 " --> pdb=" O GLU E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 746 through 755 Processing helix chain 'E' and resid 760 through 765 removed outlier: 3.689A pdb=" N ARG E 765 " --> pdb=" O GLU E 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 777 through 793 Processing helix chain 'E' and resid 809 through 817 Processing helix chain 'E' and resid 821 through 823 No H-bonds generated for 'chain 'E' and resid 821 through 823' Processing helix chain 'E' and resid 826 through 835 removed outlier: 3.557A pdb=" N ARG E 830 " --> pdb=" O ARG E 826 " (cutoff:3.500A) Processing helix chain 'E' and resid 837 through 845 Processing helix chain 'F' and resid 166 through 170 removed outlier: 3.727A pdb=" N TYR F 170 " --> pdb=" O LEU F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 190 through 200 Processing helix chain 'F' and resid 218 through 230 Processing helix chain 'F' and resid 236 through 239 No H-bonds generated for 'chain 'F' and resid 236 through 239' Processing helix chain 'F' and resid 248 through 252 Processing helix chain 'F' and resid 260 through 273 removed outlier: 3.939A pdb=" N GLY F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL F 268 " --> pdb=" O ARG F 264 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS F 270 " --> pdb=" O LYS F 266 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N GLU F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 299 through 305 Proline residue: F 303 - end of helix Processing helix chain 'F' and resid 318 through 328 Processing helix chain 'F' and resid 330 through 334 Processing helix chain 'F' and resid 345 through 363 Proline residue: F 357 - end of helix Processing helix chain 'F' and resid 369 through 382 Processing helix chain 'F' and resid 388 through 407 removed outlier: 4.185A pdb=" N LEU F 393 " --> pdb=" O PRO F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 554 Processing helix chain 'F' and resid 557 through 559 No H-bonds generated for 'chain 'F' and resid 557 through 559' Processing helix chain 'F' and resid 570 through 579 Processing helix chain 'F' and resid 584 through 600 removed outlier: 3.712A pdb=" N SER F 597 " --> pdb=" O ALA F 593 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG F 598 " --> pdb=" O VAL F 594 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N SER F 599 " --> pdb=" O ARG F 595 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLY F 600 " --> pdb=" O LEU F 596 " (cutoff:3.500A) Processing helix chain 'F' and resid 622 through 631 Processing helix chain 'F' and resid 635 through 637 No H-bonds generated for 'chain 'F' and resid 635 through 637' Processing helix chain 'F' and resid 653 through 656 No H-bonds generated for 'chain 'F' and resid 653 through 656' Processing helix chain 'F' and resid 672 through 675 No H-bonds generated for 'chain 'F' and resid 672 through 675' Processing helix chain 'F' and resid 688 through 690 No H-bonds generated for 'chain 'F' and resid 688 through 690' Processing helix chain 'F' and resid 693 through 702 Processing helix chain 'F' and resid 729 through 736 removed outlier: 4.042A pdb=" N GLU F 732 " --> pdb=" O LEU F 729 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE F 734 " --> pdb=" O ALA F 731 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASN F 735 " --> pdb=" O GLU F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 744 through 757 Processing helix chain 'F' and resid 760 through 765 removed outlier: 3.870A pdb=" N ARG F 765 " --> pdb=" O GLU F 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 777 through 794 Processing helix chain 'F' and resid 807 through 817 Processing helix chain 'F' and resid 821 through 823 No H-bonds generated for 'chain 'F' and resid 821 through 823' Processing helix chain 'F' and resid 826 through 835 removed outlier: 3.556A pdb=" N ARG F 830 " --> pdb=" O ARG F 826 " (cutoff:3.500A) Processing helix chain 'F' and resid 837 through 845 Processing sheet with id= A, first strand: chain 'A' and resid 336 through 339 removed outlier: 6.876A pdb=" N GLY A 314 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLY A 212 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N THR A 316 " --> pdb=" O GLY A 212 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 242 through 245 Processing sheet with id= C, first strand: chain 'A' and resid 768 through 772 removed outlier: 6.501A pdb=" N VAL A 723 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N PHE A 612 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N MET A 725 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N GLY A 614 " --> pdb=" O MET A 725 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER A 727 " --> pdb=" O GLY A 614 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU A 683 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N THR A 726 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N PHE A 685 " --> pdb=" O THR A 726 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 639 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ASP A 686 " --> pdb=" O ILE A 639 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 641 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 171 through 173 removed outlier: 6.618A pdb=" N LEU B 278 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE B 244 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL B 280 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU B 246 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N PHE B 282 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 315 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLN B 336 " --> pdb=" O CYS B 209 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE B 211 " --> pdb=" O GLN B 336 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE B 338 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 768 through 771 removed outlier: 6.275A pdb=" N ILE B 639 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASP B 686 " --> pdb=" O ILE B 639 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL B 641 " --> pdb=" O ASP B 686 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 855 through 857 Processing sheet with id= G, first strand: chain 'C' and resid 171 through 173 removed outlier: 3.771A pdb=" N ALA C 315 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN C 336 " --> pdb=" O CYS C 209 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE C 211 " --> pdb=" O GLN C 336 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE C 338 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 768 through 771 removed outlier: 6.511A pdb=" N ILE C 639 " --> pdb=" O LEU C 684 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 855 through 857 Processing sheet with id= J, first strand: chain 'D' and resid 171 through 173 removed outlier: 3.506A pdb=" N ALA D 315 " --> pdb=" O ILE D 283 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLN D 336 " --> pdb=" O CYS D 209 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE D 211 " --> pdb=" O GLN D 336 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ILE D 338 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 768 through 771 removed outlier: 6.671A pdb=" N ILE D 639 " --> pdb=" O LEU D 684 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 855 through 857 Processing sheet with id= M, first strand: chain 'E' and resid 171 through 173 removed outlier: 6.185A pdb=" N LEU E 278 " --> pdb=" O LYS E 242 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE E 244 " --> pdb=" O LEU E 278 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL E 280 " --> pdb=" O PHE E 244 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU E 246 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE E 282 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLN E 336 " --> pdb=" O CYS E 209 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE E 211 " --> pdb=" O GLN E 336 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE E 338 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 768 through 771 removed outlier: 6.658A pdb=" N ILE E 639 " --> pdb=" O LEU E 684 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 855 through 858 Processing sheet with id= P, first strand: chain 'F' and resid 335 through 339 removed outlier: 6.723A pdb=" N ASN F 207 " --> pdb=" O GLN F 336 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE F 338 " --> pdb=" O ASN F 207 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N CYS F 209 " --> pdb=" O ILE F 338 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL F 312 " --> pdb=" O PRO F 208 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LEU F 210 " --> pdb=" O VAL F 312 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLY F 314 " --> pdb=" O LEU F 210 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N GLY F 212 " --> pdb=" O GLY F 314 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR F 316 " --> pdb=" O GLY F 212 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE F 313 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU F 281 " --> pdb=" O ILE F 313 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ALA F 315 " --> pdb=" O LEU F 281 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE F 283 " --> pdb=" O ALA F 315 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N THR F 317 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LYS F 242 " --> pdb=" O VAL F 280 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N PHE F 282 " --> pdb=" O LYS F 242 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE F 244 " --> pdb=" O PHE F 282 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 768 through 772 removed outlier: 6.632A pdb=" N ILE F 639 " --> pdb=" O LEU F 684 " (cutoff:3.500A) 1090 hydrogen bonds defined for protein. 2985 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.51 Time building geometry restraints manager: 12.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.34: 9359 1.34 - 1.52: 15983 1.52 - 1.70: 2523 1.70 - 1.88: 173 1.88 - 2.06: 12 Bond restraints: 28050 Sorted by residual: bond pdb=" C4 AGS A1002 " pdb=" C5 AGS A1002 " ideal model delta sigma weight residual 1.386 1.476 -0.090 1.00e-02 1.00e+04 8.03e+01 bond pdb=" CB HIS E 287 " pdb=" CG HIS E 287 " ideal model delta sigma weight residual 1.497 1.375 0.122 1.40e-02 5.10e+03 7.65e+01 bond pdb=" C4 AGS F1002 " pdb=" C5 AGS F1002 " ideal model delta sigma weight residual 1.386 1.470 -0.084 1.00e-02 1.00e+04 7.02e+01 bond pdb=" C4 AGS C1002 " pdb=" C5 AGS C1002 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" CB ASN F 673 " pdb=" CG ASN F 673 " ideal model delta sigma weight residual 1.516 1.309 0.207 2.50e-02 1.60e+03 6.83e+01 ... (remaining 28045 not shown) Histogram of bond angle deviations from ideal: 92.88 - 101.75: 146 101.75 - 110.63: 9324 110.63 - 119.51: 15571 119.51 - 128.39: 12700 128.39 - 137.27: 100 Bond angle restraints: 37841 Sorted by residual: angle pdb=" N LYS F 266 " pdb=" CA LYS F 266 " pdb=" C LYS F 266 " ideal model delta sigma weight residual 112.38 130.85 -18.47 1.22e+00 6.72e-01 2.29e+02 angle pdb=" C5 AGS E1002 " pdb=" C4 AGS E1002 " pdb=" N3 AGS E1002 " ideal model delta sigma weight residual 126.80 117.84 8.96 7.41e-01 1.82e+00 1.46e+02 angle pdb=" C5 AGS A1002 " pdb=" C4 AGS A1002 " pdb=" N3 AGS A1002 " ideal model delta sigma weight residual 126.80 117.92 8.88 7.41e-01 1.82e+00 1.44e+02 angle pdb=" C5 AGS D1002 " pdb=" C4 AGS D1002 " pdb=" N3 AGS D1002 " ideal model delta sigma weight residual 126.80 117.93 8.87 7.41e-01 1.82e+00 1.43e+02 angle pdb=" C5 AGS F1002 " pdb=" C4 AGS F1002 " pdb=" N3 AGS F1002 " ideal model delta sigma weight residual 126.80 118.10 8.70 7.41e-01 1.82e+00 1.38e+02 ... (remaining 37836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.38: 17097 34.38 - 68.75: 301 68.75 - 103.12: 26 103.12 - 137.50: 7 137.50 - 171.87: 2 Dihedral angle restraints: 17433 sinusoidal: 7314 harmonic: 10119 Sorted by residual: dihedral pdb=" N LYS F 266 " pdb=" C LYS F 266 " pdb=" CA LYS F 266 " pdb=" CB LYS F 266 " ideal model delta harmonic sigma weight residual 122.80 140.71 -17.91 0 2.50e+00 1.60e-01 5.13e+01 dihedral pdb=" C LYS F 266 " pdb=" N LYS F 266 " pdb=" CA LYS F 266 " pdb=" CB LYS F 266 " ideal model delta harmonic sigma weight residual -122.60 -138.13 15.53 0 2.50e+00 1.60e-01 3.86e+01 dihedral pdb=" O1B AGS F1001 " pdb=" O3B AGS F1001 " pdb=" PB AGS F1001 " pdb=" PG AGS F1001 " ideal model delta sinusoidal sigma weight residual 68.91 -102.96 171.87 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 17430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.204: 4152 0.204 - 0.408: 226 0.408 - 0.611: 4 0.611 - 0.815: 0 0.815 - 1.019: 1 Chirality restraints: 4383 Sorted by residual: chirality pdb=" CA LYS F 266 " pdb=" N LYS F 266 " pdb=" C LYS F 266 " pdb=" CB LYS F 266 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" CA LEU C 388 " pdb=" N LEU C 388 " pdb=" C LEU C 388 " pdb=" CB LEU C 388 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CB ILE F 272 " pdb=" CA ILE F 272 " pdb=" CG1 ILE F 272 " pdb=" CG2 ILE F 272 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.63e+00 ... (remaining 4380 not shown) Planarity restraints: 4839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 170 " 0.077 2.00e-02 2.50e+03 4.16e-02 3.47e+01 pdb=" CG TYR A 170 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 170 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR A 170 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR A 170 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR A 170 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR A 170 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 170 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 819 " -0.058 2.00e-02 2.50e+03 3.49e-02 2.44e+01 pdb=" CG TYR C 819 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR C 819 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR C 819 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR C 819 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR C 819 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR C 819 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR C 819 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 321 " 0.064 2.00e-02 2.50e+03 3.34e-02 2.23e+01 pdb=" CG TYR B 321 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR B 321 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR B 321 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 321 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 321 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR B 321 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 321 " 0.044 2.00e-02 2.50e+03 ... (remaining 4836 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.86: 26 1.86 - 2.62: 756 2.62 - 3.38: 41150 3.38 - 4.14: 71781 4.14 - 4.90: 128718 Nonbonded interactions: 242431 Sorted by model distance: nonbonded pdb=" OE2 GLU D 213 " pdb=" CD ARG D 387 " model vdw 1.095 3.440 nonbonded pdb=" NZ LYS F 205 " pdb=" NH2 ARG F 333 " model vdw 1.130 3.200 nonbonded pdb=" OE2 GLU D 213 " pdb=" CG ARG D 387 " model vdw 1.178 3.440 nonbonded pdb=" CD GLU D 213 " pdb=" NE ARG D 387 " model vdw 1.267 3.350 nonbonded pdb=" OH TYR B 662 " pdb=" O LYS C 649 " model vdw 1.272 2.440 ... (remaining 242426 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.100 Check model and map are aligned: 0.380 Set scattering table: 0.270 Process input model: 72.490 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.190 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 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 : 0.024 0.207 28050 Z= 1.560 Angle : 1.942 22.921 37841 Z= 1.303 Chirality : 0.104 1.019 4383 Planarity : 0.010 0.087 4839 Dihedral : 12.779 171.874 10881 Min Nonbonded Distance : 1.095 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 1.37 % Allowed : 4.57 % Favored : 94.07 % Rotamer: Outliers : 0.77 % Allowed : 1.01 % Favored : 98.22 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3438 helix: -0.68 (0.11), residues: 1756 sheet: -0.45 (0.24), residues: 370 loop : -0.43 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.003 HIS A 883 PHE 0.042 0.006 PHE A 685 TYR 0.077 0.009 TYR A 170 ARG 0.011 0.001 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1256 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1233 time to evaluate : 2.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 HIS cc_start: 0.7075 (p90) cc_final: 0.5868 (p-80) REVERT: A 288 MET cc_start: 0.6997 (mmm) cc_final: 0.6690 (mmm) REVERT: A 643 CYS cc_start: 0.4925 (m) cc_final: 0.4595 (m) REVERT: A 762 PHE cc_start: 0.4939 (t80) cc_final: 0.4057 (t80) REVERT: B 174 MET cc_start: 0.6619 (mmm) cc_final: 0.5796 (tpp) REVERT: B 333 ARG cc_start: 0.5961 (OUTLIER) cc_final: 0.5663 (tpt90) REVERT: B 658 THR cc_start: 0.9287 (p) cc_final: 0.8985 (t) REVERT: B 704 ASP cc_start: 0.7079 (t0) cc_final: 0.6630 (t0) REVERT: B 708 ILE cc_start: 0.7204 (mt) cc_final: 0.6736 (mt) REVERT: B 877 LEU cc_start: 0.5045 (mt) cc_final: 0.4713 (mm) REVERT: B 879 VAL cc_start: 0.7057 (t) cc_final: 0.6273 (t) REVERT: C 206 SER cc_start: 0.8422 (m) cc_final: 0.8155 (p) REVERT: C 387 ARG cc_start: 0.8542 (mmp80) cc_final: 0.7874 (mmp80) REVERT: C 697 THR cc_start: 0.8493 (m) cc_final: 0.8215 (m) REVERT: C 718 CYS cc_start: 0.7171 (m) cc_final: 0.5399 (m) REVERT: C 751 MET cc_start: 0.7433 (mmm) cc_final: 0.7229 (mmm) REVERT: D 272 ILE cc_start: 0.7866 (mt) cc_final: 0.7355 (mt) REVERT: D 290 MET cc_start: 0.5522 (mtm) cc_final: 0.5306 (mtm) REVERT: D 618 SER cc_start: 0.8390 (p) cc_final: 0.8037 (t) REVERT: D 620 LYS cc_start: 0.8328 (mtmt) cc_final: 0.8040 (mtmm) REVERT: D 654 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7770 (ttmt) REVERT: D 694 ASP cc_start: 0.7355 (m-30) cc_final: 0.6958 (m-30) REVERT: D 696 LEU cc_start: 0.8613 (mt) cc_final: 0.8271 (mt) REVERT: D 800 LYS cc_start: 0.5582 (mmtm) cc_final: 0.5326 (mptt) REVERT: D 817 TYR cc_start: 0.6148 (m-80) cc_final: 0.5855 (m-10) REVERT: E 187 ILE cc_start: 0.7552 (mp) cc_final: 0.7319 (mm) REVERT: E 223 GLU cc_start: 0.6496 (mt-10) cc_final: 0.6244 (mt-10) REVERT: E 355 LEU cc_start: 0.7159 (mt) cc_final: 0.6851 (mt) REVERT: E 587 ILE cc_start: 0.8698 (mt) cc_final: 0.8480 (mm) REVERT: E 686 ASP cc_start: 0.6826 (m-30) cc_final: 0.6323 (t0) REVERT: E 819 TYR cc_start: 0.6850 (t80) cc_final: 0.6237 (t80) REVERT: F 232 ASP cc_start: 0.3847 (t0) cc_final: 0.3592 (t70) outliers start: 23 outliers final: 10 residues processed: 1249 average time/residue: 0.4892 time to fit residues: 896.0795 Evaluate side-chains 677 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 666 time to evaluate : 3.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 659 THR Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 765 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 0.9980 chunk 260 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 312 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 180 GLN C 362 HIS D 177 GLN D 287 HIS D 336 GLN D 756 GLN D 829 ASN ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 GLN ** F 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 GLN F 701 GLN F 737 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 28050 Z= 0.312 Angle : 0.852 12.505 37841 Z= 0.441 Chirality : 0.050 0.240 4383 Planarity : 0.005 0.085 4839 Dihedral : 11.786 171.138 4052 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.73 % Favored : 93.66 % Rotamer: Outliers : 3.99 % Allowed : 13.08 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3438 helix: -0.11 (0.12), residues: 1770 sheet: -0.68 (0.25), residues: 344 loop : -0.81 (0.18), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS A 692 PHE 0.029 0.003 PHE F 630 TYR 0.034 0.003 TYR E 802 ARG 0.008 0.001 ARG B 843 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 825 time to evaluate : 3.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 THR cc_start: 0.6366 (p) cc_final: 0.6107 (p) REVERT: A 287 HIS cc_start: 0.6787 (p90) cc_final: 0.6530 (p-80) REVERT: A 643 CYS cc_start: 0.4429 (m) cc_final: 0.4210 (m) REVERT: B 211 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8208 (mt) REVERT: B 281 LEU cc_start: 0.9142 (tt) cc_final: 0.8917 (mt) REVERT: B 290 MET cc_start: 0.6273 (ttm) cc_final: 0.6053 (ttm) REVERT: B 632 PHE cc_start: 0.6462 (m-80) cc_final: 0.5899 (m-80) REVERT: B 689 GLU cc_start: 0.8015 (pm20) cc_final: 0.7787 (pm20) REVERT: B 708 ILE cc_start: 0.7568 (mt) cc_final: 0.6059 (mt) REVERT: C 372 LEU cc_start: 0.8497 (mt) cc_final: 0.8229 (mt) REVERT: C 570 ILE cc_start: 0.7115 (tt) cc_final: 0.6878 (tp) REVERT: C 751 MET cc_start: 0.7345 (mmm) cc_final: 0.7064 (mmm) REVERT: D 290 MET cc_start: 0.5510 (mtm) cc_final: 0.5309 (mtm) REVERT: D 333 ARG cc_start: 0.8185 (ttt-90) cc_final: 0.7859 (ttt-90) REVERT: D 620 LYS cc_start: 0.8162 (mtmt) cc_final: 0.7757 (mtmm) REVERT: D 626 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8101 (mmmt) REVERT: D 783 ILE cc_start: 0.8470 (mt) cc_final: 0.8015 (mt) REVERT: E 827 PRO cc_start: 0.9024 (Cg_endo) cc_final: 0.8183 (Cg_exo) REVERT: F 238 LEU cc_start: 0.5402 (OUTLIER) cc_final: 0.5196 (mp) REVERT: F 283 ILE cc_start: 0.8336 (mm) cc_final: 0.8013 (mp) REVERT: F 285 GLU cc_start: 0.5169 (mp0) cc_final: 0.4850 (mp0) REVERT: F 638 MET cc_start: 0.6961 (tpp) cc_final: 0.6171 (tpt) REVERT: F 646 LEU cc_start: 0.7509 (mt) cc_final: 0.7244 (mt) REVERT: F 682 VAL cc_start: 0.8387 (p) cc_final: 0.7548 (t) REVERT: F 684 LEU cc_start: 0.7593 (tp) cc_final: 0.7346 (tp) outliers start: 119 outliers final: 70 residues processed: 897 average time/residue: 0.4222 time to fit residues: 585.5395 Evaluate side-chains 664 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 592 time to evaluate : 3.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 801 HIS Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 683 LEU Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 876 CYS Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 704 ASP Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 653 SER Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 695 VAL Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 650 TYR Chi-restraints excluded: chain F residue 720 ASN Chi-restraints excluded: chain F residue 738 GLN Chi-restraints excluded: chain F residue 821 ASP Chi-restraints excluded: chain F residue 822 ASP Chi-restraints excluded: chain F residue 876 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 173 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 312 optimal weight: 20.0000 chunk 338 optimal weight: 20.0000 chunk 278 optimal weight: 7.9990 chunk 310 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 251 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 GLN ** A 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 ASN ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 GLN C 738 GLN D 712 GLN D 756 GLN D 829 ASN ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 28050 Z= 0.314 Angle : 0.790 10.716 37841 Z= 0.403 Chirality : 0.048 0.249 4383 Planarity : 0.005 0.059 4839 Dihedral : 11.841 176.022 4039 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.02 % Favored : 93.37 % Rotamer: Outliers : 4.39 % Allowed : 16.80 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.65 (0.14), residues: 3438 helix: 0.03 (0.12), residues: 1746 sheet: -0.86 (0.25), residues: 366 loop : -0.74 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS E 363 PHE 0.019 0.002 PHE F 282 TYR 0.027 0.002 TYR B 680 ARG 0.013 0.001 ARG F 605 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 650 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 HIS cc_start: 0.6681 (p90) cc_final: 0.6471 (p90) REVERT: A 643 CYS cc_start: 0.4478 (m) cc_final: 0.4103 (m) REVERT: A 658 THR cc_start: 0.8116 (p) cc_final: 0.7891 (m) REVERT: A 663 VAL cc_start: 0.7504 (OUTLIER) cc_final: 0.7247 (p) REVERT: A 767 SER cc_start: 0.8046 (m) cc_final: 0.7760 (t) REVERT: B 211 ILE cc_start: 0.8786 (mm) cc_final: 0.8389 (mt) REVERT: B 281 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8828 (tp) REVERT: B 288 MET cc_start: 0.7216 (mmt) cc_final: 0.6731 (mmt) REVERT: B 666 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6819 (p0) REVERT: B 688 VAL cc_start: 0.9170 (m) cc_final: 0.8957 (p) REVERT: B 708 ILE cc_start: 0.7424 (mt) cc_final: 0.6893 (mt) REVERT: C 372 LEU cc_start: 0.8438 (mt) cc_final: 0.8232 (mt) REVERT: C 654 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8458 (ttmm) REVERT: C 684 LEU cc_start: 0.8784 (tt) cc_final: 0.8356 (tp) REVERT: C 702 MET cc_start: 0.7884 (tpp) cc_final: 0.7652 (tpt) REVERT: C 715 THR cc_start: 0.8083 (m) cc_final: 0.7736 (p) REVERT: C 763 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8682 (mm) REVERT: D 290 MET cc_start: 0.6119 (mtm) cc_final: 0.5711 (mtm) REVERT: D 333 ARG cc_start: 0.8596 (ttt-90) cc_final: 0.7565 (ttp80) REVERT: D 620 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7816 (mtmm) REVERT: D 767 SER cc_start: 0.8616 (m) cc_final: 0.8409 (t) REVERT: E 345 VAL cc_start: 0.8240 (m) cc_final: 0.7959 (t) REVERT: E 385 TYR cc_start: 0.6693 (m-80) cc_final: 0.6475 (m-80) REVERT: F 285 GLU cc_start: 0.5094 (mp0) cc_final: 0.4772 (mp0) REVERT: F 321 TYR cc_start: 0.6848 (t80) cc_final: 0.6609 (t80) REVERT: F 662 TYR cc_start: 0.8110 (m-80) cc_final: 0.7695 (m-80) REVERT: F 684 LEU cc_start: 0.7778 (tp) cc_final: 0.7451 (tp) outliers start: 131 outliers final: 95 residues processed: 730 average time/residue: 0.4043 time to fit residues: 463.7648 Evaluate side-chains 653 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 554 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 747 LYS Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 801 HIS Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain B residue 822 ASP Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 876 CYS Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 399 SER Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 643 CYS Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 704 ASP Chi-restraints excluded: chain D residue 720 ASN Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 653 SER Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain E residue 768 SER Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain F residue 650 TYR Chi-restraints excluded: chain F residue 709 THR Chi-restraints excluded: chain F residue 720 ASN Chi-restraints excluded: chain F residue 738 GLN Chi-restraints excluded: chain F residue 789 LYS Chi-restraints excluded: chain F residue 821 ASP Chi-restraints excluded: chain F residue 822 ASP Chi-restraints excluded: chain F residue 876 CYS Chi-restraints excluded: chain F residue 880 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 309 optimal weight: 8.9990 chunk 235 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 314 optimal weight: 1.9990 chunk 332 optimal weight: 4.9990 chunk 164 optimal weight: 8.9990 chunk 297 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 GLN ** A 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 HIS ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 GLN ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN D 829 ASN ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 28050 Z= 0.279 Angle : 0.731 10.684 37841 Z= 0.373 Chirality : 0.047 0.288 4383 Planarity : 0.004 0.046 4839 Dihedral : 11.730 172.673 4039 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.49 % Favored : 92.96 % Rotamer: Outliers : 5.06 % Allowed : 18.81 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.62 (0.14), residues: 3438 helix: 0.16 (0.12), residues: 1733 sheet: -0.95 (0.25), residues: 366 loop : -0.84 (0.18), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS D 287 PHE 0.038 0.002 PHE F 282 TYR 0.035 0.002 TYR F 817 ARG 0.011 0.001 ARG E 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 618 time to evaluate : 3.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 643 CYS cc_start: 0.4310 (m) cc_final: 0.3927 (m) REVERT: A 658 THR cc_start: 0.8122 (p) cc_final: 0.7919 (m) REVERT: A 767 SER cc_start: 0.8292 (m) cc_final: 0.8068 (t) REVERT: B 211 ILE cc_start: 0.8754 (mm) cc_final: 0.8316 (mt) REVERT: B 281 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8793 (tp) REVERT: B 387 ARG cc_start: 0.8221 (mmp80) cc_final: 0.7132 (mmt180) REVERT: B 632 PHE cc_start: 0.6576 (m-80) cc_final: 0.6283 (m-10) REVERT: B 688 VAL cc_start: 0.9215 (m) cc_final: 0.9014 (p) REVERT: B 759 ARG cc_start: 0.7247 (tpp80) cc_final: 0.6841 (ttt180) REVERT: B 762 PHE cc_start: 0.8717 (t80) cc_final: 0.8410 (t80) REVERT: B 765 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8210 (mtt-85) REVERT: C 654 LYS cc_start: 0.8782 (ttmm) cc_final: 0.8455 (ttmm) REVERT: C 684 LEU cc_start: 0.8751 (tt) cc_final: 0.8204 (tp) REVERT: C 688 VAL cc_start: 0.9211 (OUTLIER) cc_final: 0.8935 (t) REVERT: C 715 THR cc_start: 0.8034 (m) cc_final: 0.7739 (p) REVERT: D 290 MET cc_start: 0.6112 (mtm) cc_final: 0.5761 (mtm) REVERT: D 394 ASP cc_start: 0.6215 (t0) cc_final: 0.5994 (t0) REVERT: D 620 LYS cc_start: 0.8046 (mtmt) cc_final: 0.7781 (mtmm) REVERT: E 345 VAL cc_start: 0.8112 (m) cc_final: 0.7885 (t) REVERT: F 662 TYR cc_start: 0.8159 (m-80) cc_final: 0.7729 (m-80) outliers start: 151 outliers final: 100 residues processed: 703 average time/residue: 0.3989 time to fit residues: 442.5089 Evaluate side-chains 627 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 524 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 801 HIS Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 399 SER Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 643 CYS Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 720 ASN Chi-restraints excluded: chain D residue 721 CYS Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 638 MET Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain E residue 768 SER Chi-restraints excluded: chain E residue 828 LEU Chi-restraints excluded: chain E residue 880 LEU Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain F residue 643 CYS Chi-restraints excluded: chain F residue 650 TYR Chi-restraints excluded: chain F residue 680 TYR Chi-restraints excluded: chain F residue 709 THR Chi-restraints excluded: chain F residue 720 ASN Chi-restraints excluded: chain F residue 821 ASP Chi-restraints excluded: chain F residue 822 ASP Chi-restraints excluded: chain F residue 838 ASN Chi-restraints excluded: chain F residue 876 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 276 optimal weight: 7.9990 chunk 188 optimal weight: 0.0030 chunk 4 optimal weight: 9.9990 chunk 247 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 283 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 298 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 overall best weight: 2.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS D 808 GLN ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 712 GLN ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 28050 Z= 0.322 Angle : 0.750 12.756 37841 Z= 0.381 Chirality : 0.047 0.257 4383 Planarity : 0.004 0.050 4839 Dihedral : 11.717 171.240 4039 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.22 % Favored : 93.22 % Rotamer: Outliers : 5.33 % Allowed : 20.99 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.58 (0.14), residues: 3438 helix: 0.19 (0.13), residues: 1716 sheet: -1.02 (0.25), residues: 366 loop : -0.80 (0.18), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS F 692 PHE 0.034 0.002 PHE F 282 TYR 0.032 0.002 TYR A 359 ARG 0.013 0.001 ARG E 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 556 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 287 HIS cc_start: 0.7376 (p-80) cc_final: 0.6930 (p90) REVERT: A 288 MET cc_start: 0.6803 (mmm) cc_final: 0.6430 (mmm) REVERT: A 643 CYS cc_start: 0.4121 (m) cc_final: 0.3641 (m) REVERT: B 211 ILE cc_start: 0.8847 (mm) cc_final: 0.8491 (mt) REVERT: B 688 VAL cc_start: 0.9206 (m) cc_final: 0.8989 (p) REVERT: B 759 ARG cc_start: 0.7250 (tpp80) cc_final: 0.6986 (ttt180) REVERT: B 765 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7559 (mtp85) REVERT: C 654 LYS cc_start: 0.8811 (ttmm) cc_final: 0.8525 (ttmm) REVERT: C 684 LEU cc_start: 0.8801 (tt) cc_final: 0.8515 (tt) REVERT: C 702 MET cc_start: 0.7954 (tpp) cc_final: 0.7661 (tpt) REVERT: C 715 THR cc_start: 0.8008 (m) cc_final: 0.7763 (p) REVERT: C 877 LEU cc_start: 0.6887 (tp) cc_final: 0.6601 (tp) REVERT: D 618 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8512 (t) REVERT: E 345 VAL cc_start: 0.8193 (m) cc_final: 0.7965 (t) REVERT: F 174 MET cc_start: 0.6548 (mmm) cc_final: 0.6207 (mmm) REVERT: F 290 MET cc_start: 0.6305 (tmm) cc_final: 0.5949 (mtp) REVERT: F 662 TYR cc_start: 0.8259 (m-80) cc_final: 0.7995 (m-80) outliers start: 159 outliers final: 113 residues processed: 652 average time/residue: 0.3959 time to fit residues: 410.2535 Evaluate side-chains 607 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 492 time to evaluate : 3.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 801 HIS Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 399 SER Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 643 CYS Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 720 ASN Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 826 ARG Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 768 SER Chi-restraints excluded: chain E residue 828 LEU Chi-restraints excluded: chain E residue 880 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain F residue 650 TYR Chi-restraints excluded: chain F residue 680 TYR Chi-restraints excluded: chain F residue 688 VAL Chi-restraints excluded: chain F residue 716 ILE Chi-restraints excluded: chain F residue 720 ASN Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 821 ASP Chi-restraints excluded: chain F residue 822 ASP Chi-restraints excluded: chain F residue 838 ASN Chi-restraints excluded: chain F residue 876 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 111 optimal weight: 8.9990 chunk 299 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 332 optimal weight: 3.9990 chunk 276 optimal weight: 7.9990 chunk 154 optimal weight: 0.0030 chunk 27 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 538 GLN ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 856 ASN ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.6451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 28050 Z= 0.233 Angle : 0.700 16.030 37841 Z= 0.354 Chirality : 0.046 0.254 4383 Planarity : 0.004 0.053 4839 Dihedral : 11.414 165.149 4035 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.22 % Favored : 93.25 % Rotamer: Outliers : 4.63 % Allowed : 22.20 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.55 (0.15), residues: 3438 helix: 0.24 (0.13), residues: 1719 sheet: -1.03 (0.26), residues: 360 loop : -0.82 (0.18), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS F 692 PHE 0.025 0.002 PHE B 813 TYR 0.029 0.002 TYR D 677 ARG 0.009 0.001 ARG E 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 574 time to evaluate : 3.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 GLN cc_start: 0.6770 (mm110) cc_final: 0.6526 (mm-40) REVERT: A 702 MET cc_start: 0.6803 (mpp) cc_final: 0.5556 (mmp) REVERT: B 205 LYS cc_start: 0.7494 (ttpp) cc_final: 0.7269 (ttmm) REVERT: B 211 ILE cc_start: 0.8820 (mm) cc_final: 0.8497 (mt) REVERT: B 280 VAL cc_start: 0.9384 (t) cc_final: 0.9183 (m) REVERT: B 311 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8643 (mmtp) REVERT: B 387 ARG cc_start: 0.8100 (mmp80) cc_final: 0.7209 (mmt180) REVERT: B 688 VAL cc_start: 0.9208 (m) cc_final: 0.8916 (p) REVERT: B 765 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7267 (mtp85) REVERT: C 654 LYS cc_start: 0.8694 (ttmm) cc_final: 0.8395 (ttmm) REVERT: C 684 LEU cc_start: 0.8794 (tt) cc_final: 0.8472 (tt) REVERT: C 702 MET cc_start: 0.7867 (tpp) cc_final: 0.7535 (tpt) REVERT: C 715 THR cc_start: 0.7921 (m) cc_final: 0.7712 (p) REVERT: D 699 MET cc_start: 0.6584 (mmp) cc_final: 0.6169 (mmp) REVERT: E 665 TYR cc_start: 0.6921 (OUTLIER) cc_final: 0.6699 (m-80) REVERT: F 359 TYR cc_start: 0.6361 (m-10) cc_final: 0.6160 (m-10) REVERT: F 662 TYR cc_start: 0.8279 (m-80) cc_final: 0.7887 (m-80) outliers start: 138 outliers final: 100 residues processed: 658 average time/residue: 0.4110 time to fit residues: 431.5009 Evaluate side-chains 608 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 505 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 801 HIS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 399 SER Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 643 CYS Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 720 ASN Chi-restraints excluded: chain D residue 721 CYS Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 880 LEU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 768 SER Chi-restraints excluded: chain E residue 828 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 596 LEU Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 643 CYS Chi-restraints excluded: chain F residue 650 TYR Chi-restraints excluded: chain F residue 680 TYR Chi-restraints excluded: chain F residue 720 ASN Chi-restraints excluded: chain F residue 821 ASP Chi-restraints excluded: chain F residue 822 ASP Chi-restraints excluded: chain F residue 835 GLU Chi-restraints excluded: chain F residue 876 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 320 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 243 optimal weight: 7.9990 chunk 188 optimal weight: 3.9990 chunk 280 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 331 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 HIS A 538 GLN ** A 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.6716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 28050 Z= 0.296 Angle : 0.742 14.255 37841 Z= 0.372 Chirality : 0.047 0.330 4383 Planarity : 0.004 0.048 4839 Dihedral : 11.381 166.236 4035 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.63 % Favored : 92.84 % Rotamer: Outliers : 4.83 % Allowed : 22.80 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.56 (0.15), residues: 3438 helix: 0.26 (0.13), residues: 1715 sheet: -1.08 (0.26), residues: 358 loop : -0.84 (0.18), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.002 HIS D 287 PHE 0.039 0.002 PHE B 813 TYR 0.040 0.002 TYR D 677 ARG 0.008 0.001 ARG E 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 530 time to evaluate : 3.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 MET cc_start: 0.6824 (mpp) cc_final: 0.6192 (mmm) REVERT: B 211 ILE cc_start: 0.8878 (mm) cc_final: 0.8659 (mt) REVERT: B 280 VAL cc_start: 0.9108 (t) cc_final: 0.8904 (m) REVERT: B 387 ARG cc_start: 0.8016 (mmp80) cc_final: 0.7148 (mmt180) REVERT: B 765 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7268 (mtp85) REVERT: C 654 LYS cc_start: 0.8773 (ttmm) cc_final: 0.8530 (ttmm) REVERT: C 684 LEU cc_start: 0.8779 (tt) cc_final: 0.8539 (tt) REVERT: C 715 THR cc_start: 0.8026 (m) cc_final: 0.7766 (p) REVERT: D 394 ASP cc_start: 0.6179 (t0) cc_final: 0.5736 (t0) REVERT: D 699 MET cc_start: 0.6624 (mmp) cc_final: 0.5974 (mmp) REVERT: E 247 ASP cc_start: 0.6683 (t70) cc_final: 0.6179 (m-30) REVERT: E 665 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.6843 (m-80) REVERT: F 174 MET cc_start: 0.5806 (mmm) cc_final: 0.5506 (mmp) REVERT: F 662 TYR cc_start: 0.8362 (m-80) cc_final: 0.7918 (m-80) REVERT: F 673 ASN cc_start: 0.6582 (m-40) cc_final: 0.6202 (t0) outliers start: 144 outliers final: 115 residues processed: 621 average time/residue: 0.3869 time to fit residues: 384.5390 Evaluate side-chains 608 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 491 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 692 HIS Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 801 HIS Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 399 SER Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 643 CYS Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 720 ASN Chi-restraints excluded: chain D residue 721 CYS Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 826 ARG Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 768 SER Chi-restraints excluded: chain E residue 828 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 554 THR Chi-restraints excluded: chain F residue 556 ILE Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain F residue 643 CYS Chi-restraints excluded: chain F residue 650 TYR Chi-restraints excluded: chain F residue 680 TYR Chi-restraints excluded: chain F residue 720 ASN Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 789 LYS Chi-restraints excluded: chain F residue 821 ASP Chi-restraints excluded: chain F residue 822 ASP Chi-restraints excluded: chain F residue 876 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 205 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 260 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN ** A 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 701 GLN ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.6938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 28050 Z= 0.237 Angle : 0.720 13.729 37841 Z= 0.360 Chirality : 0.046 0.235 4383 Planarity : 0.004 0.046 4839 Dihedral : 11.183 161.735 4035 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.52 % Favored : 92.96 % Rotamer: Outliers : 4.29 % Allowed : 23.94 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.55 (0.15), residues: 3438 helix: 0.25 (0.13), residues: 1738 sheet: -0.99 (0.26), residues: 358 loop : -0.85 (0.18), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS C 781 PHE 0.030 0.002 PHE B 813 TYR 0.033 0.002 TYR B 802 ARG 0.007 0.001 ARG E 179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 542 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 LEU cc_start: 0.6156 (pp) cc_final: 0.5949 (tp) REVERT: A 702 MET cc_start: 0.6945 (mpp) cc_final: 0.5959 (mmm) REVERT: B 186 VAL cc_start: 0.7989 (t) cc_final: 0.7779 (p) REVERT: B 211 ILE cc_start: 0.8842 (mm) cc_final: 0.8460 (mt) REVERT: B 272 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8410 (mm) REVERT: B 321 TYR cc_start: 0.7148 (t80) cc_final: 0.6617 (t80) REVERT: B 387 ARG cc_start: 0.7877 (mmp80) cc_final: 0.7112 (mmt180) REVERT: B 765 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7326 (mtp85) REVERT: C 654 LYS cc_start: 0.8695 (ttmm) cc_final: 0.8492 (ttmm) REVERT: C 684 LEU cc_start: 0.8786 (tt) cc_final: 0.8551 (tt) REVERT: C 715 THR cc_start: 0.7933 (m) cc_final: 0.7733 (p) REVERT: C 877 LEU cc_start: 0.6693 (tp) cc_final: 0.6454 (tp) REVERT: E 247 ASP cc_start: 0.6642 (t70) cc_final: 0.6198 (m-30) REVERT: E 271 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6476 (tt0) REVERT: E 637 MET cc_start: 0.7181 (tpp) cc_final: 0.6710 (tpp) REVERT: F 174 MET cc_start: 0.5782 (mmm) cc_final: 0.5514 (mmp) REVERT: F 662 TYR cc_start: 0.8443 (m-80) cc_final: 0.8074 (m-80) outliers start: 128 outliers final: 108 residues processed: 616 average time/residue: 0.3885 time to fit residues: 382.6219 Evaluate side-chains 599 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 488 time to evaluate : 3.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 692 HIS Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 801 HIS Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain B residue 878 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 643 CYS Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 720 ASN Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 826 ARG Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 703 LEU Chi-restraints excluded: chain E residue 717 ASP Chi-restraints excluded: chain E residue 768 SER Chi-restraints excluded: chain E residue 828 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 554 THR Chi-restraints excluded: chain F residue 556 ILE Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 643 CYS Chi-restraints excluded: chain F residue 650 TYR Chi-restraints excluded: chain F residue 680 TYR Chi-restraints excluded: chain F residue 720 ASN Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 789 LYS Chi-restraints excluded: chain F residue 821 ASP Chi-restraints excluded: chain F residue 822 ASP Chi-restraints excluded: chain F residue 876 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 301 optimal weight: 2.9990 chunk 317 optimal weight: 2.9990 chunk 289 optimal weight: 9.9990 chunk 308 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 242 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 279 optimal weight: 3.9990 chunk 292 optimal weight: 4.9990 chunk 307 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 GLN ** A 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 HIS ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 HIS ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 HIS ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 781 HIS ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.7162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 28050 Z= 0.334 Angle : 0.801 14.515 37841 Z= 0.397 Chirality : 0.048 0.429 4383 Planarity : 0.005 0.049 4839 Dihedral : 11.381 165.303 4035 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 23.09 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.53 % Favored : 91.94 % Rotamer: Outliers : 4.46 % Allowed : 24.38 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.73 (0.14), residues: 3438 helix: 0.09 (0.12), residues: 1756 sheet: -0.95 (0.26), residues: 369 loop : -0.97 (0.18), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.002 HIS D 287 PHE 0.044 0.002 PHE B 813 TYR 0.020 0.002 TYR C 677 ARG 0.007 0.001 ARG E 777 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 501 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 MET cc_start: 0.6311 (mpp) cc_final: 0.5989 (mmm) REVERT: A 721 CYS cc_start: 0.7967 (p) cc_final: 0.6699 (p) REVERT: B 186 VAL cc_start: 0.8112 (OUTLIER) cc_final: 0.7905 (p) REVERT: B 765 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7467 (mtp85) REVERT: C 283 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8980 (pt) REVERT: C 634 ASP cc_start: 0.7346 (p0) cc_final: 0.7086 (p0) REVERT: C 715 THR cc_start: 0.8078 (m) cc_final: 0.7864 (p) REVERT: C 877 LEU cc_start: 0.6730 (tp) cc_final: 0.6468 (tp) REVERT: D 290 MET cc_start: 0.2809 (OUTLIER) cc_final: 0.2042 (ttt) REVERT: D 702 MET cc_start: 0.7313 (ptt) cc_final: 0.7027 (ptt) REVERT: E 247 ASP cc_start: 0.6797 (t70) cc_final: 0.6434 (m-30) REVERT: E 271 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6606 (tt0) REVERT: F 174 MET cc_start: 0.5722 (mmm) cc_final: 0.5477 (mmp) REVERT: F 662 TYR cc_start: 0.8549 (m-80) cc_final: 0.8079 (m-80) outliers start: 133 outliers final: 114 residues processed: 587 average time/residue: 0.3886 time to fit residues: 366.5196 Evaluate side-chains 604 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 485 time to evaluate : 3.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 692 HIS Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 801 HIS Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain B residue 878 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 643 CYS Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 720 ASN Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 826 ARG Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 261 PHE Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 703 LEU Chi-restraints excluded: chain E residue 717 ASP Chi-restraints excluded: chain E residue 768 SER Chi-restraints excluded: chain E residue 828 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 554 THR Chi-restraints excluded: chain F residue 556 ILE Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 643 CYS Chi-restraints excluded: chain F residue 680 TYR Chi-restraints excluded: chain F residue 716 ILE Chi-restraints excluded: chain F residue 720 ASN Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 781 HIS Chi-restraints excluded: chain F residue 789 LYS Chi-restraints excluded: chain F residue 821 ASP Chi-restraints excluded: chain F residue 822 ASP Chi-restraints excluded: chain F residue 876 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 202 optimal weight: 0.6980 chunk 326 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 154 optimal weight: 0.0040 chunk 227 optimal weight: 7.9990 chunk 342 optimal weight: 30.0000 chunk 315 optimal weight: 0.6980 chunk 272 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 210 optimal weight: 0.0170 chunk 167 optimal weight: 0.5980 overall best weight: 0.4030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 GLN ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 GLN ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 712 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 ASN ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 829 ASN ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 GLN F 781 HIS ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.7352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28050 Z= 0.209 Angle : 0.739 13.669 37841 Z= 0.367 Chirality : 0.046 0.331 4383 Planarity : 0.004 0.049 4839 Dihedral : 10.917 153.831 4035 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.05 % Favored : 93.43 % Rotamer: Outliers : 3.22 % Allowed : 25.96 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.72 (0.15), residues: 3438 helix: 0.10 (0.12), residues: 1760 sheet: -1.04 (0.26), residues: 389 loop : -0.93 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.022 0.001 HIS F 781 PHE 0.044 0.002 PHE B 813 TYR 0.022 0.002 TYR F 321 ARG 0.010 0.001 ARG E 759 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 574 time to evaluate : 3.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 MET cc_start: 0.6276 (mpp) cc_final: 0.5921 (mmm) REVERT: B 342 GLU cc_start: 0.7150 (tp30) cc_final: 0.6757 (tp30) REVERT: B 387 ARG cc_start: 0.7862 (mmp80) cc_final: 0.7183 (mmp80) REVERT: B 765 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7604 (mtp85) REVERT: C 252 THR cc_start: 0.7398 (p) cc_final: 0.7138 (t) REVERT: C 634 ASP cc_start: 0.7173 (p0) cc_final: 0.6939 (p0) REVERT: C 654 LYS cc_start: 0.8635 (ttmm) cc_final: 0.8385 (ttmm) REVERT: C 684 LEU cc_start: 0.8736 (tt) cc_final: 0.8486 (mt) REVERT: D 290 MET cc_start: 0.3123 (ttt) cc_final: 0.1744 (ttm) REVERT: D 333 ARG cc_start: 0.8479 (ttt-90) cc_final: 0.7616 (tmt-80) REVERT: D 597 SER cc_start: 0.8342 (p) cc_final: 0.7966 (t) REVERT: D 732 GLU cc_start: 0.5573 (mp0) cc_final: 0.5259 (mp0) REVERT: E 247 ASP cc_start: 0.6779 (t70) cc_final: 0.6246 (m-30) REVERT: E 271 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6580 (tt0) REVERT: F 662 TYR cc_start: 0.8456 (m-80) cc_final: 0.8181 (m-80) outliers start: 96 outliers final: 78 residues processed: 630 average time/residue: 0.4350 time to fit residues: 438.2703 Evaluate side-chains 586 residues out of total 2982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 506 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 692 HIS Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 801 HIS Chi-restraints excluded: chain B residue 878 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 826 ARG Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 703 LEU Chi-restraints excluded: chain E residue 768 SER Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 554 THR Chi-restraints excluded: chain F residue 643 CYS Chi-restraints excluded: chain F residue 680 TYR Chi-restraints excluded: chain F residue 720 ASN Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 821 ASP Chi-restraints excluded: chain F residue 822 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 216 optimal weight: 0.0970 chunk 290 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 251 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 273 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 280 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 HIS ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 712 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 829 ASN ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 GLN ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.123534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.103063 restraints weight = 63048.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.105931 restraints weight = 35901.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.107779 restraints weight = 23398.651| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.7518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 28050 Z= 0.218 Angle : 0.734 12.929 37841 Z= 0.366 Chirality : 0.046 0.265 4383 Planarity : 0.004 0.048 4839 Dihedral : 10.852 151.143 4033 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.54 % Favored : 92.96 % Rotamer: Outliers : 2.95 % Allowed : 26.89 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.64 (0.15), residues: 3438 helix: 0.17 (0.13), residues: 1757 sheet: -0.84 (0.27), residues: 361 loop : -0.96 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS D 287 PHE 0.034 0.002 PHE B 813 TYR 0.023 0.002 TYR E 802 ARG 0.011 0.001 ARG E 759 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7635.26 seconds wall clock time: 139 minutes 46.25 seconds (8386.25 seconds total)