Starting phenix.real_space_refine on Tue Mar 19 15:37:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eou_31231/03_2024/7eou_31231_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eou_31231/03_2024/7eou_31231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eou_31231/03_2024/7eou_31231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eou_31231/03_2024/7eou_31231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eou_31231/03_2024/7eou_31231_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eou_31231/03_2024/7eou_31231_trim_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 152 5.16 5 C 15769 2.51 5 N 4118 2.21 5 O 4552 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24593 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 759, 5989 Classifications: {'peptide': 759} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 28, 'TRANS': 730} Chain breaks: 5 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 6163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6163 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 32, 'TRANS': 750} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 5989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 759, 5989 Classifications: {'peptide': 759} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 28, 'TRANS': 730} Chain breaks: 5 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 6163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6163 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 32, 'TRANS': 750} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' AA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 123 Unusual residues: {'6RM': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'6RM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 12.47, per 1000 atoms: 0.51 Number of scatterers: 24593 At special positions: 0 Unit cell: (118.8, 145.8, 183.6, 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 152 16.00 F 2 9.00 O 4552 8.00 N 4118 7.00 C 15769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 745 " - pdb=" SG CYS A 800 " distance=2.03 Simple disulfide: pdb=" SG CYS A 794 " - pdb=" SG CYS D 698 " distance=2.03 Simple disulfide: pdb=" SG CYS B 79 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 420 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 698 " - pdb=" SG CYS C 794 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 429 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 745 " - pdb=" SG CYS C 800 " distance=2.03 Simple disulfide: pdb=" SG CYS D 79 " - pdb=" SG CYS D 308 " distance=2.03 Simple disulfide: pdb=" SG CYS D 420 " - pdb=" SG CYS D 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 744 " - pdb=" SG CYS D 798 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 687 " " NAG B 901 " - " ASN B 61 " " NAG B 902 " - " ASN B 203 " " NAG B 903 " - " ASN B 239 " " NAG B 904 " - " ASN B 276 " " NAG B 905 " - " ASN B 368 " " NAG B 906 " - " ASN B 471 " " NAG B 907 " - " ASN B 771 " " NAG C 901 " - " ASN C 687 " " NAG D 901 " - " ASN D 61 " " NAG D 902 " - " ASN D 203 " " NAG D 903 " - " ASN D 239 " " NAG D 904 " - " ASN D 276 " " NAG D 905 " - " ASN D 368 " " NAG D 906 " - " ASN D 471 " " NAG D 907 " - " ASN D 771 " Time building additional restraints: 9.08 Conformation dependent library (CDL) restraints added in 3.9 seconds 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5768 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 26 sheets defined 39.3% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.41 Creating SS restraints... Processing helix chain 'A' and resid 47 through 58 Proline residue: A 57 - end of helix Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 108 through 120 Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 151 through 165 Processing helix chain 'A' and resid 180 through 191 Processing helix chain 'A' and resid 214 through 220 Processing helix chain 'A' and resid 233 through 246 removed outlier: 3.876A pdb=" N VAL A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 288 through 309 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 459 through 471 removed outlier: 3.838A pdb=" N ARG A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 501 Processing helix chain 'A' and resid 516 through 521 removed outlier: 3.999A pdb=" N GLU A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 516 through 521' Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 557 through 578 Processing helix chain 'A' and resid 600 through 612 removed outlier: 4.812A pdb=" N ILE A 605 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 654 removed outlier: 3.839A pdb=" N MET A 630 " --> pdb=" O THR A 626 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE A 654 " --> pdb=" O ALA A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 671 No H-bonds generated for 'chain 'A' and resid 668 through 671' Processing helix chain 'A' and resid 673 through 675 No H-bonds generated for 'chain 'A' and resid 673 through 675' Processing helix chain 'A' and resid 690 through 694 Processing helix chain 'A' and resid 699 through 707 removed outlier: 4.062A pdb=" N LYS A 707 " --> pdb=" O GLN A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 743 through 745 No H-bonds generated for 'chain 'A' and resid 743 through 745' Processing helix chain 'A' and resid 775 through 785 Processing helix chain 'A' and resid 789 through 795 Processing helix chain 'A' and resid 814 through 836 removed outlier: 4.130A pdb=" N MET A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU A 824 " --> pdb=" O VAL A 820 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 825 " --> pdb=" O PHE A 821 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 51 removed outlier: 3.918A pdb=" N LYS B 51 " --> pdb=" O ASN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 85 removed outlier: 4.043A pdb=" N SER B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 144 through 158 Processing helix chain 'B' and resid 171 through 187 removed outlier: 4.136A pdb=" N GLU B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ARG B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 225 through 237 removed outlier: 4.239A pdb=" N ALA B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA B 235 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 236 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 261 removed outlier: 3.545A pdb=" N LEU B 259 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 295 removed outlier: 3.721A pdb=" N GLN B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N HIS B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 327 Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 458 through 470 removed outlier: 3.585A pdb=" N LEU B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 521 through 526 removed outlier: 3.783A pdb=" N TYR B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 583 removed outlier: 3.779A pdb=" N HIS B 571 " --> pdb=" O GLY B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 615 Processing helix chain 'B' and resid 627 through 656 removed outlier: 3.585A pdb=" N ILE B 631 " --> pdb=" O PHE B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 673 No H-bonds generated for 'chain 'B' and resid 670 through 673' Processing helix chain 'B' and resid 688 through 694 Processing helix chain 'B' and resid 700 through 709 removed outlier: 3.636A pdb=" N TYR B 703 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET B 706 " --> pdb=" O TYR B 703 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N GLU B 707 " --> pdb=" O ARG B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 722 Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 770 through 781 Processing helix chain 'B' and resid 784 through 792 Processing helix chain 'B' and resid 811 through 842 removed outlier: 4.456A pdb=" N VAL B 816 " --> pdb=" O ASN B 812 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE B 833 " --> pdb=" O PHE B 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 58 Proline residue: C 57 - end of helix Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 108 through 120 Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 151 through 165 Processing helix chain 'C' and resid 180 through 191 Processing helix chain 'C' and resid 214 through 220 Processing helix chain 'C' and resid 233 through 246 removed outlier: 3.867A pdb=" N VAL C 237 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 263 No H-bonds generated for 'chain 'C' and resid 261 through 263' Processing helix chain 'C' and resid 288 through 309 Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 459 through 471 removed outlier: 3.830A pdb=" N ARG C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 501 Processing helix chain 'C' and resid 516 through 521 removed outlier: 3.957A pdb=" N GLU C 520 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 521 " --> pdb=" O GLU C 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 516 through 521' Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 557 through 578 Processing helix chain 'C' and resid 600 through 612 removed outlier: 4.813A pdb=" N ILE C 605 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 654 removed outlier: 3.819A pdb=" N MET C 630 " --> pdb=" O THR C 626 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE C 654 " --> pdb=" O ALA C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 671 No H-bonds generated for 'chain 'C' and resid 668 through 671' Processing helix chain 'C' and resid 690 through 694 Processing helix chain 'C' and resid 699 through 707 removed outlier: 4.052A pdb=" N LYS C 707 " --> pdb=" O GLN C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 722 Processing helix chain 'C' and resid 732 through 741 Processing helix chain 'C' and resid 743 through 745 No H-bonds generated for 'chain 'C' and resid 743 through 745' Processing helix chain 'C' and resid 775 through 785 Processing helix chain 'C' and resid 789 through 795 Processing helix chain 'C' and resid 814 through 836 removed outlier: 4.061A pdb=" N MET C 823 " --> pdb=" O GLY C 819 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU C 824 " --> pdb=" O VAL C 820 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA C 825 " --> pdb=" O PHE C 821 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 826 " --> pdb=" O TYR C 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 51 removed outlier: 3.914A pdb=" N LYS D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 85 removed outlier: 4.033A pdb=" N SER D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N SER D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 112 Processing helix chain 'D' and resid 144 through 158 Processing helix chain 'D' and resid 171 through 187 removed outlier: 4.123A pdb=" N GLU D 186 " --> pdb=" O THR D 182 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ARG D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 212 Processing helix chain 'D' and resid 225 through 237 removed outlier: 4.247A pdb=" N ALA D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA D 236 " --> pdb=" O TYR D 232 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET D 237 " --> pdb=" O ARG D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 261 removed outlier: 3.547A pdb=" N LEU D 259 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 295 removed outlier: 3.724A pdb=" N GLN D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N HIS D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 327 Processing helix chain 'D' and resid 458 through 470 removed outlier: 3.682A pdb=" N LEU D 462 " --> pdb=" O PHE D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'D' and resid 521 through 526 removed outlier: 3.769A pdb=" N TYR D 526 " --> pdb=" O GLU D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 583 removed outlier: 3.785A pdb=" N HIS D 571 " --> pdb=" O GLY D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 615 Processing helix chain 'D' and resid 627 through 656 removed outlier: 3.587A pdb=" N ILE D 631 " --> pdb=" O PHE D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 673 No H-bonds generated for 'chain 'D' and resid 670 through 673' Processing helix chain 'D' and resid 688 through 694 Processing helix chain 'D' and resid 700 through 709 removed outlier: 3.634A pdb=" N TYR D 703 " --> pdb=" O SER D 700 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET D 706 " --> pdb=" O TYR D 703 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLU D 707 " --> pdb=" O ARG D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 722 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 770 through 781 removed outlier: 3.616A pdb=" N SER D 775 " --> pdb=" O ASN D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 792 Processing helix chain 'D' and resid 811 through 842 removed outlier: 4.453A pdb=" N VAL D 816 " --> pdb=" O ASN D 812 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE D 833 " --> pdb=" O PHE D 829 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 68 through 73 removed outlier: 3.937A pdb=" N ILE A 36 " --> pdb=" O ASN A 68 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A 70 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 72 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLY A 97 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N MET A 39 " --> pdb=" O GLY A 97 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL A 99 " --> pdb=" O MET A 39 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N PHE A 100 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A 125 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 204 through 206 removed outlier: 7.903A pdb=" N VAL A 173 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU A 228 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N THR A 175 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N TYR A 230 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE A 254 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU A 229 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE A 256 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 278 through 280 removed outlier: 3.523A pdb=" N GLU A 373 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 405 through 410 removed outlier: 7.051A pdb=" N THR A 474 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE A 408 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASP A 476 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR A 410 " --> pdb=" O ASP A 476 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR A 478 " --> pdb=" O THR A 410 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 439 through 441 removed outlier: 4.097A pdb=" N VAL A 440 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET A 450 " --> pdb=" O VAL A 440 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 727 through 731 removed outlier: 3.601A pdb=" N VAL A 748 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 30 through 32 removed outlier: 7.787A pdb=" N VAL B 92 " --> pdb=" O PRO B 117 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU B 119 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 165 through 168 Processing sheet with id= I, first strand: chain 'B' and resid 218 through 221 removed outlier: 6.383A pdb=" N VAL B 246 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N LEU B 221 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU B 248 " --> pdb=" O LEU B 221 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 267 through 271 removed outlier: 3.734A pdb=" N GLY B 365 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ASN B 355 " --> pdb=" O GLN B 363 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLN B 363 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN B 357 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEU B 361 " --> pdb=" O GLN B 357 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 399 through 401 removed outlier: 5.588A pdb=" N GLU B 475 " --> pdb=" O ILE B 400 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 409 through 413 removed outlier: 3.505A pdb=" N CYS B 455 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 434 " --> pdb=" O CYS B 455 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 746 through 749 removed outlier: 4.283A pdb=" N ALA B 682 " --> pdb=" O ALA B 728 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE B 730 " --> pdb=" O ALA B 682 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 68 through 73 removed outlier: 3.915A pdb=" N ILE C 36 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL C 70 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 72 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLY C 97 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N MET C 39 " --> pdb=" O GLY C 97 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL C 99 " --> pdb=" O MET C 39 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE C 100 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 204 through 206 removed outlier: 7.957A pdb=" N VAL C 173 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU C 228 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR C 175 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N TYR C 230 " --> pdb=" O THR C 175 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE C 254 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU C 229 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE C 256 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 278 through 280 removed outlier: 3.537A pdb=" N GLU C 373 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 407 through 410 removed outlier: 6.094A pdb=" N ASP C 476 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR C 410 " --> pdb=" O ASP C 476 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR C 478 " --> pdb=" O THR C 410 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 439 through 441 removed outlier: 4.107A pdb=" N VAL C 440 " --> pdb=" O MET C 450 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N MET C 450 " --> pdb=" O VAL C 440 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 727 through 731 removed outlier: 3.600A pdb=" N VAL C 748 " --> pdb=" O VAL C 537 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 30 through 32 removed outlier: 7.711A pdb=" N VAL D 92 " --> pdb=" O PRO D 117 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU D 119 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 165 through 168 Processing sheet with id= V, first strand: chain 'D' and resid 218 through 221 removed outlier: 6.422A pdb=" N VAL D 246 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N LEU D 221 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU D 248 " --> pdb=" O LEU D 221 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'D' and resid 267 through 271 removed outlier: 3.752A pdb=" N GLY D 365 " --> pdb=" O ILE D 353 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASN D 355 " --> pdb=" O GLN D 363 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLN D 363 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN D 357 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LEU D 361 " --> pdb=" O GLN D 357 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 397 through 401 removed outlier: 5.885A pdb=" N THR D 473 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE D 400 " --> pdb=" O THR D 473 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N GLU D 475 " --> pdb=" O ILE D 400 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'D' and resid 409 through 413 removed outlier: 3.535A pdb=" N CYS D 455 " --> pdb=" O VAL D 434 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL D 434 " --> pdb=" O CYS D 455 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 746 through 749 removed outlier: 3.547A pdb=" N ILE D 540 " --> pdb=" O THR D 749 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA D 682 " --> pdb=" O ALA D 728 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE D 730 " --> pdb=" O ALA D 682 " (cutoff:3.500A) 823 hydrogen bonds defined for protein. 2403 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: 7.29 Time building geometry restraints manager: 9.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3982 1.32 - 1.44: 6899 1.44 - 1.57: 14016 1.57 - 1.69: 0 1.69 - 1.81: 260 Bond restraints: 25157 Sorted by residual: bond pdb=" C9 AA A 902 " pdb=" N9 AA A 902 " ideal model delta sigma weight residual 1.314 1.422 -0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" N 6RM B 908 " pdb=" C2 6RM B 908 " ideal model delta sigma weight residual 1.412 1.370 0.042 2.00e-02 2.50e+03 4.39e+00 bond pdb=" N 6RM C 902 " pdb=" C2 6RM C 902 " ideal model delta sigma weight residual 1.412 1.371 0.041 2.00e-02 2.50e+03 4.17e+00 bond pdb=" C13 AA A 902 " pdb=" C9 AA A 902 " ideal model delta sigma weight residual 1.435 1.399 0.036 2.00e-02 2.50e+03 3.30e+00 bond pdb=" C12 AA A 902 " pdb=" C9 AA A 902 " ideal model delta sigma weight residual 1.434 1.399 0.035 2.00e-02 2.50e+03 3.12e+00 ... (remaining 25152 not shown) Histogram of bond angle deviations from ideal: 59.16 - 74.13: 6 74.13 - 89.10: 0 89.10 - 104.08: 361 104.08 - 119.05: 20437 119.05 - 134.02: 13308 Bond angle restraints: 34112 Sorted by residual: angle pdb=" N VAL A 662 " pdb=" CA VAL A 662 " pdb=" C VAL A 662 " ideal model delta sigma weight residual 111.90 109.20 2.70 8.10e-01 1.52e+00 1.11e+01 angle pdb=" N ILE D 254 " pdb=" CA ILE D 254 " pdb=" C ILE D 254 " ideal model delta sigma weight residual 113.42 109.61 3.81 1.17e+00 7.31e-01 1.06e+01 angle pdb=" N ILE B 254 " pdb=" CA ILE B 254 " pdb=" C ILE B 254 " ideal model delta sigma weight residual 113.42 109.61 3.81 1.17e+00 7.31e-01 1.06e+01 angle pdb=" N GLY B 457 " pdb=" CA GLY B 457 " pdb=" C GLY B 457 " ideal model delta sigma weight residual 110.58 114.84 -4.26 1.35e+00 5.49e-01 9.97e+00 angle pdb=" N VAL C 662 " pdb=" CA VAL C 662 " pdb=" C VAL C 662 " ideal model delta sigma weight residual 111.56 109.22 2.34 8.60e-01 1.35e+00 7.39e+00 ... (remaining 34107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 14484 17.44 - 34.87: 564 34.87 - 52.31: 107 52.31 - 69.75: 3 69.75 - 87.19: 2 Dihedral angle restraints: 15160 sinusoidal: 6230 harmonic: 8930 Sorted by residual: dihedral pdb=" N LEU B 752 " pdb=" CA LEU B 752 " pdb=" CB LEU B 752 " pdb=" CG LEU B 752 " ideal model delta sinusoidal sigma weight residual -60.00 -117.61 57.61 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" N LEU D 752 " pdb=" CA LEU D 752 " pdb=" CB LEU D 752 " pdb=" CG LEU D 752 " ideal model delta sinusoidal sigma weight residual -60.00 -111.78 51.78 3 1.50e+01 4.44e-03 9.05e+00 dihedral pdb=" N MET C 162 " pdb=" CA MET C 162 " pdb=" CB MET C 162 " pdb=" CG MET C 162 " ideal model delta sinusoidal sigma weight residual -180.00 -129.29 -50.71 3 1.50e+01 4.44e-03 8.93e+00 ... (remaining 15157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2519 0.031 - 0.063: 904 0.063 - 0.094: 249 0.094 - 0.126: 199 0.126 - 0.157: 9 Chirality restraints: 3880 Sorted by residual: chirality pdb=" C1 NAG D 903 " pdb=" ND2 ASN D 239 " pdb=" C2 NAG D 903 " pdb=" O5 NAG D 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" C1 NAG B 903 " pdb=" ND2 ASN B 239 " pdb=" C2 NAG B 903 " pdb=" O5 NAG B 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" C1 NAG D 906 " pdb=" ND2 ASN D 471 " pdb=" C2 NAG D 906 " pdb=" O5 NAG D 906 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 3877 not shown) Planarity restraints: 4303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N 6RM C 902 " 0.021 2.00e-02 2.50e+03 5.52e-02 9.89e+01 pdb=" C 6RM C 902 " -0.107 2.00e-02 2.50e+03 pdb=" O 6RM C 902 " -0.065 2.00e-02 2.50e+03 pdb=" C1 6RM C 902 " -0.014 2.00e-02 2.50e+03 pdb=" C14 6RM C 902 " 0.084 2.00e-02 2.50e+03 pdb=" C2 6RM C 902 " 0.011 2.00e-02 2.50e+03 pdb=" C3 6RM C 902 " -0.007 2.00e-02 2.50e+03 pdb=" C4 6RM C 902 " 0.005 2.00e-02 2.50e+03 pdb=" C5 6RM C 902 " 0.029 2.00e-02 2.50e+03 pdb=" C6 6RM C 902 " 0.046 2.00e-02 2.50e+03 pdb=" C7 6RM C 902 " -0.091 2.00e-02 2.50e+03 pdb=" N1 6RM C 902 " 0.065 2.00e-02 2.50e+03 pdb=" S 6RM C 902 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 6RM B 908 " 0.021 2.00e-02 2.50e+03 5.51e-02 9.88e+01 pdb=" C 6RM B 908 " -0.107 2.00e-02 2.50e+03 pdb=" O 6RM B 908 " -0.064 2.00e-02 2.50e+03 pdb=" C1 6RM B 908 " -0.014 2.00e-02 2.50e+03 pdb=" C14 6RM B 908 " 0.083 2.00e-02 2.50e+03 pdb=" C2 6RM B 908 " 0.011 2.00e-02 2.50e+03 pdb=" C3 6RM B 908 " -0.008 2.00e-02 2.50e+03 pdb=" C4 6RM B 908 " 0.005 2.00e-02 2.50e+03 pdb=" C5 6RM B 908 " 0.029 2.00e-02 2.50e+03 pdb=" C6 6RM B 908 " 0.046 2.00e-02 2.50e+03 pdb=" C7 6RM B 908 " -0.091 2.00e-02 2.50e+03 pdb=" N1 6RM B 908 " 0.066 2.00e-02 2.50e+03 pdb=" S 6RM B 908 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 6RM C 902 " 0.006 2.00e-02 2.50e+03 2.08e-02 8.68e+00 pdb=" C11 6RM C 902 " -0.011 2.00e-02 2.50e+03 pdb=" C12 6RM C 902 " -0.002 2.00e-02 2.50e+03 pdb=" C13 6RM C 902 " 0.024 2.00e-02 2.50e+03 pdb=" C8 6RM C 902 " 0.021 2.00e-02 2.50e+03 pdb=" C9 6RM C 902 " 0.018 2.00e-02 2.50e+03 pdb=" F 6RM C 902 " -0.016 2.00e-02 2.50e+03 pdb=" O1 6RM C 902 " -0.041 2.00e-02 2.50e+03 ... (remaining 4300 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4456 2.77 - 3.31: 25123 3.31 - 3.84: 40549 3.84 - 4.37: 45107 4.37 - 4.90: 77244 Nonbonded interactions: 192479 Sorted by model distance: nonbonded pdb=" O GLN A 703 " pdb=" OG1 THR A 706 " model vdw 2.243 2.440 nonbonded pdb=" O GLN C 703 " pdb=" OG1 THR C 706 " model vdw 2.244 2.440 nonbonded pdb=" O ASN C 404 " pdb=" OG1 THR C 474 " model vdw 2.262 2.440 nonbonded pdb=" O ASN A 404 " pdb=" OG1 THR A 474 " model vdw 2.271 2.440 nonbonded pdb=" O THR B 396 " pdb=" OG1 THR B 473 " model vdw 2.273 2.440 ... (remaining 192474 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 34 through 837 or resid 901)) selection = (chain 'C' and (resid 34 through 837 or resid 901)) } ncs_group { reference = (chain 'B' and (resid 25 through 844 or resid 901 through 907)) selection = chain 'D' } 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: 0.760 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: 0.030 Extract box with map and model: 5.280 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 60.720 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 : 0.002 0.108 25157 Z= 0.139 Angle : 0.450 6.725 34112 Z= 0.231 Chirality : 0.041 0.157 3880 Planarity : 0.003 0.055 4287 Dihedral : 9.119 87.186 9344 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 1.92 % Allowed : 6.11 % Favored : 91.97 % 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: 0.78 (0.16), residues: 3040 helix: 2.21 (0.15), residues: 1220 sheet: 0.11 (0.32), residues: 306 loop : -0.85 (0.17), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 636 HIS 0.002 0.000 HIS C 119 PHE 0.005 0.001 PHE D 753 TYR 0.007 0.001 TYR A 321 ARG 0.002 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 485 time to evaluate : 2.858 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: A 162 MET cc_start: 0.8752 (tpp) cc_final: 0.8508 (mmm) REVERT: A 200 MET cc_start: 0.6986 (tpt) cc_final: 0.6746 (tpt) REVERT: A 491 ASN cc_start: 0.8402 (m-40) cc_final: 0.8150 (t0) REVERT: A 787 GLU cc_start: 0.8305 (mp0) cc_final: 0.7916 (mp0) REVERT: B 41 MET cc_start: 0.8493 (ptp) cc_final: 0.7989 (ptm) REVERT: B 123 THR cc_start: 0.8514 (m) cc_final: 0.8169 (p) REVERT: B 514 VAL cc_start: 0.9311 (OUTLIER) cc_final: 0.8719 (m) REVERT: B 607 MET cc_start: 0.2926 (ptt) cc_final: 0.2306 (ptt) REVERT: B 611 TRP cc_start: 0.7340 (m-10) cc_final: 0.6833 (m100) REVERT: B 730 ILE cc_start: 0.8435 (mp) cc_final: 0.8170 (tp) REVERT: C 82 LEU cc_start: 0.8602 (mt) cc_final: 0.8150 (mt) REVERT: C 113 LEU cc_start: 0.9443 (mt) cc_final: 0.8695 (mt) REVERT: C 200 MET cc_start: 0.7148 (tpt) cc_final: 0.6716 (tpt) REVERT: C 252 ASP cc_start: 0.8752 (p0) cc_final: 0.8238 (p0) REVERT: C 320 CYS cc_start: 0.2525 (OUTLIER) cc_final: 0.1683 (m) REVERT: C 509 VAL cc_start: 0.8898 (t) cc_final: 0.8619 (t) REVERT: C 782 PHE cc_start: 0.8440 (m-10) cc_final: 0.7792 (m-10) REVERT: D 240 MET cc_start: 0.8620 (mmp) cc_final: 0.7857 (mmm) REVERT: D 249 VAL cc_start: 0.7434 (t) cc_final: 0.6813 (p) REVERT: D 386 THR cc_start: 0.8183 (p) cc_final: 0.7530 (p) REVERT: D 427 ASN cc_start: 0.8249 (m-40) cc_final: 0.8005 (t0) REVERT: D 616 ASN cc_start: 0.6723 (m-40) cc_final: 0.6145 (p0) REVERT: D 639 PHE cc_start: 0.9312 (t80) cc_final: 0.9003 (t80) REVERT: D 736 LEU cc_start: 0.8524 (mt) cc_final: 0.8252 (mt) outliers start: 51 outliers final: 21 residues processed: 531 average time/residue: 0.3720 time to fit residues: 300.8016 Evaluate side-chains 324 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 301 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 20.0000 chunk 231 optimal weight: 20.0000 chunk 128 optimal weight: 30.0000 chunk 79 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 239 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 178 optimal weight: 7.9990 chunk 277 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 201 GLN A 482 ASN ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 GLN B 525 GLN ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 201 GLN C 482 ASN ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** D 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 25157 Z= 0.432 Angle : 0.789 10.658 34112 Z= 0.408 Chirality : 0.048 0.255 3880 Planarity : 0.006 0.071 4287 Dihedral : 5.639 89.026 3672 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 25.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.48 % Favored : 93.45 % Rotamer: Outliers : 0.08 % Allowed : 4.94 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 3040 helix: 0.91 (0.15), residues: 1240 sheet: -1.48 (0.26), residues: 366 loop : -1.14 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 151 HIS 0.010 0.002 HIS C 168 PHE 0.036 0.003 PHE A 183 TYR 0.037 0.003 TYR B 692 ARG 0.008 0.001 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 285 time to evaluate : 3.032 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 135 MET cc_start: 0.6266 (ptm) cc_final: 0.5945 (tpt) REVERT: A 200 MET cc_start: 0.8101 (tpt) cc_final: 0.7778 (tpt) REVERT: A 252 ASP cc_start: 0.8930 (p0) cc_final: 0.8611 (p0) REVERT: A 472 LYS cc_start: 0.8585 (ptpp) cc_final: 0.7999 (ptmt) REVERT: B 316 LYS cc_start: 0.8541 (pttp) cc_final: 0.8164 (tptt) REVERT: B 354 MET cc_start: 0.9010 (mmp) cc_final: 0.8522 (mmm) REVERT: B 639 PHE cc_start: 0.9323 (t80) cc_final: 0.8920 (t80) REVERT: B 667 ILE cc_start: 0.8528 (pt) cc_final: 0.8270 (mm) REVERT: C 82 LEU cc_start: 0.9056 (mt) cc_final: 0.8743 (mt) REVERT: C 113 LEU cc_start: 0.9740 (mt) cc_final: 0.9092 (mt) REVERT: C 200 MET cc_start: 0.7896 (tpt) cc_final: 0.7444 (tmm) REVERT: C 412 GLU cc_start: 0.7177 (tt0) cc_final: 0.6968 (tt0) REVERT: C 558 TRP cc_start: 0.6222 (t60) cc_final: 0.5417 (t-100) REVERT: D 119 LEU cc_start: 0.8433 (mm) cc_final: 0.8117 (mt) REVERT: D 240 MET cc_start: 0.8951 (mmp) cc_final: 0.8568 (mmm) REVERT: D 316 LYS cc_start: 0.8389 (pttm) cc_final: 0.7976 (tptt) REVERT: D 639 PHE cc_start: 0.9378 (t80) cc_final: 0.9004 (t80) outliers start: 2 outliers final: 1 residues processed: 287 average time/residue: 0.3623 time to fit residues: 163.4404 Evaluate side-chains 208 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 189 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 278 optimal weight: 0.9990 chunk 300 optimal weight: 0.9980 chunk 247 optimal weight: 2.9990 chunk 276 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 223 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 766 GLN B 40 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 GLN D 40 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25157 Z= 0.171 Angle : 0.533 6.161 34112 Z= 0.273 Chirality : 0.043 0.247 3880 Planarity : 0.004 0.061 4287 Dihedral : 4.637 40.700 3672 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.10 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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: -0.18 (0.16), residues: 3040 helix: 1.25 (0.15), residues: 1250 sheet: -1.35 (0.26), residues: 394 loop : -0.98 (0.18), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 608 HIS 0.004 0.001 HIS B 727 PHE 0.019 0.001 PHE A 183 TYR 0.019 0.001 TYR D 578 ARG 0.005 0.000 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 2.769 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: A 135 MET cc_start: 0.5798 (ptm) cc_final: 0.5592 (tpt) REVERT: A 200 MET cc_start: 0.7767 (tpt) cc_final: 0.7514 (tpt) REVERT: A 252 ASP cc_start: 0.8691 (p0) cc_final: 0.8306 (p0) REVERT: A 472 LYS cc_start: 0.8500 (ptpp) cc_final: 0.7807 (ptmt) REVERT: A 491 ASN cc_start: 0.8586 (m-40) cc_final: 0.8201 (t0) REVERT: A 564 MET cc_start: 0.3816 (mpp) cc_final: 0.3560 (ptp) REVERT: B 41 MET cc_start: 0.8339 (ptp) cc_final: 0.8079 (ptp) REVERT: B 316 LYS cc_start: 0.8351 (pttp) cc_final: 0.7992 (tptt) REVERT: B 354 MET cc_start: 0.8956 (mmp) cc_final: 0.8653 (mmm) REVERT: B 639 PHE cc_start: 0.9320 (t80) cc_final: 0.8848 (t80) REVERT: B 667 ILE cc_start: 0.8701 (pt) cc_final: 0.8336 (mm) REVERT: C 82 LEU cc_start: 0.8898 (mt) cc_final: 0.8594 (mt) REVERT: C 113 LEU cc_start: 0.9705 (mt) cc_final: 0.9090 (mt) REVERT: C 200 MET cc_start: 0.7629 (tpt) cc_final: 0.7088 (tmm) REVERT: D 119 LEU cc_start: 0.8395 (mm) cc_final: 0.8037 (mt) REVERT: D 240 MET cc_start: 0.8835 (mmp) cc_final: 0.8418 (mmm) REVERT: D 316 LYS cc_start: 0.8329 (pttm) cc_final: 0.7876 (tptt) REVERT: D 354 MET cc_start: 0.9183 (mmp) cc_final: 0.8956 (mmm) REVERT: D 785 MET cc_start: 0.8946 (mmm) cc_final: 0.8657 (tpp) REVERT: D 787 ASP cc_start: 0.8620 (t0) cc_final: 0.8346 (t0) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.3532 time to fit residues: 158.4259 Evaluate side-chains 211 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 0.6980 chunk 209 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 132 optimal weight: 40.0000 chunk 186 optimal weight: 0.4980 chunk 279 optimal weight: 3.9990 chunk 295 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 264 optimal weight: 0.7980 chunk 79 optimal weight: 20.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 812 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS D 724 ASN D 812 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25157 Z= 0.137 Angle : 0.513 9.963 34112 Z= 0.261 Chirality : 0.043 0.231 3880 Planarity : 0.003 0.053 4287 Dihedral : 4.251 39.972 3672 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.72 % Favored : 94.21 % Rotamer: Outliers : 0.04 % Allowed : 3.21 % Favored : 96.76 % 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: -0.03 (0.16), residues: 3040 helix: 1.32 (0.15), residues: 1248 sheet: -1.20 (0.26), residues: 394 loop : -0.86 (0.18), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 255 HIS 0.003 0.001 HIS D 146 PHE 0.017 0.001 PHE D 639 TYR 0.018 0.001 TYR B 578 ARG 0.004 0.000 ARG B 755 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 283 time to evaluate : 2.937 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 135 MET cc_start: 0.5725 (ptm) cc_final: 0.5515 (tpt) REVERT: A 151 ILE cc_start: 0.9461 (mm) cc_final: 0.8969 (tt) REVERT: A 200 MET cc_start: 0.7722 (tpt) cc_final: 0.7466 (tpt) REVERT: A 252 ASP cc_start: 0.8610 (p0) cc_final: 0.8263 (p0) REVERT: A 472 LYS cc_start: 0.8301 (ptpp) cc_final: 0.7529 (ptmt) REVERT: A 491 ASN cc_start: 0.8521 (m-40) cc_final: 0.8195 (t0) REVERT: B 316 LYS cc_start: 0.8253 (pttp) cc_final: 0.7929 (tptt) REVERT: B 354 MET cc_start: 0.8834 (mmp) cc_final: 0.8604 (mmm) REVERT: B 639 PHE cc_start: 0.9314 (t80) cc_final: 0.8890 (t80) REVERT: B 667 ILE cc_start: 0.8710 (pt) cc_final: 0.8350 (mm) REVERT: C 82 LEU cc_start: 0.8830 (mt) cc_final: 0.8545 (mt) REVERT: C 113 LEU cc_start: 0.9709 (mt) cc_final: 0.9139 (mt) REVERT: C 200 MET cc_start: 0.7550 (tpt) cc_final: 0.7001 (tmm) REVERT: C 252 ASP cc_start: 0.8833 (p0) cc_final: 0.8333 (p0) REVERT: D 181 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8825 (mm-30) REVERT: D 185 GLU cc_start: 0.8201 (pp20) cc_final: 0.7666 (pp20) REVERT: D 240 MET cc_start: 0.8791 (mmp) cc_final: 0.8494 (mmm) REVERT: D 316 LYS cc_start: 0.8254 (pttm) cc_final: 0.7818 (tptt) REVERT: D 354 MET cc_start: 0.9081 (mmp) cc_final: 0.8776 (mmm) REVERT: D 702 MET cc_start: 0.8739 (mmt) cc_final: 0.8385 (mmt) REVERT: D 706 MET cc_start: 0.8993 (mmm) cc_final: 0.8208 (mmp) REVERT: D 785 MET cc_start: 0.8992 (mmm) cc_final: 0.8668 (tpp) REVERT: D 787 ASP cc_start: 0.8615 (t0) cc_final: 0.8351 (t0) outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 0.3464 time to fit residues: 156.8704 Evaluate side-chains 215 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 5.9990 chunk 167 optimal weight: 0.1980 chunk 4 optimal weight: 7.9990 chunk 220 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 252 optimal weight: 3.9990 chunk 204 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 151 optimal weight: 20.0000 chunk 265 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25157 Z= 0.264 Angle : 0.586 9.065 34112 Z= 0.303 Chirality : 0.044 0.272 3880 Planarity : 0.004 0.050 4287 Dihedral : 4.717 39.143 3672 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.91 % Favored : 93.03 % Rotamer: Outliers : 0.04 % Allowed : 3.05 % Favored : 96.91 % 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: -0.24 (0.16), residues: 3040 helix: 1.20 (0.15), residues: 1252 sheet: -1.45 (0.26), residues: 398 loop : -0.99 (0.18), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 255 HIS 0.006 0.001 HIS B 171 PHE 0.018 0.001 PHE A 183 TYR 0.016 0.002 TYR C 281 ARG 0.013 0.001 ARG B 704 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 247 time to evaluate : 2.952 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 200 MET cc_start: 0.7935 (tpt) cc_final: 0.7603 (tpt) REVERT: A 252 ASP cc_start: 0.8807 (p0) cc_final: 0.8594 (p0) REVERT: A 255 TRP cc_start: 0.7866 (m100) cc_final: 0.7071 (m100) REVERT: B 185 GLU cc_start: 0.8131 (pp20) cc_final: 0.7890 (pp20) REVERT: B 316 LYS cc_start: 0.8374 (pttp) cc_final: 0.7951 (tptt) REVERT: B 354 MET cc_start: 0.8946 (mmp) cc_final: 0.8577 (mmm) REVERT: B 639 PHE cc_start: 0.9369 (t80) cc_final: 0.8992 (t80) REVERT: B 667 ILE cc_start: 0.8855 (pt) cc_final: 0.8577 (mm) REVERT: C 82 LEU cc_start: 0.8989 (mt) cc_final: 0.8704 (mt) REVERT: C 113 LEU cc_start: 0.9735 (mt) cc_final: 0.9143 (mt) REVERT: C 200 MET cc_start: 0.7631 (tpt) cc_final: 0.7121 (tmm) REVERT: D 185 GLU cc_start: 0.8323 (pp20) cc_final: 0.7814 (pp20) REVERT: D 240 MET cc_start: 0.8885 (mmp) cc_final: 0.8549 (mmm) REVERT: D 316 LYS cc_start: 0.8385 (pttm) cc_final: 0.7917 (tptt) REVERT: D 354 MET cc_start: 0.9185 (mmp) cc_final: 0.8941 (mmm) REVERT: D 639 PHE cc_start: 0.9420 (t80) cc_final: 0.9215 (t80) REVERT: D 785 MET cc_start: 0.9054 (mmm) cc_final: 0.8719 (tpp) REVERT: D 787 ASP cc_start: 0.8713 (t0) cc_final: 0.8447 (t0) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.3257 time to fit residues: 132.6049 Evaluate side-chains 200 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 0.9990 chunk 266 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 173 optimal weight: 0.1980 chunk 73 optimal weight: 5.9990 chunk 296 optimal weight: 0.7980 chunk 245 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 97 optimal weight: 0.0020 chunk 155 optimal weight: 9.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 146 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25157 Z= 0.137 Angle : 0.531 9.164 34112 Z= 0.270 Chirality : 0.043 0.297 3880 Planarity : 0.003 0.050 4287 Dihedral : 4.290 37.887 3672 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.43 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: -0.09 (0.16), residues: 3040 helix: 1.27 (0.15), residues: 1246 sheet: -1.22 (0.27), residues: 368 loop : -0.90 (0.18), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 378 HIS 0.006 0.001 HIS A 405 PHE 0.016 0.001 PHE A 183 TYR 0.014 0.001 TYR A 281 ARG 0.005 0.000 ARG B 755 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 3.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ILE cc_start: 0.9562 (mm) cc_final: 0.9025 (tt) REVERT: A 200 MET cc_start: 0.7711 (tpt) cc_final: 0.7468 (tpt) REVERT: A 252 ASP cc_start: 0.8710 (p0) cc_final: 0.8452 (p0) REVERT: A 255 TRP cc_start: 0.7493 (m100) cc_final: 0.7016 (m100) REVERT: A 491 ASN cc_start: 0.8552 (m-40) cc_final: 0.8199 (t0) REVERT: A 787 GLU cc_start: 0.8198 (mp0) cc_final: 0.7872 (mp0) REVERT: B 185 GLU cc_start: 0.7946 (pp20) cc_final: 0.7726 (pp20) REVERT: B 240 MET cc_start: 0.9089 (mmm) cc_final: 0.8832 (mmm) REVERT: B 316 LYS cc_start: 0.8191 (pttp) cc_final: 0.7789 (tptt) REVERT: B 501 MET cc_start: 0.9328 (ptm) cc_final: 0.8859 (ppp) REVERT: B 639 PHE cc_start: 0.9335 (t80) cc_final: 0.9011 (t80) REVERT: B 667 ILE cc_start: 0.8904 (pt) cc_final: 0.8583 (mm) REVERT: C 82 LEU cc_start: 0.8930 (mt) cc_final: 0.8679 (mt) REVERT: C 113 LEU cc_start: 0.9729 (mt) cc_final: 0.9182 (mt) REVERT: C 200 MET cc_start: 0.7478 (tpt) cc_final: 0.6963 (tmm) REVERT: C 252 ASP cc_start: 0.8658 (p0) cc_final: 0.8180 (p0) REVERT: D 41 MET cc_start: 0.8559 (ptp) cc_final: 0.8291 (ptm) REVERT: D 181 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8759 (mm-30) REVERT: D 185 GLU cc_start: 0.8195 (pp20) cc_final: 0.7669 (pp20) REVERT: D 240 MET cc_start: 0.8809 (mmp) cc_final: 0.8478 (mmm) REVERT: D 316 LYS cc_start: 0.8257 (pttm) cc_final: 0.7810 (tptt) REVERT: D 354 MET cc_start: 0.9098 (mmp) cc_final: 0.8678 (mmm) REVERT: D 702 MET cc_start: 0.8780 (mmt) cc_final: 0.8442 (mmt) REVERT: D 706 MET cc_start: 0.8881 (mmm) cc_final: 0.8140 (mmp) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.3435 time to fit residues: 148.1284 Evaluate side-chains 214 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 0.0470 chunk 33 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 216 optimal weight: 9.9990 chunk 167 optimal weight: 0.8980 chunk 249 optimal weight: 10.0000 chunk 165 optimal weight: 0.6980 chunk 294 optimal weight: 0.8980 chunk 184 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 146 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 25157 Z= 0.133 Angle : 0.514 8.116 34112 Z= 0.260 Chirality : 0.043 0.289 3880 Planarity : 0.003 0.047 4287 Dihedral : 4.093 39.828 3672 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.18 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: -0.03 (0.16), residues: 3040 helix: 1.28 (0.15), residues: 1256 sheet: -1.08 (0.28), residues: 364 loop : -0.88 (0.18), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 55 HIS 0.003 0.001 HIS A 405 PHE 0.023 0.001 PHE D 639 TYR 0.015 0.001 TYR C 281 ARG 0.003 0.000 ARG B 755 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 3.162 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 151 ILE cc_start: 0.9529 (mm) cc_final: 0.8997 (tt) REVERT: A 200 MET cc_start: 0.7576 (tpt) cc_final: 0.7375 (tpt) REVERT: A 252 ASP cc_start: 0.8638 (p0) cc_final: 0.8341 (p0) REVERT: A 255 TRP cc_start: 0.7425 (m100) cc_final: 0.7072 (m100) REVERT: A 507 MET cc_start: 0.8003 (ttp) cc_final: 0.7770 (ttp) REVERT: B 119 LEU cc_start: 0.8184 (mm) cc_final: 0.7962 (mt) REVERT: B 185 GLU cc_start: 0.7988 (pp20) cc_final: 0.7608 (pp20) REVERT: B 240 MET cc_start: 0.9080 (mmm) cc_final: 0.8811 (mmm) REVERT: B 316 LYS cc_start: 0.8203 (pttp) cc_final: 0.7812 (tptt) REVERT: B 501 MET cc_start: 0.9353 (ptm) cc_final: 0.8953 (ppp) REVERT: B 639 PHE cc_start: 0.9336 (t80) cc_final: 0.8951 (t80) REVERT: B 667 ILE cc_start: 0.8927 (pt) cc_final: 0.8610 (mm) REVERT: C 82 LEU cc_start: 0.8964 (mt) cc_final: 0.8646 (mt) REVERT: C 113 LEU cc_start: 0.9712 (mt) cc_final: 0.9170 (mt) REVERT: C 200 MET cc_start: 0.7508 (tpt) cc_final: 0.6989 (tmm) REVERT: C 252 ASP cc_start: 0.8618 (p0) cc_final: 0.8147 (p0) REVERT: D 181 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8784 (mm-30) REVERT: D 185 GLU cc_start: 0.8133 (pp20) cc_final: 0.7588 (pp20) REVERT: D 240 MET cc_start: 0.8783 (mmp) cc_final: 0.8483 (mmm) REVERT: D 316 LYS cc_start: 0.8257 (pttm) cc_final: 0.7835 (tptt) REVERT: D 354 MET cc_start: 0.8964 (mmp) cc_final: 0.8593 (mmm) REVERT: D 702 MET cc_start: 0.8720 (mmt) cc_final: 0.8332 (mmt) REVERT: D 706 MET cc_start: 0.8894 (mmm) cc_final: 0.8090 (mmp) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.3281 time to fit residues: 141.2479 Evaluate side-chains 213 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 176 optimal weight: 0.0060 chunk 88 optimal weight: 0.2980 chunk 57 optimal weight: 8.9990 chunk 187 optimal weight: 7.9990 chunk 200 optimal weight: 0.9990 chunk 145 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 231 optimal weight: 20.0000 chunk 268 optimal weight: 5.9990 overall best weight: 2.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 146 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN B 727 HIS ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25157 Z= 0.188 Angle : 0.551 10.064 34112 Z= 0.280 Chirality : 0.043 0.292 3880 Planarity : 0.003 0.045 4287 Dihedral : 4.266 39.660 3672 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.22 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % 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: -0.13 (0.16), residues: 3040 helix: 1.27 (0.15), residues: 1244 sheet: -1.35 (0.25), residues: 412 loop : -0.89 (0.18), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 151 HIS 0.004 0.001 HIS B 705 PHE 0.017 0.001 PHE A 183 TYR 0.017 0.001 TYR C 281 ARG 0.005 0.000 ARG A 386 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ILE cc_start: 0.9548 (mm) cc_final: 0.9094 (tt) REVERT: A 200 MET cc_start: 0.7796 (tpt) cc_final: 0.7512 (tpt) REVERT: A 255 TRP cc_start: 0.7833 (m100) cc_final: 0.7461 (m100) REVERT: B 119 LEU cc_start: 0.8218 (mm) cc_final: 0.7973 (mt) REVERT: B 185 GLU cc_start: 0.8097 (pp20) cc_final: 0.7745 (pp20) REVERT: B 240 MET cc_start: 0.9016 (mmm) cc_final: 0.8791 (mmm) REVERT: B 316 LYS cc_start: 0.8274 (pttp) cc_final: 0.7869 (tptt) REVERT: B 501 MET cc_start: 0.9371 (ptm) cc_final: 0.8948 (ppp) REVERT: B 639 PHE cc_start: 0.9363 (t80) cc_final: 0.8848 (t80) REVERT: B 667 ILE cc_start: 0.8938 (pt) cc_final: 0.8675 (mm) REVERT: C 82 LEU cc_start: 0.8903 (mt) cc_final: 0.8666 (mt) REVERT: C 113 LEU cc_start: 0.9733 (mt) cc_final: 0.9178 (mt) REVERT: C 200 MET cc_start: 0.7553 (tpt) cc_final: 0.7031 (tmm) REVERT: C 252 ASP cc_start: 0.8752 (p0) cc_final: 0.8303 (p0) REVERT: D 41 MET cc_start: 0.8483 (ptp) cc_final: 0.8233 (ptm) REVERT: D 181 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8789 (mm-30) REVERT: D 185 GLU cc_start: 0.8331 (pp20) cc_final: 0.7801 (pp20) REVERT: D 240 MET cc_start: 0.8801 (mmp) cc_final: 0.8521 (mmm) REVERT: D 316 LYS cc_start: 0.8286 (pttm) cc_final: 0.7823 (tptt) REVERT: D 501 MET cc_start: 0.9394 (ptm) cc_final: 0.8694 (ppp) REVERT: D 784 PHE cc_start: 0.7576 (m-80) cc_final: 0.7351 (m-80) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.3305 time to fit residues: 135.8399 Evaluate side-chains 204 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 6.9990 chunk 257 optimal weight: 2.9990 chunk 274 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 215 optimal weight: 0.3980 chunk 84 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 chunk 273 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 146 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25157 Z= 0.220 Angle : 0.580 9.971 34112 Z= 0.298 Chirality : 0.044 0.281 3880 Planarity : 0.004 0.047 4287 Dihedral : 4.496 39.105 3672 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.94 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -0.29 (0.16), residues: 3040 helix: 1.14 (0.15), residues: 1248 sheet: -1.41 (0.26), residues: 416 loop : -0.99 (0.18), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 151 HIS 0.003 0.001 HIS B 705 PHE 0.018 0.001 PHE A 183 TYR 0.027 0.002 TYR A 730 ARG 0.006 0.000 ARG A 386 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 2.697 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 151 ILE cc_start: 0.9560 (mm) cc_final: 0.9156 (tt) REVERT: A 200 MET cc_start: 0.7812 (tpt) cc_final: 0.7517 (tpt) REVERT: A 255 TRP cc_start: 0.8061 (m100) cc_final: 0.7744 (m100) REVERT: B 119 LEU cc_start: 0.8247 (mm) cc_final: 0.7970 (mt) REVERT: B 185 GLU cc_start: 0.8169 (pp20) cc_final: 0.7875 (pp20) REVERT: B 316 LYS cc_start: 0.8340 (pttp) cc_final: 0.7893 (tptt) REVERT: B 470 MET cc_start: 0.8696 (pmm) cc_final: 0.8053 (pmm) REVERT: B 501 MET cc_start: 0.9397 (ptm) cc_final: 0.8896 (ppp) REVERT: B 667 ILE cc_start: 0.8937 (pt) cc_final: 0.8698 (mm) REVERT: C 113 LEU cc_start: 0.9750 (mt) cc_final: 0.9234 (mt) REVERT: C 200 MET cc_start: 0.7462 (tpt) cc_final: 0.7000 (tmm) REVERT: C 252 ASP cc_start: 0.9002 (p0) cc_final: 0.8504 (p0) REVERT: D 41 MET cc_start: 0.8740 (ptp) cc_final: 0.8493 (ptm) REVERT: D 123 THR cc_start: 0.8488 (m) cc_final: 0.8230 (p) REVERT: D 181 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8733 (mm-30) REVERT: D 185 GLU cc_start: 0.8439 (pp20) cc_final: 0.7900 (pp20) REVERT: D 240 MET cc_start: 0.8811 (mmp) cc_final: 0.8580 (mmm) REVERT: D 316 LYS cc_start: 0.8309 (pttm) cc_final: 0.7804 (tptt) REVERT: D 501 MET cc_start: 0.9389 (ptm) cc_final: 0.8736 (ppp) REVERT: D 786 GLU cc_start: 0.8601 (pm20) cc_final: 0.8394 (pm20) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.3271 time to fit residues: 131.9545 Evaluate side-chains 200 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.0470 chunk 177 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 304 optimal weight: 4.9990 chunk 280 optimal weight: 0.0370 chunk 242 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25157 Z= 0.142 Angle : 0.559 9.008 34112 Z= 0.282 Chirality : 0.044 0.265 3880 Planarity : 0.003 0.046 4287 Dihedral : 4.246 38.760 3672 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.72 % Favored : 94.21 % Rotamer: Outliers : 0.04 % Allowed : 0.15 % Favored : 99.81 % 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: -0.14 (0.16), residues: 3040 helix: 1.20 (0.15), residues: 1252 sheet: -1.17 (0.27), residues: 384 loop : -0.93 (0.18), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 55 HIS 0.006 0.001 HIS D 477 PHE 0.017 0.001 PHE C 170 TYR 0.017 0.001 TYR C 281 ARG 0.006 0.000 ARG A 392 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 3.022 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 151 ILE cc_start: 0.9435 (mm) cc_final: 0.9075 (tt) REVERT: A 200 MET cc_start: 0.7565 (tpt) cc_final: 0.7345 (tpt) REVERT: A 255 TRP cc_start: 0.7766 (m100) cc_final: 0.7414 (m100) REVERT: B 119 LEU cc_start: 0.8220 (mm) cc_final: 0.7976 (mt) REVERT: B 185 GLU cc_start: 0.8096 (pp20) cc_final: 0.7716 (pp20) REVERT: B 240 MET cc_start: 0.9020 (mmm) cc_final: 0.8792 (mmm) REVERT: B 316 LYS cc_start: 0.8301 (pttp) cc_final: 0.7823 (tptt) REVERT: B 501 MET cc_start: 0.9362 (ptm) cc_final: 0.8815 (ppp) REVERT: B 667 ILE cc_start: 0.8967 (pt) cc_final: 0.8666 (mm) REVERT: C 113 LEU cc_start: 0.9739 (mt) cc_final: 0.9266 (mt) REVERT: C 200 MET cc_start: 0.7434 (tpt) cc_final: 0.6901 (tmm) REVERT: C 252 ASP cc_start: 0.8660 (p0) cc_final: 0.8203 (p0) REVERT: D 181 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8746 (mm-30) REVERT: D 185 GLU cc_start: 0.8321 (pp20) cc_final: 0.7707 (pp20) REVERT: D 240 MET cc_start: 0.8839 (mmp) cc_final: 0.8586 (mmm) REVERT: D 316 LYS cc_start: 0.8253 (pttm) cc_final: 0.7720 (tptt) REVERT: D 501 MET cc_start: 0.9335 (ptm) cc_final: 0.8779 (ppp) REVERT: D 706 MET cc_start: 0.8800 (mmm) cc_final: 0.8549 (mmm) outliers start: 1 outliers final: 1 residues processed: 258 average time/residue: 0.3290 time to fit residues: 138.4998 Evaluate side-chains 203 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 202 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.3980 chunk 74 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 243 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 249 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 213 optimal weight: 0.5980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 146 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.069976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.053897 restraints weight = 146290.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.055229 restraints weight = 90875.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.056129 restraints weight = 64357.481| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25157 Z= 0.174 Angle : 0.562 9.970 34112 Z= 0.284 Chirality : 0.043 0.259 3880 Planarity : 0.003 0.046 4287 Dihedral : 4.291 39.787 3672 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.28 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 3040 helix: 1.20 (0.15), residues: 1252 sheet: -1.24 (0.27), residues: 396 loop : -1.01 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 55 HIS 0.004 0.001 HIS B 146 PHE 0.030 0.001 PHE C 613 TYR 0.021 0.001 TYR A 730 ARG 0.003 0.000 ARG B 755 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4311.85 seconds wall clock time: 79 minutes 49.45 seconds (4789.45 seconds total)