Starting phenix.real_space_refine on Tue Feb 20 10:43:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vjh_8697/02_2024/5vjh_8697_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vjh_8697/02_2024/5vjh_8697.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/5vjh_8697/02_2024/5vjh_8697.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vjh_8697/02_2024/5vjh_8697.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vjh_8697/02_2024/5vjh_8697_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vjh_8697/02_2024/5vjh_8697_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= 0.006 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 17230 2.51 5 N 4835 2.21 5 O 5356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 667": "OE1" <-> "OE2" Residue "D ARG 765": "NH1" <-> "NH2" Residue "E ARG 826": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27577 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: 4424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4424 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 17, 'TRANS': 546} Chain breaks: 3 Chain: "P" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 131 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'UNK:plan-1': 25} Unresolved non-hydrogen planarities: 25 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: 14.51, per 1000 atoms: 0.53 Number of scatterers: 27577 At special positions: 0 Unit cell: (135, 143, 131, 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 5356 8.00 N 4835 7.00 C 17230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 718 " - pdb=" SG CYS F 721 " distance=2.22 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.83 Conformation dependent library (CDL) restraints added in 5.2 seconds 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6524 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 194 helices and 21 sheets defined 52.1% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.67 Creating SS restraints... Processing helix chain 'A' and resid 166 through 170 removed outlier: 3.504A pdb=" N TYR A 170 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 180 Processing helix chain 'A' and resid 190 through 201 Processing helix chain 'A' and resid 218 through 230 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 252 Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 286 through 289 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 303 through 306 Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'A' and resid 330 through 334 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 removed outlier: 3.771A pdb=" N LEU A 393 " --> pdb=" O PRO A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 563 through 568 Processing helix chain 'A' and resid 570 through 579 Processing helix chain 'A' and resid 584 through 598 Processing helix chain 'A' and resid 620 through 632 Processing helix chain 'A' and resid 635 through 637 No H-bonds generated for 'chain 'A' and resid 635 through 637' 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 Processing helix chain 'A' and resid 729 through 736 removed outlier: 4.337A pdb=" N GLU A 732 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN A 735 " --> pdb=" O GLU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 757 removed outlier: 5.272A pdb=" N LEU A 749 " --> pdb=" O SER A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 764 Processing helix chain 'A' and resid 777 through 794 Processing helix chain 'A' and resid 809 through 818 Processing helix chain 'A' and resid 826 through 834 Processing helix chain 'A' and resid 837 through 845 Processing helix chain 'B' and resid 166 through 170 removed outlier: 4.064A pdb=" N TYR B 170 " --> pdb=" O LEU B 167 " (cutoff:3.500A) 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 231 Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 260 through 274 Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 318 through 328 removed outlier: 4.660A 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 Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 557 through 559 No H-bonds generated for 'chain 'B' and resid 557 through 559' Processing helix chain 'B' and resid 563 through 579 removed outlier: 4.821A pdb=" N GLU B 573 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ARG B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU B 579 " --> pdb=" O ASP B 575 " (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 648 through 656 removed outlier: 4.553A pdb=" N VAL B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N SER B 653 " --> pdb=" O LYS B 649 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 677 No H-bonds generated for 'chain 'B' and resid 674 through 677' 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 703 Processing helix chain 'B' and resid 729 through 736 removed outlier: 3.850A pdb=" N GLU B 732 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASN B 735 " --> pdb=" O GLU B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 Processing helix chain 'B' and resid 760 through 765 removed outlier: 4.132A 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 817 Processing helix chain 'B' and resid 826 through 835 removed outlier: 3.503A pdb=" N ARG B 830 " --> pdb=" O ARG B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 845 Processing helix chain 'C' and resid 166 through 169 No H-bonds generated for 'chain 'C' and resid 166 through 169' 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 249 through 252 No H-bonds generated for 'chain 'C' and resid 249 through 252' Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 286 through 290 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 306 Processing helix chain 'C' and resid 318 through 328 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 removed outlier: 4.059A pdb=" N LEU C 393 " --> pdb=" O PRO C 389 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER C 409 " --> pdb=" O VAL C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 554 Processing helix chain 'C' and resid 557 through 559 No H-bonds generated for 'chain 'C' and resid 557 through 559' Processing helix chain 'C' and resid 563 through 570 Processing helix chain 'C' and resid 572 through 579 Processing helix chain 'C' and resid 584 through 598 Processing helix chain 'C' and resid 620 through 632 Processing helix chain 'C' and resid 643 through 645 No H-bonds generated for 'chain 'C' and resid 643 through 645' Processing helix chain 'C' and resid 648 through 656 removed outlier: 5.174A pdb=" N SER C 653 " --> pdb=" O LYS C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 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 695 through 702 Processing helix chain 'C' and resid 729 through 736 removed outlier: 5.004A 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: 4.049A pdb=" N ARG C 765 " --> pdb=" O GLU C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 793 Processing helix chain 'C' and resid 809 through 817 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 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 248 through 252 Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 286 through 290 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 removed outlier: 3.570A pdb=" N ARG D 307 " --> pdb=" O PRO D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 removed outlier: 4.559A pdb=" N LYS D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) 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 removed outlier: 4.128A pdb=" N LEU D 393 " --> pdb=" O PRO D 389 " (cutoff:3.500A) 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 570 removed outlier: 3.815A pdb=" N GLU D 567 " --> pdb=" O GLU D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 579 removed outlier: 3.500A pdb=" N GLU D 579 " --> pdb=" O ASP D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 599 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 648 through 656 removed outlier: 4.472A pdb=" N VAL D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N SER D 653 " --> pdb=" O LYS D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 675 Processing helix chain 'D' and resid 688 through 690 No H-bonds generated for 'chain 'D' and resid 688 through 690' Processing helix chain 'D' and resid 693 through 702 Processing helix chain 'D' and resid 729 through 736 removed outlier: 4.173A pdb=" N GLU D 732 " --> pdb=" O LEU D 729 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN D 735 " --> pdb=" O GLU D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 755 Processing helix chain 'D' and resid 760 through 765 removed outlier: 4.861A pdb=" N ARG D 765 " --> pdb=" O GLU D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 793 Processing helix chain 'D' and resid 809 through 818 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 Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'E' and resid 190 through 201 Processing helix chain 'E' and resid 218 through 230 Processing helix chain 'E' and resid 236 through 238 No H-bonds generated for 'chain 'E' and resid 236 through 238' 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 327 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 406 Processing helix chain 'E' and resid 543 through 554 Processing helix chain 'E' and resid 557 through 559 No H-bonds generated for 'chain 'E' and resid 557 through 559' Processing helix chain 'E' and resid 563 through 578 removed outlier: 4.704A pdb=" N GLU E 573 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG E 574 " --> pdb=" O ILE E 570 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER E 577 " --> pdb=" O GLU E 573 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER E 578 " --> pdb=" O ARG E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 598 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 643 through 645 No H-bonds generated for 'chain 'E' and resid 643 through 645' Processing helix chain 'E' and resid 648 through 656 removed outlier: 5.743A pdb=" N SER E 653 " --> pdb=" O LYS E 649 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 729 through 736 removed outlier: 4.301A pdb=" N ASN E 735 " --> pdb=" O GLU E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 746 through 757 Processing helix chain 'E' and resid 760 through 765 removed outlier: 3.943A 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 826 through 835 Processing helix chain 'E' and resid 837 through 845 Processing helix chain 'F' and resid 166 through 170 Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 189 through 201 Processing helix chain 'F' and resid 218 through 231 Processing helix chain 'F' and resid 248 through 253 Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 294 through 299 Processing helix chain 'F' and resid 302 through 307 Processing helix chain 'F' and resid 318 through 327 Processing helix chain 'F' and resid 329 through 334 removed outlier: 3.558A pdb=" N ARG F 334 " --> pdb=" O PHE F 331 " (cutoff:3.500A) 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 409 removed outlier: 4.663A pdb=" N LEU F 393 " --> pdb=" O PRO F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 554 Processing helix chain 'F' and resid 563 through 570 removed outlier: 3.949A pdb=" N LEU F 569 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 578 removed outlier: 3.779A pdb=" N SER F 578 " --> pdb=" O ARG F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 599 Processing helix chain 'F' and resid 620 through 632 Processing helix chain 'F' and resid 643 through 645 No H-bonds generated for 'chain 'F' and resid 643 through 645' Processing helix chain 'F' and resid 648 through 654 removed outlier: 5.740A pdb=" N SER F 653 " --> pdb=" O LYS F 649 " (cutoff:3.500A) Processing helix chain 'F' and resid 673 through 677 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 703 Processing helix chain 'F' and resid 729 through 736 removed outlier: 4.829A pdb=" N ASN F 735 " --> pdb=" O GLU F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 746 through 756 removed outlier: 3.742A pdb=" N GLN F 756 " --> pdb=" O GLY F 752 " (cutoff:3.500A) Processing helix chain 'F' and resid 760 through 763 No H-bonds generated for 'chain 'F' and resid 760 through 763' Processing helix chain 'F' and resid 777 through 794 removed outlier: 3.551A pdb=" N LYS F 782 " --> pdb=" O LYS F 778 " (cutoff:3.500A) Processing helix chain 'F' and resid 807 through 816 Processing helix chain 'F' and resid 826 through 835 Processing helix chain 'F' and resid 837 through 845 Processing sheet with id= A, first strand: chain 'A' and resid 171 through 173 Processing sheet with id= B, first strand: chain 'A' and resid 336 through 339 removed outlier: 6.921A pdb=" N GLY A 314 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 768 through 772 removed outlier: 6.495A pdb=" N VAL A 723 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N PHE A 612 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N MET A 725 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY A 614 " --> pdb=" O MET A 725 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N SER A 727 " --> pdb=" O GLY A 614 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 855 through 857 Processing sheet with id= E, first strand: chain 'B' and resid 171 through 173 removed outlier: 6.378A pdb=" N LYS B 311 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE B 283 " --> pdb=" O LYS B 311 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE B 313 " --> pdb=" O ILE B 283 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 336 through 339 removed outlier: 6.490A pdb=" N GLY B 314 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 768 through 771 removed outlier: 6.683A pdb=" N ILE B 639 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASP B 686 " --> pdb=" O ILE B 639 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL B 641 " --> pdb=" O ASP B 686 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 855 through 857 Processing sheet with id= I, first strand: chain 'C' and resid 171 through 173 removed outlier: 3.563A pdb=" N GLY C 212 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN C 336 " --> pdb=" O CYS C 209 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE C 211 " --> pdb=" O GLN C 336 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE C 338 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 768 through 771 removed outlier: 6.378A pdb=" N ILE C 639 " --> pdb=" O LEU C 684 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 855 through 857 Processing sheet with id= L, first strand: chain 'D' and resid 171 through 173 removed outlier: 6.183A pdb=" N GLN D 336 " --> pdb=" O CYS D 209 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE D 211 " --> pdb=" O GLN D 336 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE D 338 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 768 through 771 removed outlier: 6.474A pdb=" N ILE D 639 " --> pdb=" O LEU D 684 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ASP D 686 " --> pdb=" O ILE D 639 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL D 641 " --> pdb=" O ASP D 686 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 855 through 857 Processing sheet with id= O, first strand: chain 'E' and resid 171 through 173 removed outlier: 5.312A pdb=" N ASP E 284 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLN E 336 " --> pdb=" O CYS E 209 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE E 211 " --> pdb=" O GLN E 336 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ILE E 338 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 365 through 367 removed outlier: 6.377A pdb=" N ASN E 539 " --> pdb=" O ARG E 366 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 768 through 771 removed outlier: 6.438A pdb=" N ILE E 639 " --> pdb=" O LEU E 684 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 855 through 857 Processing sheet with id= S, first strand: chain 'F' and resid 171 through 173 Processing sheet with id= T, first strand: chain 'F' and resid 768 through 771 removed outlier: 6.493A pdb=" N VAL F 723 " --> pdb=" O PHE F 610 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE F 612 " --> pdb=" O VAL F 723 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N MET F 725 " --> pdb=" O PHE F 612 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 802 through 804 removed outlier: 6.429A pdb=" N GLU F 853 " --> pdb=" O LYS F 803 " (cutoff:3.500A) 1175 hydrogen bonds defined for protein. 3258 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: 9.18 Time building geometry restraints manager: 12.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 9739 1.36 - 1.54: 17333 1.54 - 1.72: 677 1.72 - 1.90: 171 1.90 - 2.08: 12 Bond restraints: 27932 Sorted by residual: bond pdb=" C4 AGS F1002 " pdb=" C5 AGS F1002 " ideal model delta sigma weight residual 1.386 1.477 -0.091 1.00e-02 1.00e+04 8.28e+01 bond pdb=" C4 AGS A1001 " pdb=" C5 AGS A1001 " ideal model delta sigma weight residual 1.386 1.473 -0.087 1.00e-02 1.00e+04 7.50e+01 bond pdb=" C5 AGS C1002 " pdb=" N7 AGS C1002 " ideal model delta sigma weight residual 1.387 1.302 0.085 1.00e-02 1.00e+04 7.27e+01 bond pdb=" CB LEU F 383 " pdb=" CG LEU F 383 " ideal model delta sigma weight residual 1.530 1.360 0.170 2.00e-02 2.50e+03 7.24e+01 bond pdb=" C4 AGS A1002 " pdb=" C5 AGS A1002 " ideal model delta sigma weight residual 1.386 1.468 -0.082 1.00e-02 1.00e+04 6.75e+01 ... (remaining 27927 not shown) Histogram of bond angle deviations from ideal: 91.43 - 100.65: 82 100.65 - 109.86: 6714 109.86 - 119.08: 17304 119.08 - 128.30: 13482 128.30 - 137.51: 98 Bond angle restraints: 37680 Sorted by residual: angle pdb=" C5 AGS E1001 " pdb=" C4 AGS E1001 " pdb=" N3 AGS E1001 " ideal model delta sigma weight residual 126.80 117.37 9.43 7.41e-01 1.82e+00 1.62e+02 angle pdb=" N ASP D 799 " pdb=" CA ASP D 799 " pdb=" C ASP D 799 " ideal model delta sigma weight residual 113.41 97.95 15.46 1.22e+00 6.72e-01 1.61e+02 angle pdb=" N ASN B 882 " pdb=" CA ASN B 882 " pdb=" C ASN B 882 " ideal model delta sigma weight residual 113.88 98.57 15.31 1.23e+00 6.61e-01 1.55e+02 angle pdb=" N ASP E 799 " pdb=" CA ASP E 799 " pdb=" C ASP E 799 " ideal model delta sigma weight residual 113.88 98.67 15.21 1.23e+00 6.61e-01 1.53e+02 angle pdb=" C5 AGS F1002 " pdb=" C4 AGS F1002 " pdb=" N3 AGS F1002 " ideal model delta sigma weight residual 126.80 117.65 9.15 7.41e-01 1.82e+00 1.53e+02 ... (remaining 37675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.06: 16939 30.06 - 60.11: 381 60.11 - 90.17: 51 90.17 - 120.22: 0 120.22 - 150.28: 1 Dihedral angle restraints: 17372 sinusoidal: 7295 harmonic: 10077 Sorted by residual: dihedral pdb=" CB CYS F 718 " pdb=" SG CYS F 718 " pdb=" SG CYS F 721 " pdb=" CB CYS F 721 " ideal model delta sinusoidal sigma weight residual 93.00 40.15 52.85 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CA LYS A 302 " pdb=" C LYS A 302 " pdb=" N PRO A 303 " pdb=" CA PRO A 303 " ideal model delta harmonic sigma weight residual -180.00 -156.26 -23.74 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLU E 274 " pdb=" C GLU E 274 " pdb=" N SER E 275 " pdb=" CA SER E 275 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 17369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 3159 0.108 - 0.215: 1013 0.215 - 0.323: 177 0.323 - 0.430: 16 0.430 - 0.538: 3 Chirality restraints: 4368 Sorted by residual: chirality pdb=" CG LEU C 700 " pdb=" CB LEU C 700 " pdb=" CD1 LEU C 700 " pdb=" CD2 LEU C 700 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.23e+00 chirality pdb=" CB ILE F 216 " pdb=" CA ILE F 216 " pdb=" CG1 ILE F 216 " pdb=" CG2 ILE F 216 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CB VAL D 695 " pdb=" CA VAL D 695 " pdb=" CG1 VAL D 695 " pdb=" CG2 VAL D 695 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.45 2.00e-01 2.50e+01 5.16e+00 ... (remaining 4365 not shown) Planarity restraints: 4817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 680 " -0.073 2.00e-02 2.50e+03 3.92e-02 3.08e+01 pdb=" CG TYR F 680 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR F 680 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR F 680 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR F 680 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR F 680 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR F 680 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR F 680 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 302 " -0.089 5.00e-02 4.00e+02 1.36e-01 2.94e+01 pdb=" N PRO A 303 " 0.234 5.00e-02 4.00e+02 pdb=" CA PRO A 303 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO A 303 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 650 " 0.066 2.00e-02 2.50e+03 3.36e-02 2.25e+01 pdb=" CG TYR E 650 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR E 650 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR E 650 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR E 650 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR E 650 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR E 650 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 650 " 0.044 2.00e-02 2.50e+03 ... (remaining 4814 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 24 1.94 - 2.68: 2119 2.68 - 3.42: 42067 3.42 - 4.16: 72226 4.16 - 4.90: 125803 Nonbonded interactions: 242239 Sorted by model distance: nonbonded pdb=" OE2 GLU C 326 " pdb=" OE1 GLN D 712 " model vdw 1.198 3.040 nonbonded pdb=" NZ LYS C 205 " pdb=" NH1 ARG C 333 " model vdw 1.355 3.200 nonbonded pdb=" OE2 GLU C 326 " pdb=" CD GLN D 712 " model vdw 1.356 3.270 nonbonded pdb=" CE2 TYR E 665 " pdb=" NE2 GLN E 712 " model vdw 1.386 3.420 nonbonded pdb=" CE2 TYR E 662 " pdb=" OH TYR F 650 " model vdw 1.400 3.340 ... (remaining 242234 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 165 through 656 or resid 672 through 884 or resid 1001 thr \ ough 1002)) selection = (chain 'B' and (resid 165 through 656 or resid 672 through 884 or resid 1001 thr \ ough 1002)) selection = (chain 'C' and (resid 165 through 656 or resid 672 through 884 or resid 1001 thr \ ough 1002)) selection = (chain 'D' and (resid 165 through 656 or resid 672 through 884 or resid 1001 thr \ ough 1002)) selection = (chain 'E' and (resid 165 through 656 or resid 672 through 884 or resid 1001 thr \ ough 1002)) 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: 1.080 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: 5.110 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 72.530 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.120 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 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 0.179 27932 Z= 1.558 Angle : 1.940 18.420 37680 Z= 1.315 Chirality : 0.104 0.538 4368 Planarity : 0.010 0.136 4817 Dihedral : 12.364 150.281 10845 Min Nonbonded Distance : 1.198 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.96 % Allowed : 3.77 % Favored : 95.26 % Rotamer: Outliers : 0.94 % Allowed : 0.81 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3421 helix: -0.60 (0.11), residues: 1760 sheet: 0.38 (0.25), residues: 358 loop : -0.20 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.003 HIS E 363 PHE 0.040 0.007 PHE A 685 TYR 0.073 0.009 TYR F 680 ARG 0.012 0.001 ARG D 595 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1184 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1156 time to evaluate : 3.624 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 206 SER cc_start: 0.9386 (m) cc_final: 0.8772 (p) REVERT: A 216 ILE cc_start: 0.8662 (pt) cc_final: 0.8454 (mt) REVERT: A 352 LEU cc_start: 0.8439 (mt) cc_final: 0.8150 (mp) REVERT: B 238 LEU cc_start: 0.8348 (mt) cc_final: 0.8110 (mt) REVERT: B 320 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7137 (mt-10) REVERT: B 580 VAL cc_start: 0.8397 (t) cc_final: 0.7950 (p) REVERT: B 791 ILE cc_start: 0.7953 (mm) cc_final: 0.7643 (mm) REVERT: C 271 GLU cc_start: 0.6042 (tt0) cc_final: 0.5758 (tm-30) REVERT: C 280 VAL cc_start: 0.8614 (t) cc_final: 0.8269 (m) REVERT: C 310 LEU cc_start: 0.7109 (mt) cc_final: 0.6635 (mt) REVERT: C 349 VAL cc_start: 0.9105 (t) cc_final: 0.8877 (t) REVERT: C 547 SER cc_start: 0.8828 (m) cc_final: 0.8619 (t) REVERT: C 680 TYR cc_start: 0.7655 (OUTLIER) cc_final: 0.7080 (p90) REVERT: C 765 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7760 (mtt-85) REVERT: D 183 LEU cc_start: 0.7379 (mt) cc_final: 0.6637 (mt) REVERT: D 269 LEU cc_start: 0.8373 (mt) cc_final: 0.8010 (tp) REVERT: D 271 GLU cc_start: 0.6471 (tt0) cc_final: 0.6042 (tp30) REVERT: D 310 LEU cc_start: 0.8552 (mt) cc_final: 0.8031 (mt) REVERT: D 333 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6961 (ttp-110) REVERT: D 626 LYS cc_start: 0.8608 (mmtt) cc_final: 0.8100 (mmmt) REVERT: D 686 ASP cc_start: 0.7380 (m-30) cc_final: 0.7177 (m-30) REVERT: D 727 SER cc_start: 0.8332 (t) cc_final: 0.7778 (t) REVERT: D 746 THR cc_start: 0.8202 (m) cc_final: 0.7895 (m) REVERT: D 783 ILE cc_start: 0.8749 (mt) cc_final: 0.8524 (mt) REVERT: E 238 LEU cc_start: 0.6015 (pt) cc_final: 0.5684 (tp) REVERT: E 348 THR cc_start: 0.7797 (m) cc_final: 0.7544 (m) REVERT: E 359 TYR cc_start: 0.8072 (m-80) cc_final: 0.7609 (m-10) REVERT: E 578 SER cc_start: 0.8169 (p) cc_final: 0.7759 (t) REVERT: E 587 ILE cc_start: 0.8554 (mt) cc_final: 0.7884 (mt) REVERT: E 708 ILE cc_start: 0.7631 (mm) cc_final: 0.7116 (tt) REVERT: E 826 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8248 (mmt180) REVERT: F 174 MET cc_start: 0.6244 (mmm) cc_final: 0.5770 (tpp) REVERT: F 216 ILE cc_start: 0.5154 (tt) cc_final: 0.4424 (tt) REVERT: F 310 LEU cc_start: 0.7852 (tp) cc_final: 0.7523 (tt) REVERT: F 361 ILE cc_start: 0.7177 (mt) cc_final: 0.6935 (mt) REVERT: F 615 LEU cc_start: 0.7599 (mt) cc_final: 0.7360 (mt) outliers start: 28 outliers final: 18 residues processed: 1178 average time/residue: 0.4850 time to fit residues: 841.4642 Evaluate side-chains 630 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 608 time to evaluate : 3.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 643 CYS Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 680 TYR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 826 ARG Chi-restraints excluded: chain F residue 334 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 6.9990 chunk 259 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 175 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 347 GLN A 538 GLN ** A 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN B 377 GLN ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 743 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 HIS ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 HIS ** D 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 781 HIS ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 HIS E 764 ASN F 177 GLN ** F 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 27932 Z= 0.320 Angle : 0.837 10.625 37680 Z= 0.443 Chirality : 0.050 0.272 4368 Planarity : 0.006 0.103 4817 Dihedral : 11.515 143.947 4068 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.38 % Favored : 94.24 % Rotamer: Outliers : 4.04 % Allowed : 12.21 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.21 % 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: -0.44 (0.14), residues: 3421 helix: -0.06 (0.12), residues: 1798 sheet: -0.03 (0.25), residues: 387 loop : -0.49 (0.19), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS B 692 PHE 0.032 0.003 PHE E 630 TYR 0.032 0.002 TYR C 677 ARG 0.009 0.001 ARG E 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 754 time to evaluate : 3.056 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 202 ARG cc_start: 0.7940 (mtp180) cc_final: 0.7700 (mtp-110) REVERT: A 287 HIS cc_start: 0.7037 (p-80) cc_final: 0.5258 (p-80) REVERT: A 325 VAL cc_start: 0.7766 (p) cc_final: 0.6868 (p) REVERT: A 638 MET cc_start: 0.7538 (tpp) cc_final: 0.6621 (ttp) REVERT: A 831 LEU cc_start: 0.5293 (mt) cc_final: 0.5093 (mt) REVERT: B 183 LEU cc_start: 0.7783 (pt) cc_final: 0.7550 (pp) REVERT: B 192 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7761 (mm-30) REVERT: B 243 LEU cc_start: 0.9115 (tp) cc_final: 0.8878 (tt) REVERT: B 333 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8236 (ttp80) REVERT: B 355 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8206 (tp) REVERT: B 580 VAL cc_start: 0.8267 (t) cc_final: 0.7959 (p) REVERT: B 605 ARG cc_start: 0.6351 (mtp180) cc_final: 0.6016 (mtp180) REVERT: B 692 HIS cc_start: 0.7339 (t-90) cc_final: 0.6985 (t-90) REVERT: C 200 LEU cc_start: 0.9234 (mt) cc_final: 0.8890 (mt) REVERT: C 280 VAL cc_start: 0.8774 (t) cc_final: 0.8335 (m) REVERT: C 363 HIS cc_start: 0.6798 (m170) cc_final: 0.6440 (m170) REVERT: C 382 TYR cc_start: 0.8100 (m-10) cc_final: 0.7784 (m-10) REVERT: C 680 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.7360 (p90) REVERT: D 183 LEU cc_start: 0.7968 (mt) cc_final: 0.7709 (mt) REVERT: D 192 GLU cc_start: 0.7385 (mp0) cc_final: 0.6354 (mp0) REVERT: D 310 LEU cc_start: 0.8724 (mt) cc_final: 0.7981 (mt) REVERT: D 333 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7310 (ttp-170) REVERT: D 368 LEU cc_start: 0.8939 (tp) cc_final: 0.8738 (tp) REVERT: D 626 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8566 (mmmt) REVERT: D 720 ASN cc_start: 0.8118 (t0) cc_final: 0.7772 (t0) REVERT: D 766 ILE cc_start: 0.8904 (mm) cc_final: 0.8485 (tp) REVERT: D 795 PHE cc_start: 0.6494 (m-10) cc_final: 0.6137 (m-10) REVERT: E 183 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6667 (mm) REVERT: E 290 MET cc_start: 0.6777 (mmp) cc_final: 0.6530 (mmp) REVERT: E 578 SER cc_start: 0.7814 (p) cc_final: 0.7204 (t) REVERT: E 587 ILE cc_start: 0.8204 (mt) cc_final: 0.7727 (mt) REVERT: E 591 SER cc_start: 0.8276 (m) cc_final: 0.7227 (m) REVERT: E 637 MET cc_start: 0.5976 (tpp) cc_final: 0.5196 (tpp) REVERT: E 708 ILE cc_start: 0.7766 (mm) cc_final: 0.7544 (tt) REVERT: E 720 ASN cc_start: 0.8006 (OUTLIER) cc_final: 0.7424 (t0) REVERT: E 838 ASN cc_start: 0.7470 (m-40) cc_final: 0.7153 (m110) REVERT: F 338 ILE cc_start: 0.7974 (mt) cc_final: 0.7694 (mt) REVERT: F 801 HIS cc_start: 0.6289 (OUTLIER) cc_final: 0.5805 (m-70) outliers start: 120 outliers final: 70 residues processed: 829 average time/residue: 0.4193 time to fit residues: 534.0050 Evaluate side-chains 646 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 569 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 261 PHE Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 720 ASN Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 560 LYS Chi-restraints excluded: chain C residue 643 CYS Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 777 ARG Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 680 TYR Chi-restraints excluded: chain D residue 765 ARG Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 697 THR Chi-restraints excluded: chain E residue 703 LEU Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 762 PHE Chi-restraints excluded: chain F residue 801 HIS Chi-restraints excluded: chain F residue 857 VAL Chi-restraints excluded: chain F residue 877 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 173 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 259 optimal weight: 7.9990 chunk 212 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 312 optimal weight: 0.0870 chunk 337 optimal weight: 0.9980 chunk 277 optimal weight: 1.9990 chunk 309 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** A 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS C 363 HIS ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 HIS ** D 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 743 GLN E 347 GLN E 808 GLN F 728 ASN F 737 GLN F 756 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27932 Z= 0.245 Angle : 0.736 10.794 37680 Z= 0.380 Chirality : 0.047 0.350 4368 Planarity : 0.005 0.092 4817 Dihedral : 10.778 142.190 4041 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.17 % Favored : 94.45 % Rotamer: Outliers : 4.51 % Allowed : 15.78 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.15 % 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: -0.53 (0.14), residues: 3421 helix: 0.05 (0.12), residues: 1779 sheet: -0.30 (0.24), residues: 390 loop : -0.76 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.028 0.002 HIS A 781 PHE 0.034 0.002 PHE E 685 TYR 0.037 0.002 TYR C 170 ARG 0.009 0.001 ARG C 334 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 672 time to evaluate : 3.389 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 167 LEU cc_start: 0.8010 (mm) cc_final: 0.7761 (mm) REVERT: A 274 GLU cc_start: 0.5260 (OUTLIER) cc_final: 0.5034 (pp20) REVERT: A 325 VAL cc_start: 0.7810 (p) cc_final: 0.6908 (p) REVERT: A 612 PHE cc_start: 0.6465 (t80) cc_final: 0.6111 (t80) REVERT: A 833 GLN cc_start: 0.6171 (OUTLIER) cc_final: 0.4859 (mp10) REVERT: B 183 LEU cc_start: 0.7505 (pt) cc_final: 0.7247 (pp) REVERT: B 243 LEU cc_start: 0.9122 (tp) cc_final: 0.8919 (tt) REVERT: B 580 VAL cc_start: 0.8314 (t) cc_final: 0.7931 (p) REVERT: B 705 ASP cc_start: 0.7005 (m-30) cc_final: 0.6730 (m-30) REVERT: B 762 PHE cc_start: 0.8963 (t80) cc_final: 0.8711 (t80) REVERT: B 840 LEU cc_start: 0.7651 (tp) cc_final: 0.7324 (tt) REVERT: C 200 LEU cc_start: 0.9233 (mt) cc_final: 0.9031 (mt) REVERT: C 280 VAL cc_start: 0.8673 (t) cc_final: 0.8295 (m) REVERT: D 183 LEU cc_start: 0.8066 (mt) cc_final: 0.7789 (mt) REVERT: D 210 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8748 (mp) REVERT: D 699 MET cc_start: 0.6825 (tpp) cc_final: 0.6569 (tpp) REVERT: D 720 ASN cc_start: 0.8293 (t0) cc_final: 0.7964 (t0) REVERT: E 174 MET cc_start: 0.6913 (mmm) cc_final: 0.6255 (mmm) REVERT: E 578 SER cc_start: 0.7751 (p) cc_final: 0.7482 (t) REVERT: E 591 SER cc_start: 0.8707 (m) cc_final: 0.7721 (m) REVERT: E 708 ILE cc_start: 0.7686 (mm) cc_final: 0.7291 (tt) REVERT: E 838 ASN cc_start: 0.7101 (m-40) cc_final: 0.6871 (m-40) REVERT: F 221 ILE cc_start: 0.6444 (mt) cc_final: 0.6149 (mt) REVERT: F 338 ILE cc_start: 0.8065 (mt) cc_final: 0.7808 (mt) REVERT: F 615 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7030 (pt) outliers start: 134 outliers final: 82 residues processed: 754 average time/residue: 0.3971 time to fit residues: 469.2343 Evaluate side-chains 628 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 542 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 720 ASN Chi-restraints excluded: chain B residue 802 TYR Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 618 SER Chi-restraints excluded: chain C residue 638 MET Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 777 ARG Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 680 TYR Chi-restraints excluded: chain D residue 686 ASP Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 765 ARG Chi-restraints excluded: chain D residue 773 ASN Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 697 THR Chi-restraints excluded: chain E residue 703 LEU Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 697 THR Chi-restraints excluded: chain F residue 803 LYS Chi-restraints excluded: chain F residue 857 VAL Chi-restraints excluded: chain F residue 877 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 308 optimal weight: 2.9990 chunk 234 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 313 optimal weight: 10.0000 chunk 331 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 296 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 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 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 ASN A 728 ASN A 781 HIS ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 HIS ** D 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 737 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 27932 Z= 0.308 Angle : 0.734 10.493 37680 Z= 0.376 Chirality : 0.047 0.237 4368 Planarity : 0.005 0.083 4817 Dihedral : 10.627 142.621 4031 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.73 % Favored : 93.86 % Rotamer: Outliers : 4.54 % Allowed : 17.22 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.12 % 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 (0.14), residues: 3421 helix: 0.09 (0.12), residues: 1785 sheet: -0.41 (0.24), residues: 403 loop : -0.85 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.002 HIS B 692 PHE 0.026 0.002 PHE A 630 TYR 0.028 0.002 TYR A 680 ARG 0.007 0.001 ARG D 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 593 time to evaluate : 3.050 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 167 LEU cc_start: 0.8184 (mm) cc_final: 0.7935 (mm) REVERT: A 173 ASP cc_start: 0.6680 (t70) cc_final: 0.6162 (t0) REVERT: A 274 GLU cc_start: 0.5312 (OUTLIER) cc_final: 0.5088 (pp20) REVERT: A 833 GLN cc_start: 0.6141 (OUTLIER) cc_final: 0.4761 (mp10) REVERT: B 223 GLU cc_start: 0.6612 (mt-10) cc_final: 0.6377 (mt-10) REVERT: B 243 LEU cc_start: 0.9118 (tp) cc_final: 0.8862 (tt) REVERT: B 584 MET cc_start: 0.7859 (mmm) cc_final: 0.7466 (mmm) REVERT: B 707 ARG cc_start: 0.7261 (ttm110) cc_final: 0.7014 (ttm110) REVERT: B 883 HIS cc_start: 0.1420 (OUTLIER) cc_final: -0.0836 (m90) REVERT: C 200 LEU cc_start: 0.9260 (mt) cc_final: 0.9014 (mt) REVERT: C 280 VAL cc_start: 0.8764 (t) cc_final: 0.8442 (m) REVERT: C 333 ARG cc_start: 0.8147 (tmm160) cc_final: 0.7043 (tmm160) REVERT: C 385 TYR cc_start: 0.7553 (m-10) cc_final: 0.7261 (m-80) REVERT: C 394 ASP cc_start: 0.7827 (t0) cc_final: 0.7600 (t0) REVERT: C 579 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7126 (mm-30) REVERT: C 649 LYS cc_start: 0.6003 (tttt) cc_final: 0.5622 (mtpt) REVERT: C 680 TYR cc_start: 0.7820 (OUTLIER) cc_final: 0.7087 (p90) REVERT: C 712 GLN cc_start: 0.6499 (pt0) cc_final: 0.6293 (pt0) REVERT: D 192 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6863 (mp0) REVERT: D 305 LEU cc_start: 0.8534 (mp) cc_final: 0.8282 (mp) REVERT: D 333 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7651 (ttp-170) REVERT: D 391 SER cc_start: 0.8457 (m) cc_final: 0.8238 (m) REVERT: D 727 SER cc_start: 0.8787 (t) cc_final: 0.8584 (t) REVERT: E 174 MET cc_start: 0.7040 (mmm) cc_final: 0.6688 (mmm) REVERT: E 177 GLN cc_start: 0.6371 (tt0) cc_final: 0.6168 (tt0) REVERT: E 192 GLU cc_start: 0.4835 (mp0) cc_final: 0.3920 (mp0) REVERT: E 578 SER cc_start: 0.8067 (p) cc_final: 0.7654 (t) REVERT: E 763 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.6483 (tp) REVERT: E 838 ASN cc_start: 0.7117 (m-40) cc_final: 0.6728 (m-40) REVERT: F 208 PRO cc_start: 0.8688 (Cg_exo) cc_final: 0.8460 (Cg_endo) REVERT: F 221 ILE cc_start: 0.6290 (mt) cc_final: 0.5985 (mt) REVERT: F 338 ILE cc_start: 0.8018 (mt) cc_final: 0.7750 (mt) REVERT: F 538 GLN cc_start: 0.2822 (mm-40) cc_final: 0.2399 (tp-100) REVERT: F 620 LYS cc_start: 0.6700 (ttmt) cc_final: 0.6473 (ttmm) outliers start: 135 outliers final: 95 residues processed: 678 average time/residue: 0.3885 time to fit residues: 415.4496 Evaluate side-chains 624 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 523 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 720 ASN Chi-restraints excluded: chain B residue 802 TYR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 618 SER Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 638 MET Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 694 ASP Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 686 ASP Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 773 ASN Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 573 GLU Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 688 VAL Chi-restraints excluded: chain E residue 703 LEU Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 697 THR Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 770 VAL Chi-restraints excluded: chain F residue 857 VAL Chi-restraints excluded: chain F residue 877 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 276 optimal weight: 1.9990 chunk 188 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 246 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 282 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 728 ASN A 737 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 HIS ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 HIS ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 798 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27932 Z= 0.280 Angle : 0.696 9.137 37680 Z= 0.357 Chirality : 0.046 0.216 4368 Planarity : 0.005 0.075 4817 Dihedral : 10.399 139.345 4025 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.55 % Favored : 94.04 % Rotamer: Outliers : 4.61 % Allowed : 18.87 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % 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: -0.53 (0.14), residues: 3421 helix: 0.18 (0.12), residues: 1780 sheet: -0.54 (0.24), residues: 402 loop : -0.90 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS B 692 PHE 0.023 0.002 PHE A 630 TYR 0.021 0.002 TYR B 170 ARG 0.005 0.000 ARG D 787 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 551 time to evaluate : 3.407 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 167 LEU cc_start: 0.8234 (mm) cc_final: 0.7987 (mm) REVERT: A 173 ASP cc_start: 0.6752 (t70) cc_final: 0.6343 (t0) REVERT: A 274 GLU cc_start: 0.5211 (OUTLIER) cc_final: 0.4954 (pp20) REVERT: A 613 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7228 (mt) REVERT: A 833 GLN cc_start: 0.6104 (OUTLIER) cc_final: 0.4834 (mp10) REVERT: B 243 LEU cc_start: 0.9089 (tp) cc_final: 0.8830 (tt) REVERT: B 307 ARG cc_start: 0.7438 (mmp-170) cc_final: 0.7119 (mmp-170) REVERT: B 584 MET cc_start: 0.7798 (mmm) cc_final: 0.7546 (mmm) REVERT: B 707 ARG cc_start: 0.7324 (ttm110) cc_final: 0.7092 (ttm110) REVERT: B 883 HIS cc_start: 0.1415 (OUTLIER) cc_final: -0.0799 (m90) REVERT: C 200 LEU cc_start: 0.9254 (mt) cc_final: 0.9009 (mt) REVERT: C 280 VAL cc_start: 0.8805 (t) cc_final: 0.8449 (m) REVERT: C 385 TYR cc_start: 0.7398 (m-10) cc_final: 0.7129 (m-80) REVERT: C 394 ASP cc_start: 0.7829 (t0) cc_final: 0.7600 (t0) REVERT: C 591 SER cc_start: 0.8963 (m) cc_final: 0.7684 (m) REVERT: C 680 TYR cc_start: 0.7878 (OUTLIER) cc_final: 0.7173 (p90) REVERT: D 192 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6933 (mp0) REVERT: D 666 ASP cc_start: 0.6813 (m-30) cc_final: 0.6536 (m-30) REVERT: E 262 GLU cc_start: 0.6423 (mm-30) cc_final: 0.6151 (mp0) REVERT: E 578 SER cc_start: 0.8009 (p) cc_final: 0.7649 (t) REVERT: E 838 ASN cc_start: 0.7079 (m-40) cc_final: 0.6732 (m110) REVERT: F 221 ILE cc_start: 0.6316 (mt) cc_final: 0.5961 (mt) REVERT: F 290 MET cc_start: 0.5178 (tmm) cc_final: 0.4822 (tmm) REVERT: F 538 GLN cc_start: 0.2629 (mm-40) cc_final: 0.2015 (tp40) outliers start: 137 outliers final: 94 residues processed: 636 average time/residue: 0.3783 time to fit residues: 384.7698 Evaluate side-chains 605 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 506 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 720 ASN Chi-restraints excluded: chain B residue 802 TYR Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 618 SER Chi-restraints excluded: chain C residue 638 MET Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain D residue 773 ASN Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 875 GLU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 688 VAL Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 697 THR Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 770 VAL Chi-restraints excluded: chain F residue 857 VAL Chi-restraints excluded: chain F residue 877 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 111 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 331 optimal weight: 0.9990 chunk 275 optimal weight: 0.3980 chunk 153 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 chunk 109 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 HIS C 712 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 HIS ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 773 ASN D 798 ASN D 805 ASN E 362 HIS E 738 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 27932 Z= 0.210 Angle : 0.670 12.934 37680 Z= 0.340 Chirality : 0.045 0.207 4368 Planarity : 0.004 0.070 4817 Dihedral : 9.936 133.672 4021 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.58 % Favored : 94.01 % Rotamer: Outliers : 4.10 % Allowed : 20.08 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % 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: -0.49 (0.14), residues: 3421 helix: 0.25 (0.12), residues: 1788 sheet: -0.54 (0.24), residues: 404 loop : -0.93 (0.18), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS C 287 PHE 0.028 0.002 PHE C 244 TYR 0.018 0.001 TYR E 677 ARG 0.005 0.000 ARG D 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 587 time to evaluate : 3.053 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 167 LEU cc_start: 0.8234 (mm) cc_final: 0.7976 (mm) REVERT: A 173 ASP cc_start: 0.6698 (t70) cc_final: 0.6230 (t0) REVERT: A 274 GLU cc_start: 0.5009 (OUTLIER) cc_final: 0.4725 (pp20) REVERT: A 833 GLN cc_start: 0.5892 (OUTLIER) cc_final: 0.4645 (mp10) REVERT: B 243 LEU cc_start: 0.8992 (tp) cc_final: 0.8765 (tt) REVERT: B 584 MET cc_start: 0.7608 (mmm) cc_final: 0.7389 (mmm) REVERT: B 670 PHE cc_start: 0.7407 (m-10) cc_final: 0.6901 (m-10) REVERT: B 699 MET cc_start: 0.6258 (ttt) cc_final: 0.5442 (ttt) REVERT: B 883 HIS cc_start: 0.1280 (OUTLIER) cc_final: -0.0865 (m90) REVERT: C 200 LEU cc_start: 0.9186 (mt) cc_final: 0.8972 (mt) REVERT: C 280 VAL cc_start: 0.8734 (t) cc_final: 0.8392 (m) REVERT: C 336 GLN cc_start: 0.8272 (tp40) cc_final: 0.8050 (tp40) REVERT: C 394 ASP cc_start: 0.7858 (t0) cc_final: 0.7584 (t0) REVERT: C 572 MET cc_start: 0.6915 (ppp) cc_final: 0.6510 (ppp) REVERT: C 649 LYS cc_start: 0.5701 (tttt) cc_final: 0.5391 (mtpt) REVERT: C 680 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.6922 (p90) REVERT: D 192 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6784 (mp0) REVERT: D 305 LEU cc_start: 0.8479 (mp) cc_final: 0.8246 (mp) REVERT: D 572 MET cc_start: 0.8132 (ttp) cc_final: 0.7716 (ttt) REVERT: D 666 ASP cc_start: 0.6771 (m-30) cc_final: 0.6470 (m-30) REVERT: D 801 HIS cc_start: 0.5744 (p-80) cc_final: 0.4799 (p-80) REVERT: D 826 ARG cc_start: 0.8229 (mtt-85) cc_final: 0.7852 (mtt-85) REVERT: E 203 ARG cc_start: 0.7241 (tpp-160) cc_final: 0.6599 (tpp80) REVERT: E 572 MET cc_start: 0.7757 (ppp) cc_final: 0.7244 (ppp) REVERT: E 578 SER cc_start: 0.7974 (p) cc_final: 0.7520 (t) REVERT: E 689 GLU cc_start: 0.7609 (pm20) cc_final: 0.6979 (mp0) REVERT: E 758 PHE cc_start: 0.7159 (m-80) cc_final: 0.6876 (m-10) REVERT: E 763 LEU cc_start: 0.7137 (mt) cc_final: 0.6423 (tp) REVERT: E 838 ASN cc_start: 0.6941 (m-40) cc_final: 0.6475 (m-40) REVERT: F 221 ILE cc_start: 0.6242 (mt) cc_final: 0.6005 (mt) REVERT: F 290 MET cc_start: 0.5154 (tmm) cc_final: 0.4932 (tmm) REVERT: F 538 GLN cc_start: 0.2619 (mm-40) cc_final: 0.2028 (tp40) REVERT: F 638 MET cc_start: 0.6389 (pp-130) cc_final: 0.5855 (pp-130) REVERT: F 737 GLN cc_start: 0.4746 (mp-120) cc_final: 0.4438 (mp-120) outliers start: 122 outliers final: 86 residues processed: 660 average time/residue: 0.3707 time to fit residues: 391.8659 Evaluate side-chains 611 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 521 time to evaluate : 3.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 720 ASN Chi-restraints excluded: chain B residue 802 TYR Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 618 SER Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 741 LYS Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain D residue 773 ASN Chi-restraints excluded: chain D residue 798 ASN Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 875 GLU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 688 VAL Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 697 THR Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 770 VAL Chi-restraints excluded: chain F residue 857 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 319 optimal weight: 0.0980 chunk 37 optimal weight: 3.9990 chunk 189 optimal weight: 0.6980 chunk 242 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 chunk 279 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 330 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 152 optimal weight: 0.6980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 712 GLN C 781 HIS ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.6448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 27932 Z= 0.282 Angle : 0.702 11.303 37680 Z= 0.356 Chirality : 0.047 0.347 4368 Planarity : 0.004 0.069 4817 Dihedral : 9.832 131.370 4019 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.85 % Favored : 93.80 % Rotamer: Outliers : 4.57 % Allowed : 21.12 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % 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: -0.54 (0.14), residues: 3421 helix: 0.24 (0.12), residues: 1793 sheet: -0.59 (0.24), residues: 411 loop : -1.01 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS C 287 PHE 0.029 0.002 PHE B 265 TYR 0.023 0.002 TYR E 677 ARG 0.007 0.001 ARG D 759 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 553 time to evaluate : 5.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8182 (mm) cc_final: 0.7905 (mm) REVERT: A 237 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8545 (mt) REVERT: A 720 ASN cc_start: 0.6880 (OUTLIER) cc_final: 0.6635 (t0) REVERT: A 833 GLN cc_start: 0.6030 (OUTLIER) cc_final: 0.4846 (mp10) REVERT: B 243 LEU cc_start: 0.8986 (tp) cc_final: 0.8683 (tt) REVERT: B 638 MET cc_start: 0.7148 (ttm) cc_final: 0.6805 (ttp) REVERT: B 883 HIS cc_start: 0.1255 (OUTLIER) cc_final: -0.0872 (m90) REVERT: C 200 LEU cc_start: 0.9264 (mt) cc_final: 0.8973 (mt) REVERT: C 280 VAL cc_start: 0.8849 (t) cc_final: 0.8473 (m) REVERT: C 385 TYR cc_start: 0.7456 (m-10) cc_final: 0.7113 (m-80) REVERT: C 394 ASP cc_start: 0.7873 (t0) cc_final: 0.7572 (t0) REVERT: C 639 ILE cc_start: 0.8577 (mt) cc_final: 0.8092 (mt) REVERT: C 665 TYR cc_start: 0.6516 (OUTLIER) cc_final: 0.5584 (m-80) REVERT: C 680 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7143 (p90) REVERT: C 684 LEU cc_start: 0.8760 (tp) cc_final: 0.8542 (tt) REVERT: D 192 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6885 (mp0) REVERT: D 282 PHE cc_start: 0.8820 (t80) cc_final: 0.8536 (t80) REVERT: D 598 ARG cc_start: 0.6727 (tmt170) cc_final: 0.6413 (tpt-90) REVERT: D 666 ASP cc_start: 0.6848 (m-30) cc_final: 0.6595 (m-30) REVERT: D 690 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7634 (mttt) REVERT: D 727 SER cc_start: 0.9124 (t) cc_final: 0.8904 (m) REVERT: D 801 HIS cc_start: 0.5761 (p-80) cc_final: 0.4626 (p-80) REVERT: D 826 ARG cc_start: 0.8353 (mtt-85) cc_final: 0.8124 (mtt-85) REVERT: E 203 ARG cc_start: 0.7326 (tpp-160) cc_final: 0.6644 (tpp80) REVERT: E 328 ASP cc_start: 0.4479 (t70) cc_final: 0.4022 (m-30) REVERT: E 331 PHE cc_start: 0.6582 (m-80) cc_final: 0.5936 (m-80) REVERT: E 572 MET cc_start: 0.7852 (ppp) cc_final: 0.7187 (ppp) REVERT: E 578 SER cc_start: 0.8058 (p) cc_final: 0.7483 (t) REVERT: E 689 GLU cc_start: 0.7771 (pm20) cc_final: 0.7550 (pm20) REVERT: E 763 LEU cc_start: 0.7297 (mt) cc_final: 0.6334 (tp) REVERT: F 221 ILE cc_start: 0.6342 (mt) cc_final: 0.5906 (mt) REVERT: F 290 MET cc_start: 0.5152 (tmm) cc_final: 0.4903 (tmm) REVERT: F 338 ILE cc_start: 0.7741 (mt) cc_final: 0.7535 (mt) REVERT: F 538 GLN cc_start: 0.2594 (mm-40) cc_final: 0.1963 (tp40) REVERT: F 638 MET cc_start: 0.6431 (pp-130) cc_final: 0.5843 (pp-130) REVERT: F 808 GLN cc_start: 0.5663 (mm-40) cc_final: 0.4587 (mm-40) REVERT: F 817 TYR cc_start: 0.5562 (m-80) cc_final: 0.5259 (m-10) outliers start: 136 outliers final: 101 residues processed: 636 average time/residue: 0.4122 time to fit residues: 424.8444 Evaluate side-chains 618 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 510 time to evaluate : 3.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 720 ASN Chi-restraints excluded: chain B residue 802 TYR Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 618 SER Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 643 CYS Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 690 LYS Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 875 GLU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 573 GLU Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 672 THR Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 806 LEU Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 697 THR Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 770 VAL Chi-restraints excluded: chain F residue 857 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 204 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 197 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 259 optimal weight: 0.9990 chunk 300 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 HIS C 781 HIS D 309 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 798 ASN ** F 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 757 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.6664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 27932 Z= 0.229 Angle : 0.696 15.172 37680 Z= 0.350 Chirality : 0.045 0.303 4368 Planarity : 0.004 0.067 4817 Dihedral : 9.666 125.468 4019 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.96 % Favored : 93.69 % Rotamer: Outliers : 3.97 % Allowed : 22.64 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % 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: -0.54 (0.14), residues: 3421 helix: 0.25 (0.12), residues: 1784 sheet: -0.58 (0.25), residues: 393 loop : -1.03 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS B 287 PHE 0.047 0.002 PHE B 265 TYR 0.024 0.001 TYR C 170 ARG 0.007 0.000 ARG D 759 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 554 time to evaluate : 3.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8029 (mm) cc_final: 0.7815 (mm) REVERT: A 638 MET cc_start: 0.7769 (tpp) cc_final: 0.7480 (tpp) REVERT: A 720 ASN cc_start: 0.6846 (OUTLIER) cc_final: 0.6601 (t0) REVERT: A 833 GLN cc_start: 0.5407 (OUTLIER) cc_final: 0.3808 (mt0) REVERT: B 243 LEU cc_start: 0.8967 (tp) cc_final: 0.8634 (tt) REVERT: B 883 HIS cc_start: 0.1200 (OUTLIER) cc_final: -0.0859 (m90) REVERT: C 200 LEU cc_start: 0.9210 (mt) cc_final: 0.8939 (mt) REVERT: C 638 MET cc_start: 0.8341 (ppp) cc_final: 0.8140 (tmm) REVERT: C 665 TYR cc_start: 0.6255 (OUTLIER) cc_final: 0.5525 (m-80) REVERT: D 192 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6734 (mp0) REVERT: D 282 PHE cc_start: 0.8808 (t80) cc_final: 0.8575 (t80) REVERT: D 307 ARG cc_start: 0.6783 (mmp80) cc_final: 0.6396 (mmp80) REVERT: D 598 ARG cc_start: 0.6714 (tmt170) cc_final: 0.6377 (tpt-90) REVERT: D 626 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8607 (mmmt) REVERT: D 666 ASP cc_start: 0.6901 (m-30) cc_final: 0.6631 (m-30) REVERT: D 690 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7578 (mttm) REVERT: D 699 MET cc_start: 0.7007 (tpp) cc_final: 0.6792 (tpp) REVERT: D 725 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.7039 (mtp) REVERT: D 727 SER cc_start: 0.9229 (t) cc_final: 0.8966 (m) REVERT: D 801 HIS cc_start: 0.5500 (p-80) cc_final: 0.4373 (p-80) REVERT: E 203 ARG cc_start: 0.7291 (tpp-160) cc_final: 0.6760 (tpp80) REVERT: E 328 ASP cc_start: 0.4566 (t70) cc_final: 0.4188 (m-30) REVERT: E 331 PHE cc_start: 0.6598 (m-80) cc_final: 0.6173 (m-80) REVERT: E 572 MET cc_start: 0.7592 (ppp) cc_final: 0.7083 (ppp) REVERT: E 578 SER cc_start: 0.8072 (p) cc_final: 0.7577 (t) REVERT: E 763 LEU cc_start: 0.7159 (mt) cc_final: 0.6399 (tp) REVERT: E 838 ASN cc_start: 0.6973 (m-40) cc_final: 0.6644 (m110) REVERT: F 221 ILE cc_start: 0.6205 (mt) cc_final: 0.5857 (mt) REVERT: F 538 GLN cc_start: 0.2731 (mm-40) cc_final: 0.2043 (tp40) REVERT: F 638 MET cc_start: 0.6486 (pp-130) cc_final: 0.5910 (pp-130) REVERT: F 737 GLN cc_start: 0.4801 (mp-120) cc_final: 0.4540 (mp-120) REVERT: F 817 TYR cc_start: 0.5602 (m-80) cc_final: 0.5393 (m-10) outliers start: 118 outliers final: 92 residues processed: 627 average time/residue: 0.3714 time to fit residues: 373.9743 Evaluate side-chains 611 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 513 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 720 ASN Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain B residue 802 TYR Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 618 SER Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 741 LYS Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 690 LYS Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 875 GLU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 596 LEU Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 672 THR Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 806 LEU Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 697 THR Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 770 VAL Chi-restraints excluded: chain F residue 857 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 316 optimal weight: 0.2980 chunk 288 optimal weight: 0.9990 chunk 308 optimal weight: 9.9990 chunk 185 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 241 optimal weight: 4.9990 chunk 94 optimal weight: 0.4980 chunk 278 optimal weight: 10.0000 chunk 291 optimal weight: 1.9990 chunk 306 optimal weight: 0.9990 chunk 202 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN B 362 HIS ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C 781 HIS C 801 HIS ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 798 ASN ** F 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 757 HIS ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.6858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27932 Z= 0.219 Angle : 0.714 16.122 37680 Z= 0.354 Chirality : 0.045 0.391 4368 Planarity : 0.004 0.067 4817 Dihedral : 9.557 122.365 4019 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.93 % Favored : 93.74 % Rotamer: Outliers : 3.77 % Allowed : 23.31 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % 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 (0.14), residues: 3421 helix: 0.25 (0.12), residues: 1788 sheet: -0.50 (0.25), residues: 398 loop : -1.08 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS B 287 PHE 0.051 0.002 PHE B 265 TYR 0.021 0.001 TYR C 170 ARG 0.008 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 566 time to evaluate : 3.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8067 (mm) cc_final: 0.7844 (mm) REVERT: A 216 ILE cc_start: 0.9063 (pt) cc_final: 0.8833 (mt) REVERT: A 662 TYR cc_start: 0.7599 (m-80) cc_final: 0.6812 (m-80) REVERT: A 720 ASN cc_start: 0.6943 (OUTLIER) cc_final: 0.6671 (t0) REVERT: A 833 GLN cc_start: 0.5478 (OUTLIER) cc_final: 0.3870 (mt0) REVERT: B 243 LEU cc_start: 0.8930 (tp) cc_final: 0.8644 (tt) REVERT: B 883 HIS cc_start: 0.1074 (OUTLIER) cc_final: -0.0977 (m90) REVERT: C 183 LEU cc_start: 0.7363 (mt) cc_final: 0.6552 (mt) REVERT: C 200 LEU cc_start: 0.9212 (mt) cc_final: 0.8935 (mt) REVERT: C 223 GLU cc_start: 0.6683 (mm-30) cc_final: 0.6253 (mm-30) REVERT: C 280 VAL cc_start: 0.8948 (t) cc_final: 0.8525 (m) REVERT: C 665 TYR cc_start: 0.6091 (OUTLIER) cc_final: 0.5386 (m-80) REVERT: D 192 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6863 (mp0) REVERT: D 282 PHE cc_start: 0.8799 (t80) cc_final: 0.8575 (t80) REVERT: D 307 ARG cc_start: 0.6723 (mmp80) cc_final: 0.6493 (mmp80) REVERT: D 598 ARG cc_start: 0.6652 (tmt170) cc_final: 0.6344 (tpt-90) REVERT: D 666 ASP cc_start: 0.6846 (m-30) cc_final: 0.6543 (m-30) REVERT: D 690 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7529 (mttm) REVERT: D 702 MET cc_start: 0.7788 (tmm) cc_final: 0.7580 (tmm) REVERT: D 725 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.7009 (mtp) REVERT: D 727 SER cc_start: 0.9191 (t) cc_final: 0.8949 (m) REVERT: D 761 GLU cc_start: 0.6659 (mt-10) cc_final: 0.5687 (mt-10) REVERT: D 801 HIS cc_start: 0.5672 (p-80) cc_final: 0.4354 (p-80) REVERT: E 189 ARG cc_start: 0.7728 (mmt-90) cc_final: 0.7491 (mmt180) REVERT: E 203 ARG cc_start: 0.7284 (tpp-160) cc_final: 0.6756 (tpp80) REVERT: E 328 ASP cc_start: 0.4910 (t70) cc_final: 0.4535 (m-30) REVERT: E 331 PHE cc_start: 0.6585 (m-80) cc_final: 0.6244 (m-80) REVERT: E 572 MET cc_start: 0.7570 (ppp) cc_final: 0.7247 (ppp) REVERT: E 578 SER cc_start: 0.8065 (p) cc_final: 0.7542 (t) REVERT: E 689 GLU cc_start: 0.7419 (pm20) cc_final: 0.6704 (mt-10) REVERT: E 728 ASN cc_start: 0.7217 (p0) cc_final: 0.6231 (p0) REVERT: E 763 LEU cc_start: 0.7261 (mt) cc_final: 0.6621 (tp) REVERT: E 838 ASN cc_start: 0.6882 (m-40) cc_final: 0.6604 (m110) REVERT: F 221 ILE cc_start: 0.6210 (mt) cc_final: 0.5863 (mt) REVERT: F 538 GLN cc_start: 0.2782 (mm-40) cc_final: 0.2001 (tp40) REVERT: F 638 MET cc_start: 0.6355 (pp-130) cc_final: 0.5716 (pp-130) REVERT: F 817 TYR cc_start: 0.5595 (m-80) cc_final: 0.5318 (m-10) outliers start: 112 outliers final: 92 residues processed: 634 average time/residue: 0.3819 time to fit residues: 388.2725 Evaluate side-chains 616 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 518 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 720 ASN Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain B residue 802 TYR Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 618 SER Chi-restraints excluded: chain C residue 643 CYS Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 741 LYS Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 690 LYS Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 798 ASN Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 875 GLU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 637 MET Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 672 THR Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 806 LEU Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 770 VAL Chi-restraints excluded: chain F residue 857 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 325 optimal weight: 20.0000 chunk 198 optimal weight: 3.9990 chunk 154 optimal weight: 0.0970 chunk 226 optimal weight: 2.9990 chunk 341 optimal weight: 10.0000 chunk 314 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 216 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 798 ASN ** F 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 757 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.6952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 27932 Z= 0.269 Angle : 0.754 15.581 37680 Z= 0.373 Chirality : 0.048 0.622 4368 Planarity : 0.005 0.130 4817 Dihedral : 9.600 122.017 4019 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.05 % Favored : 93.63 % Rotamer: Outliers : 3.83 % Allowed : 23.78 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % 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: -0.61 (0.14), residues: 3421 helix: 0.21 (0.12), residues: 1791 sheet: -0.53 (0.26), residues: 383 loop : -1.13 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.001 HIS C 287 PHE 0.060 0.002 PHE C 813 TYR 0.041 0.002 TYR C 817 ARG 0.022 0.001 ARG A 381 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 522 time to evaluate : 4.333 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 167 LEU cc_start: 0.8071 (mm) cc_final: 0.7838 (mm) REVERT: A 216 ILE cc_start: 0.9095 (pt) cc_final: 0.8868 (mt) REVERT: A 720 ASN cc_start: 0.6891 (OUTLIER) cc_final: 0.6566 (t0) REVERT: A 833 GLN cc_start: 0.5418 (OUTLIER) cc_final: 0.3742 (mt0) REVERT: B 243 LEU cc_start: 0.8926 (tp) cc_final: 0.8629 (tt) REVERT: B 883 HIS cc_start: 0.1081 (OUTLIER) cc_final: -0.0958 (m90) REVERT: C 200 LEU cc_start: 0.9234 (mt) cc_final: 0.8994 (mt) REVERT: C 665 TYR cc_start: 0.6331 (OUTLIER) cc_final: 0.5630 (m-80) REVERT: D 192 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6737 (mp0) REVERT: D 307 ARG cc_start: 0.7006 (mmp80) cc_final: 0.6744 (mmp80) REVERT: D 598 ARG cc_start: 0.6642 (tmt170) cc_final: 0.6338 (tpt-90) REVERT: D 666 ASP cc_start: 0.6882 (m-30) cc_final: 0.6552 (m-30) REVERT: D 727 SER cc_start: 0.9259 (t) cc_final: 0.9035 (m) REVERT: D 801 HIS cc_start: 0.5178 (p-80) cc_final: 0.4210 (p-80) REVERT: E 203 ARG cc_start: 0.7266 (tpp-160) cc_final: 0.6811 (tpp80) REVERT: E 328 ASP cc_start: 0.4936 (t70) cc_final: 0.4326 (m-30) REVERT: E 572 MET cc_start: 0.7743 (ppp) cc_final: 0.7278 (ppp) REVERT: E 578 SER cc_start: 0.8083 (p) cc_final: 0.7548 (t) REVERT: E 838 ASN cc_start: 0.7056 (m-40) cc_final: 0.6653 (m110) REVERT: F 221 ILE cc_start: 0.6137 (mt) cc_final: 0.5781 (mt) REVERT: F 538 GLN cc_start: 0.2784 (mm-40) cc_final: 0.1995 (tp40) REVERT: F 817 TYR cc_start: 0.5668 (m-80) cc_final: 0.5407 (m-10) outliers start: 114 outliers final: 100 residues processed: 592 average time/residue: 0.3773 time to fit residues: 361.9908 Evaluate side-chains 608 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 504 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 720 ASN Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain B residue 802 TYR Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 618 SER Chi-restraints excluded: chain C residue 643 CYS Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 741 LYS Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 798 ASN Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 875 GLU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 672 THR Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 806 LEU Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 770 VAL Chi-restraints excluded: chain F residue 802 TYR Chi-restraints excluded: chain F residue 857 VAL Chi-restraints excluded: chain F residue 877 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 250 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 272 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 279 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 50 optimal weight: 0.0870 chunk 239 optimal weight: 7.9990 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS E 538 GLN ** F 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 757 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.151073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.127798 restraints weight = 51556.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.129700 restraints weight = 34563.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130877 restraints weight = 23969.051| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.7116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 27932 Z= 0.216 Angle : 0.722 15.977 37680 Z= 0.361 Chirality : 0.046 0.376 4368 Planarity : 0.005 0.114 4817 Dihedral : 9.486 118.895 4019 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.05 % Favored : 93.66 % Rotamer: Outliers : 3.70 % Allowed : 23.71 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % 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: -0.53 (0.14), residues: 3421 helix: 0.25 (0.12), residues: 1777 sheet: -0.49 (0.25), residues: 394 loop : -1.04 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.001 HIS C 287 PHE 0.045 0.002 PHE C 813 TYR 0.041 0.002 TYR D 680 ARG 0.011 0.001 ARG A 381 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7460.68 seconds wall clock time: 135 minutes 7.48 seconds (8107.48 seconds total)