Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 03:59:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eou_31231/04_2023/7eou_31231_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eou_31231/04_2023/7eou_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_31231/04_2023/7eou_31231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eou_31231/04_2023/7eou_31231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eou_31231/04_2023/7eou_31231_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eou_31231/04_2023/7eou_31231_trim_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 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 chiralities: 7 Time building chain proxies: 12.36, per 1000 atoms: 0.50 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: 9.30 Conformation dependent library (CDL) restraints added in 3.4 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: 2.98 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: 7.46 Time building geometry restraints manager: 10.15 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: 14154 17.44 - 34.87: 548 34.87 - 52.31: 87 52.31 - 69.75: 1 69.75 - 87.19: 2 Dihedral angle restraints: 14792 sinusoidal: 5862 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 14789 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.910 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 57.280 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.910 ------------------------------------------------------------------------------- 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 : 8.937 87.186 8976 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 % 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 *********************** 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 : 2.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 21 residues processed: 531 average time/residue: 0.4082 time to fit residues: 333.3878 Evaluate side-chains 315 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 294 time to evaluate : 2.967 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2440 time to fit residues: 13.3106 ------------------------------------------------------------------------------- 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: 9.9990 chunk 156 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 277 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 40 GLN ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 0.7975 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 25157 Z= 0.392 Angle : 0.735 10.031 34112 Z= 0.380 Chirality : 0.046 0.204 3880 Planarity : 0.005 0.067 4287 Dihedral : 4.872 72.683 3304 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 23.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.22 % Favored : 93.72 % Rotamer Outliers : 0.34 % 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: -0.23 (0.16), residues: 3040 helix: 1.11 (0.15), residues: 1244 sheet: -1.49 (0.25), residues: 392 loop : -0.86 (0.18), residues: 1404 *********************** 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 309 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 300 time to evaluate : 2.998 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 outliers start: 9 outliers final: 8 residues processed: 309 average time/residue: 0.3724 time to fit residues: 181.0215 Evaluate side-chains 211 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 203 time to evaluate : 2.972 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2141 time to fit residues: 7.3593 ------------------------------------------------------------------------------- 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: 0.0020 chunk 86 optimal weight: 10.0000 chunk 231 optimal weight: 50.0000 chunk 189 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 278 optimal weight: 4.9990 chunk 300 optimal weight: 5.9990 chunk 247 optimal weight: 0.6980 chunk 276 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 223 optimal weight: 4.9990 overall best weight: 3.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 332 HIS B 40 GLN B 405 GLN ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 25157 Z= 0.241 Angle : 0.558 6.062 34112 Z= 0.289 Chirality : 0.043 0.225 3880 Planarity : 0.004 0.061 4287 Dihedral : 4.509 71.972 3304 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.66 % Favored : 94.28 % Rotamer Outliers : 0.04 % 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: -0.17 (0.16), residues: 3040 helix: 1.24 (0.15), residues: 1252 sheet: -1.44 (0.25), residues: 410 loop : -0.91 (0.18), residues: 1378 *********************** 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 267 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 266 time to evaluate : 2.956 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 outliers start: 1 outliers final: 1 residues processed: 267 average time/residue: 0.3519 time to fit residues: 152.8383 Evaluate side-chains 203 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 202 time to evaluate : 2.969 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2617 time to fit residues: 4.4519 ------------------------------------------------------------------------------- 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: 6.9990 chunk 209 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 132 optimal weight: 50.0000 chunk 186 optimal weight: 8.9990 chunk 279 optimal weight: 4.9990 chunk 295 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 264 optimal weight: 9.9990 chunk 79 optimal weight: 0.0270 overall best weight: 2.5444 ------------------------------------------------------------------------------- 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 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** D 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 724 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4812 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= 0.213 Angle : 0.548 6.560 34112 Z= 0.282 Chirality : 0.043 0.218 3880 Planarity : 0.004 0.052 4287 Dihedral : 4.455 60.843 3304 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.12 % Favored : 93.82 % Rotamer Outliers : 0.11 % 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: -0.22 (0.16), residues: 3040 helix: 1.22 (0.15), residues: 1250 sheet: -1.50 (0.26), residues: 372 loop : -0.98 (0.18), residues: 1418 *********************** 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 262 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 259 time to evaluate : 2.898 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 outliers start: 3 outliers final: 1 residues processed: 262 average time/residue: 0.3445 time to fit residues: 147.5283 Evaluate side-chains 201 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 2.983 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2762 time to fit residues: 4.5629 ------------------------------------------------------------------------------- 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: 0.3980 chunk 167 optimal weight: 0.0970 chunk 4 optimal weight: 8.9990 chunk 220 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 204 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 151 optimal weight: 30.0000 chunk 265 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 812 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 GLN D 40 GLN 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 D 812 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 25157 Z= 0.151 Angle : 0.525 6.402 34112 Z= 0.269 Chirality : 0.043 0.269 3880 Planarity : 0.003 0.049 4287 Dihedral : 4.260 52.954 3304 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.56 % Favored : 94.38 % Rotamer Outliers : 0.04 % 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: -0.19 (0.16), residues: 3040 helix: 1.23 (0.15), residues: 1248 sheet: -1.49 (0.26), residues: 396 loop : -0.92 (0.18), residues: 1396 *********************** 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 266 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 265 time to evaluate : 2.992 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 outliers start: 1 outliers final: 1 residues processed: 266 average time/residue: 0.3502 time to fit residues: 152.7217 Evaluate side-chains 205 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 2.954 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2533 time to fit residues: 4.6345 ------------------------------------------------------------------------------- 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: 0.6980 chunk 266 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 173 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 296 optimal weight: 7.9990 chunk 245 optimal weight: 0.5980 chunk 137 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 375 ASN ** 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 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: 0.7971 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 25157 Z= 0.189 Angle : 0.540 7.970 34112 Z= 0.276 Chirality : 0.043 0.294 3880 Planarity : 0.003 0.048 4287 Dihedral : 4.274 49.650 3304 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.05 % Favored : 93.88 % Rotamer Outliers : 0.00 % 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: 1.18 (0.15), residues: 1248 sheet: -1.30 (0.26), residues: 388 loop : -0.97 (0.18), residues: 1404 *********************** 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 252 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 3.240 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 outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.3542 time to fit residues: 147.3135 Evaluate side-chains 196 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 2.968 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0303 ------------------------------------------------------------------------------- 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: 20.0000 chunk 33 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 216 optimal weight: 8.9990 chunk 167 optimal weight: 0.9990 chunk 249 optimal weight: 6.9990 chunk 165 optimal weight: 0.7980 chunk 294 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 375 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 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: 0.8020 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 25157 Z= 0.225 Angle : 0.563 6.656 34112 Z= 0.290 Chirality : 0.043 0.290 3880 Planarity : 0.004 0.046 4287 Dihedral : 4.452 46.761 3304 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.11 % Favored : 92.83 % Rotamer Outliers : 0.00 % 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: -0.33 (0.16), residues: 3040 helix: 1.12 (0.15), residues: 1246 sheet: -1.56 (0.26), residues: 398 loop : -1.00 (0.18), residues: 1396 *********************** 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 243 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.980 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 outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.3491 time to fit residues: 140.0327 Evaluate side-chains 191 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.953 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0346 ------------------------------------------------------------------------------- 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: 9.9990 chunk 117 optimal weight: 6.9990 chunk 176 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 57 optimal weight: 20.0000 chunk 187 optimal weight: 5.9990 chunk 200 optimal weight: 0.0050 chunk 145 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 231 optimal weight: 3.9990 chunk 268 optimal weight: 0.0470 overall best weight: 1.1494 ------------------------------------------------------------------------------- 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 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: 0.7966 moved from start: 0.5405 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= 0.152 Angle : 0.541 8.867 34112 Z= 0.275 Chirality : 0.043 0.277 3880 Planarity : 0.003 0.046 4287 Dihedral : 4.312 43.960 3304 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.18 % Favored : 93.75 % Rotamer Outliers : 0.00 % 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: 1.13 (0.15), residues: 1242 sheet: -1.52 (0.25), residues: 408 loop : -0.94 (0.18), residues: 1390 *********************** 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 245 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.981 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 outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.3378 time to fit residues: 136.9244 Evaluate side-chains 187 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 2.844 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8727 ------------------------------------------------------------------------------- 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: 10.0000 chunk 257 optimal weight: 0.8980 chunk 274 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 248 optimal weight: 0.9980 chunk 259 optimal weight: 0.9980 chunk 273 optimal weight: 3.9990 chunk 180 optimal weight: 20.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 25157 Z= 0.168 Angle : 0.558 9.352 34112 Z= 0.283 Chirality : 0.044 0.268 3880 Planarity : 0.003 0.045 4287 Dihedral : 4.301 39.618 3304 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.22 % Favored : 93.72 % Rotamer Outliers : 0.00 % 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: -0.33 (0.16), residues: 3040 helix: 1.07 (0.15), residues: 1240 sheet: -1.56 (0.26), residues: 396 loop : -0.95 (0.18), residues: 1404 *********************** 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 239 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 2.898 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 outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.3506 time to fit residues: 139.8215 Evaluate side-chains 184 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 3.184 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2367 ------------------------------------------------------------------------------- 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: 4.9990 chunk 177 optimal weight: 0.8980 chunk 137 optimal weight: 0.0870 chunk 202 optimal weight: 5.9990 chunk 304 optimal weight: 6.9990 chunk 280 optimal weight: 0.4980 chunk 242 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 overall best weight: 1.2962 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 25157 Z= 0.161 Angle : 0.560 10.533 34112 Z= 0.284 Chirality : 0.044 0.261 3880 Planarity : 0.003 0.046 4287 Dihedral : 4.305 35.891 3304 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.09 % Favored : 93.85 % Rotamer Outliers : 0.00 % 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: -0.35 (0.16), residues: 3040 helix: 1.05 (0.15), residues: 1240 sheet: -1.55 (0.26), residues: 386 loop : -0.96 (0.18), residues: 1414 ********************** 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 239 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 3.007 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 outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.3379 time to fit residues: 134.9987 Evaluate side-chains 189 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.987 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9234 ------------------------------------------------------------------------------- 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: 0.7980 chunk 74 optimal weight: 8.9990 chunk 223 optimal weight: 0.0070 chunk 35 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 243 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 249 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 213 optimal weight: 0.0870 overall best weight: 2.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.069230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.052957 restraints weight = 149421.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.054294 restraints weight = 92774.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.055208 restraints weight = 65604.680| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 25157 Z= 0.198 Angle : 0.577 9.868 34112 Z= 0.294 Chirality : 0.044 0.256 3880 Planarity : 0.004 0.045 4287 Dihedral : 4.373 29.085 3304 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.71 % Favored : 93.22 % Rotamer Outliers : 0.00 % 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: -0.41 (0.16), residues: 3040 helix: 1.02 (0.15), residues: 1240 sheet: -1.59 (0.26), residues: 396 loop : -1.01 (0.18), residues: 1404 =============================================================================== Job complete usr+sys time: 4198.65 seconds wall clock time: 79 minutes 2.04 seconds (4742.04 seconds total)