Starting phenix.real_space_refine (version: dev) on Sat Feb 25 01:04:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eor_31228/02_2023/7eor_31228_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eor_31228/02_2023/7eor_31228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eor_31228/02_2023/7eor_31228.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eor_31228/02_2023/7eor_31228.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eor_31228/02_2023/7eor_31228_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eor_31228/02_2023/7eor_31228_trim_updated.pdb" } resolution = 4.0 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 Process input model Symmetric amino acids flipped Residue "B PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 24204 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5886 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 6093 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 770, 6088 Classifications: {'peptide': 770} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 32, 'TRANS': 737} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 770, 6088 Classifications: {'peptide': 770} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 32, 'TRANS': 737} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 6215 Chain: "C" Number of atoms: 5886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5886 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 6093 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 770, 6088 Classifications: {'peptide': 770} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 32, 'TRANS': 737} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 770, 6088 Classifications: {'peptide': 770} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 32, 'TRANS': 737} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 6215 Chain: "A" 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: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 19.33, per 1000 atoms: 0.80 Number of scatterers: 24204 At special positions: 0 Unit cell: (116.61, 145.002, 185.562, 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 150 16.00 F 2 9.00 O 4468 8.00 N 4040 7.00 C 15544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 456 " distance=2.03 Simple disulfide: pdb=" SG CYS A 794 " - pdb=" SG CYS D 698 " 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 C 87 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 456 " 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 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=2, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 687 " " NAG B 901 " - " ASN B 61 " " NAG B 902 " - " ASN B 276 " " NAG B 903 " - " ASN B 239 " " NAG B 904 " - " ASN B 203 " " NAG B 905 " - " ASN B 771 " " NAG B 906 " - " ASN B 471 " " NAG C 901 " - " ASN C 687 " " NAG D 901 " - " ASN D 61 " " NAG D 902 " - " ASN D 276 " " NAG D 903 " - " ASN D 239 " " NAG D 904 " - " ASN D 203 " " NAG D 905 " - " ASN D 771 " " NAG D 906 " - " ASN D 471 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.30 Conformation dependent library (CDL) restraints added in 4.8 seconds 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5676 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 28 sheets defined 39.8% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.747A pdb=" N GLY A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Proline residue: A 57 - end of helix Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 111 through 119 removed outlier: 4.559A pdb=" N PHE A 115 " --> pdb=" O MET A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 153 through 164 removed outlier: 3.679A pdb=" N VAL A 157 " --> pdb=" O GLN A 153 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET A 162 " --> pdb=" O MET A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 192 Processing helix chain 'A' and resid 215 through 221 removed outlier: 4.718A pdb=" N LYS A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 246 removed outlier: 3.527A pdb=" N SER A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 262 No H-bonds generated for 'chain 'A' and resid 259 through 262' Processing helix chain 'A' and resid 288 through 309 removed outlier: 3.920A pdb=" N LYS A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 337 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 459 through 471 removed outlier: 3.565A pdb=" N ARG A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.806A 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 519 No H-bonds generated for 'chain 'A' and resid 516 through 519' Processing helix chain 'A' and resid 557 through 568 removed outlier: 3.718A pdb=" N LEU A 566 " --> pdb=" O PHE A 562 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 567 " --> pdb=" O VAL A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 601 through 611 Processing helix chain 'A' and resid 626 through 652 removed outlier: 4.123A pdb=" N ILE A 629 " --> pdb=" O THR A 626 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET A 630 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A 633 " --> pdb=" O MET A 630 " (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 690 through 697 Processing helix chain 'A' and resid 699 through 708 removed outlier: 3.926A pdb=" N HIS A 702 " --> pdb=" O PRO A 699 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN A 703 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR A 706 " --> pdb=" O GLN A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 722 removed outlier: 4.154A pdb=" N LEU A 717 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 718 " --> pdb=" O GLU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 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 772 through 785 removed outlier: 4.075A pdb=" N LEU A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 795 removed outlier: 4.175A pdb=" N THR A 793 " --> pdb=" O GLU A 789 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS A 794 " --> pdb=" O GLU A 790 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 836 Processing helix chain 'B' and resid 36 through 52 Processing helix chain 'B' and resid 73 through 85 removed outlier: 3.693A pdb=" N SER B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.897A pdb=" N PHE B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 144 through 158 removed outlier: 3.589A pdb=" N VAL B 150 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG B 156 " --> pdb=" O GLU B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 187 removed outlier: 4.383A pdb=" N GLU B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.860A 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: 3.920A pdb=" N MET B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 256 through 260 Processing helix chain 'B' and resid 277 through 295 removed outlier: 3.867A pdb=" N GLN B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 327 removed outlier: 3.540A pdb=" N LYS B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 469 removed outlier: 3.621A 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 524 No H-bonds generated for 'chain 'B' and resid 521 through 524' Processing helix chain 'B' and resid 560 through 582 removed outlier: 4.201A pdb=" N LEU B 564 " --> pdb=" O THR B 561 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 572 " --> pdb=" O SER B 569 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL B 573 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 575 " --> pdb=" O VAL B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 614 Processing helix chain 'B' and resid 627 through 657 removed outlier: 3.745A pdb=" N VAL B 656 " --> pdb=" O ALA B 652 " (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 695 Processing helix chain 'B' and resid 700 through 709 removed outlier: 3.816A pdb=" N MET B 706 " --> pdb=" O TYR B 703 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLU B 707 " --> pdb=" O ARG B 704 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS B 709 " --> pdb=" O MET B 706 " (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 769 through 781 removed outlier: 3.670A pdb=" N SER B 775 " --> pdb=" O ASN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 792 Processing helix chain 'B' and resid 811 through 843 removed outlier: 3.860A pdb=" N ALA B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 829 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 836 " --> pdb=" O PHE B 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 59 removed outlier: 3.752A pdb=" N GLY C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Proline residue: C 57 - end of helix Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 111 through 120 removed outlier: 4.554A pdb=" N PHE C 115 " --> pdb=" O MET C 112 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR C 120 " --> pdb=" O SER C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 153 through 164 removed outlier: 3.677A pdb=" N VAL C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET C 162 " --> pdb=" O MET C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 192 Processing helix chain 'C' and resid 215 through 221 removed outlier: 4.719A pdb=" N LYS C 221 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 246 removed outlier: 3.528A pdb=" N SER C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 262 No H-bonds generated for 'chain 'C' and resid 259 through 262' Processing helix chain 'C' and resid 288 through 309 removed outlier: 3.908A pdb=" N LYS C 309 " --> pdb=" O SER C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 337 Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 459 through 471 removed outlier: 3.571A pdb=" N ARG C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 3.806A 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 519 No H-bonds generated for 'chain 'C' and resid 516 through 519' Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.674A pdb=" N LEU C 566 " --> pdb=" O PHE C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 580 Processing helix chain 'C' and resid 601 through 611 Processing helix chain 'C' and resid 628 through 654 removed outlier: 3.630A pdb=" N TRP C 634 " --> pdb=" O MET C 630 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET C 653 " --> pdb=" O LEU C 649 " (cutoff:3.500A) removed outlier: 4.485A 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 697 Processing helix chain 'C' and resid 699 through 708 removed outlier: 3.929A pdb=" N HIS C 702 " --> pdb=" O PRO C 699 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN C 703 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR C 706 " --> pdb=" O GLN C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 721 removed outlier: 4.187A pdb=" N LEU C 717 " --> pdb=" O VAL C 713 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL C 718 " --> pdb=" O GLU C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 removed outlier: 3.594A pdb=" N TYR C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) 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 772 through 785 removed outlier: 4.121A pdb=" N LEU C 777 " --> pdb=" O ARG C 773 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 795 removed outlier: 4.177A pdb=" N THR C 793 " --> pdb=" O GLU C 789 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N CYS C 794 " --> pdb=" O GLU C 790 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TRP C 795 " --> pdb=" O LEU C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 836 Processing helix chain 'D' and resid 36 through 52 Processing helix chain 'D' and resid 72 through 85 removed outlier: 3.704A pdb=" N SER D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 113 removed outlier: 3.905A pdb=" N PHE D 113 " --> pdb=" O TYR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 128 No H-bonds generated for 'chain 'D' and resid 126 through 128' Processing helix chain 'D' and resid 144 through 158 removed outlier: 3.565A pdb=" N VAL D 150 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG D 156 " --> pdb=" O GLU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 187 removed outlier: 4.372A pdb=" N GLU D 186 " --> pdb=" O THR D 182 " (cutoff:3.500A) removed outlier: 4.852A 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: 3.917A pdb=" N MET D 237 " --> pdb=" O ARG D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 256 through 260 Processing helix chain 'D' and resid 277 through 295 removed outlier: 3.867A pdb=" N GLN D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 327 removed outlier: 3.536A pdb=" N LYS D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 469 removed outlier: 3.635A 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 524 No H-bonds generated for 'chain 'D' and resid 521 through 524' Processing helix chain 'D' and resid 560 through 582 removed outlier: 4.245A pdb=" N LEU D 564 " --> pdb=" O THR D 561 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D 572 " --> pdb=" O SER D 569 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL D 573 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL D 575 " --> pdb=" O VAL D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 614 Processing helix chain 'D' and resid 627 through 657 removed outlier: 3.798A pdb=" N VAL D 656 " --> pdb=" O ALA D 652 " (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 695 Processing helix chain 'D' and resid 700 through 709 removed outlier: 3.771A pdb=" N MET D 706 " --> pdb=" O TYR D 703 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLU D 707 " --> pdb=" O ARG D 704 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS D 709 " --> pdb=" O MET D 706 " (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 769 through 781 removed outlier: 3.673A 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 843 removed outlier: 3.800A pdb=" N ALA D 821 " --> pdb=" O PHE D 817 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE D 829 " --> pdb=" O VAL D 825 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 836 " --> pdb=" O PHE D 832 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 36 through 40 removed outlier: 6.031A pdb=" N GLY A 97 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N MET A 39 " --> pdb=" O GLY A 97 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL A 99 " --> pdb=" O MET A 39 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N PHE A 100 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU A 125 " --> pdb=" O PHE A 100 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.056A pdb=" N PHE A 254 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU A 229 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 256 " --> pdb=" O LEU A 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 277 through 280 Processing sheet with id= D, first strand: chain 'A' and resid 406 through 410 removed outlier: 3.826A pdb=" N ASP A 476 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR A 410 " --> pdb=" O TYR A 478 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 417 through 419 Processing sheet with id= F, first strand: chain 'A' and resid 436 through 440 removed outlier: 3.563A pdb=" N CYS A 436 " --> pdb=" O LYS A 454 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 452 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 533 through 536 removed outlier: 3.501A pdb=" N SER A 534 " --> pdb=" O TYR A 730 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 730 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET A 536 " --> pdb=" O PHE A 728 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 728 " --> pdb=" O MET A 536 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 60 through 65 removed outlier: 6.434A pdb=" N VAL B 27 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR B 63 " --> pdb=" O VAL B 27 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE B 29 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL B 65 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA B 31 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLY B 30 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE B 90 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL B 32 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL B 92 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL B 92 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 194 through 197 removed outlier: 6.575A pdb=" N LEU B 165 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N PHE B 197 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL B 167 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 168 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL B 246 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU B 221 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 248 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 267 through 270 Processing sheet with id= K, first strand: chain 'B' and resid 365 through 367 Processing sheet with id= L, first strand: chain 'B' and resid 397 through 402 removed outlier: 6.002A pdb=" N THR B 473 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 400 " --> pdb=" O THR B 473 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU B 475 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR B 402 " --> pdb=" O GLU B 475 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N HIS B 477 " --> pdb=" O THR B 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 409 through 412 removed outlier: 3.582A pdb=" N VAL B 451 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY B 438 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS B 455 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL B 434 " --> pdb=" O CYS B 455 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 729 through 732 removed outlier: 3.859A pdb=" N TRP B 731 " --> pdb=" O THR B 539 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 36 through 40 removed outlier: 6.022A pdb=" N GLY C 97 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N MET C 39 " --> pdb=" O GLY C 97 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL C 99 " --> pdb=" O MET C 39 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N PHE C 100 " --> pdb=" O PRO C 123 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU C 125 " --> pdb=" O PHE C 100 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 226 through 229 removed outlier: 6.067A pdb=" N PHE C 254 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU C 229 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 256 " --> pdb=" O LEU C 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 277 through 280 Processing sheet with id= R, first strand: chain 'C' and resid 406 through 410 removed outlier: 3.849A pdb=" N ASP C 476 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR C 410 " --> pdb=" O TYR C 478 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 417 through 419 Processing sheet with id= T, first strand: chain 'C' and resid 436 through 440 removed outlier: 3.516A pdb=" N CYS C 436 " --> pdb=" O LYS C 454 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 452 " --> pdb=" O LYS C 438 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 533 through 536 removed outlier: 3.546A pdb=" N TYR C 730 " --> pdb=" O SER C 534 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET C 536 " --> pdb=" O PHE C 728 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE C 728 " --> pdb=" O MET C 536 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 60 through 65 removed outlier: 6.438A pdb=" N VAL D 27 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR D 63 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE D 29 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL D 65 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA D 31 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLY D 30 " --> pdb=" O TYR D 88 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE D 90 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL D 32 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL D 92 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL D 92 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 194 through 197 removed outlier: 6.575A pdb=" N LEU D 165 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N PHE D 197 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL D 167 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 168 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL D 246 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU D 221 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU D 248 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 267 through 270 Processing sheet with id= Y, first strand: chain 'D' and resid 365 through 367 Processing sheet with id= Z, first strand: chain 'D' and resid 397 through 402 removed outlier: 5.982A pdb=" N THR D 473 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE D 400 " --> pdb=" O THR D 473 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLU D 475 " --> pdb=" O ILE D 400 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR D 402 " --> pdb=" O GLU D 475 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N HIS D 477 " --> pdb=" O THR D 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'D' and resid 409 through 412 removed outlier: 3.582A pdb=" N VAL D 451 " --> pdb=" O GLY D 438 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY D 438 " --> pdb=" O VAL D 451 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N CYS D 455 " --> pdb=" O VAL D 434 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL D 434 " --> pdb=" O CYS D 455 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 729 through 732 removed outlier: 3.834A pdb=" N TRP D 731 " --> pdb=" O THR D 539 " (cutoff:3.500A) 780 hydrogen bonds defined for protein. 1993 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.08 Time building geometry restraints manager: 10.54 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: 3908 1.32 - 1.44: 6770 1.44 - 1.56: 13822 1.56 - 1.69: 0 1.69 - 1.81: 258 Bond restraints: 24758 Sorted by residual: bond pdb=" N 6RM A 902 " pdb=" C2 6RM A 902 " ideal model delta sigma weight residual 1.412 1.371 0.041 2.00e-02 2.50e+03 4.21e+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 4.13e+00 bond pdb=" C1 NAG D 905 " pdb=" O5 NAG D 905 " ideal model delta sigma weight residual 1.426 1.482 -0.056 3.20e-02 9.77e+02 3.01e+00 bond pdb=" C1 NAG B 905 " pdb=" O5 NAG B 905 " ideal model delta sigma weight residual 1.426 1.481 -0.055 3.20e-02 9.77e+02 2.96e+00 bond pdb=" C14 6RM C 902 " pdb=" C2 6RM C 902 " ideal model delta sigma weight residual 1.477 1.502 -0.025 2.00e-02 2.50e+03 1.53e+00 ... (remaining 24753 not shown) Histogram of bond angle deviations from ideal: 59.16 - 74.15: 6 74.15 - 89.13: 0 89.13 - 104.12: 369 104.12 - 119.10: 20211 119.10 - 134.09: 12980 Bond angle restraints: 33566 Sorted by residual: angle pdb=" C1 NAG B 905 " pdb=" O5 NAG B 905 " pdb=" C5 NAG B 905 " ideal model delta sigma weight residual 113.34 117.76 -4.42 1.74e+00 3.30e-01 6.44e+00 angle pdb=" C1 NAG D 905 " pdb=" O5 NAG D 905 " pdb=" C5 NAG D 905 " ideal model delta sigma weight residual 113.34 117.73 -4.39 1.74e+00 3.30e-01 6.37e+00 angle pdb=" C GLU A 211 " pdb=" N ASP A 212 " pdb=" CA ASP A 212 " ideal model delta sigma weight residual 121.54 126.24 -4.70 1.91e+00 2.74e-01 6.06e+00 angle pdb=" C5 6RM A 902 " pdb=" C7 6RM A 902 " pdb=" O1 6RM A 902 " ideal model delta sigma weight residual 107.46 114.20 -6.74 3.00e+00 1.11e-01 5.05e+00 angle pdb=" C CYS A 399 " pdb=" N GLU A 400 " pdb=" CA GLU A 400 " ideal model delta sigma weight residual 121.80 127.24 -5.44 2.44e+00 1.68e-01 4.96e+00 ... (remaining 33561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 14248 21.85 - 43.70: 367 43.70 - 65.55: 29 65.55 - 87.40: 6 87.40 - 109.25: 2 Dihedral angle restraints: 14652 sinusoidal: 5868 harmonic: 8784 Sorted by residual: dihedral pdb=" C2 NAG D 905 " pdb=" C1 NAG D 905 " pdb=" O5 NAG D 905 " pdb=" C5 NAG D 905 " ideal model delta sinusoidal sigma weight residual -50.00 59.25 -109.25 1 2.00e+01 2.50e-03 3.19e+01 dihedral pdb=" C2 NAG B 905 " pdb=" C1 NAG B 905 " pdb=" O5 NAG B 905 " pdb=" C5 NAG B 905 " ideal model delta sinusoidal sigma weight residual -50.00 59.18 -109.18 1 2.00e+01 2.50e-03 3.19e+01 dihedral pdb=" C1 NAG B 905 " pdb=" C5 NAG B 905 " pdb=" O5 NAG B 905 " pdb=" C4 NAG B 905 " ideal model delta sinusoidal sigma weight residual -50.00 35.20 -85.20 1 2.00e+01 2.50e-03 2.20e+01 ... (remaining 14649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3308 0.058 - 0.116: 491 0.116 - 0.174: 25 0.174 - 0.233: 0 0.233 - 0.291: 2 Chirality restraints: 3826 Sorted by residual: chirality pdb=" C1 NAG D 902 " pdb=" ND2 ASN D 276 " pdb=" C2 NAG D 902 " pdb=" O5 NAG D 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C1 NAG B 902 " pdb=" ND2 ASN B 276 " pdb=" C2 NAG B 902 " pdb=" O5 NAG B 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C1 NAG B 905 " pdb=" ND2 ASN B 771 " pdb=" C2 NAG B 905 " pdb=" O5 NAG B 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.05e-01 ... (remaining 3823 not shown) Planarity restraints: 4220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N 6RM C 902 " 0.020 2.00e-02 2.50e+03 5.51e-02 9.87e+01 pdb=" C 6RM C 902 " -0.106 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 " -0.008 2.00e-02 2.50e+03 pdb=" C4 6RM C 902 " 0.006 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 A 902 " 0.021 2.00e-02 2.50e+03 5.50e-02 9.84e+01 pdb=" C 6RM A 902 " -0.107 2.00e-02 2.50e+03 pdb=" O 6RM A 902 " -0.064 2.00e-02 2.50e+03 pdb=" C1 6RM A 902 " -0.014 2.00e-02 2.50e+03 pdb=" C14 6RM A 902 " 0.083 2.00e-02 2.50e+03 pdb=" C2 6RM A 902 " 0.011 2.00e-02 2.50e+03 pdb=" C3 6RM A 902 " -0.008 2.00e-02 2.50e+03 pdb=" C4 6RM A 902 " 0.005 2.00e-02 2.50e+03 pdb=" C5 6RM A 902 " 0.029 2.00e-02 2.50e+03 pdb=" C6 6RM A 902 " 0.045 2.00e-02 2.50e+03 pdb=" C7 6RM A 902 " -0.091 2.00e-02 2.50e+03 pdb=" N1 6RM A 902 " 0.065 2.00e-02 2.50e+03 pdb=" S 6RM A 902 " 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 8.69e+00 pdb=" C11 6RM C 902 " -0.010 2.00e-02 2.50e+03 pdb=" C12 6RM C 902 " -0.001 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 " -0.017 2.00e-02 2.50e+03 pdb=" O1 6RM C 902 " -0.041 2.00e-02 2.50e+03 ... (remaining 4217 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3657 2.76 - 3.30: 23935 3.30 - 3.83: 38766 3.83 - 4.37: 42465 4.37 - 4.90: 73313 Nonbonded interactions: 182136 Sorted by model distance: nonbonded pdb=" O THR B 396 " pdb=" OG1 THR B 473 " model vdw 2.227 2.440 nonbonded pdb=" OG1 THR C 446 " pdb=" OE1 GLU C 448 " model vdw 2.228 2.440 nonbonded pdb=" O THR D 396 " pdb=" OG1 THR D 473 " model vdw 2.229 2.440 nonbonded pdb=" O GLU A 577 " pdb=" OG SER A 580 " model vdw 2.231 2.440 nonbonded pdb=" OG1 THR A 446 " pdb=" OE1 GLU A 448 " model vdw 2.231 2.440 ... (remaining 182131 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 25 through 775 or resid 777 through 844 or resid 901 throu \ gh 906)) selection = (chain 'D' and (resid 25 through 775 or resid 777 through 844 or resid 901 throu \ gh 906)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 150 5.16 5 C 15544 2.51 5 N 4040 2.21 5 O 4468 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.710 Check model and map are aligned: 0.330 Process input model: 67.970 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.250 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 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 0.056 24758 Z= 0.113 Angle : 0.423 7.849 33566 Z= 0.216 Chirality : 0.041 0.291 3826 Planarity : 0.003 0.055 4206 Dihedral : 9.091 109.255 8946 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 1.64 % 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: 0.66 (0.17), residues: 2980 helix: 2.18 (0.16), residues: 1162 sheet: -0.18 (0.32), residues: 344 loop : -0.86 (0.17), residues: 1474 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 546 time to evaluate : 2.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 8 residues processed: 587 average time/residue: 0.3934 time to fit residues: 347.7143 Evaluate side-chains 304 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 296 time to evaluate : 3.341 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2320 time to fit residues: 7.7549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 20.0000 chunk 228 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 236 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 274 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN A 674 HIS A 736 ASN B 363 GLN B 477 HIS ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN C 490 ASN C 674 HIS D 363 GLN D 477 HIS D 650 ASN ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 24758 Z= 0.414 Angle : 0.758 9.050 33566 Z= 0.387 Chirality : 0.047 0.246 3826 Planarity : 0.006 0.098 4206 Dihedral : 6.148 110.529 3332 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 2.48 % 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: -0.34 (0.16), residues: 2980 helix: 1.13 (0.15), residues: 1220 sheet: -0.96 (0.28), residues: 370 loop : -1.24 (0.17), residues: 1390 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 270 time to evaluate : 2.950 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 outliers start: 65 outliers final: 42 residues processed: 320 average time/residue: 0.3556 time to fit residues: 180.6588 Evaluate side-chains 275 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 233 time to evaluate : 2.885 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.2426 time to fit residues: 22.8495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 152 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 228 optimal weight: 8.9990 chunk 186 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 274 optimal weight: 0.7980 chunk 296 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 272 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 chunk 220 optimal weight: 0.0070 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN B 134 HIS B 559 GLN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN C 153 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 24758 Z= 0.164 Angle : 0.587 11.487 33566 Z= 0.288 Chirality : 0.044 0.300 3826 Planarity : 0.003 0.041 4206 Dihedral : 5.791 109.935 3332 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 0.91 % 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: -0.18 (0.16), residues: 2980 helix: 1.27 (0.16), residues: 1190 sheet: -0.87 (0.28), residues: 384 loop : -1.10 (0.17), residues: 1406 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 278 time to evaluate : 2.946 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: 24 outliers final: 7 residues processed: 296 average time/residue: 0.3539 time to fit residues: 166.7123 Evaluate side-chains 234 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 227 time to evaluate : 2.935 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2477 time to fit residues: 7.2055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 271 optimal weight: 10.0000 chunk 206 optimal weight: 0.3980 chunk 142 optimal weight: 0.3980 chunk 30 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 chunk 184 optimal weight: 0.4980 chunk 275 optimal weight: 1.9990 chunk 291 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 261 optimal weight: 0.3980 chunk 78 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 24758 Z= 0.151 Angle : 0.572 10.553 33566 Z= 0.280 Chirality : 0.044 0.312 3826 Planarity : 0.003 0.049 4206 Dihedral : 5.744 110.097 3332 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 1.37 % 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: 2980 helix: 1.12 (0.16), residues: 1206 sheet: -0.74 (0.27), residues: 410 loop : -1.12 (0.17), residues: 1364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 252 time to evaluate : 3.180 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: 36 outliers final: 15 residues processed: 275 average time/residue: 0.3551 time to fit residues: 155.1796 Evaluate side-chains 244 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 229 time to evaluate : 3.019 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2461 time to fit residues: 10.4040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 243 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 217 optimal weight: 0.6980 chunk 120 optimal weight: 8.9990 chunk 249 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 149 optimal weight: 50.0000 chunk 262 optimal weight: 5.9990 chunk 73 optimal weight: 30.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 HIS A 515 ASN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN C 515 ASN C 736 ASN ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 24758 Z= 0.326 Angle : 0.671 12.217 33566 Z= 0.336 Chirality : 0.045 0.301 3826 Planarity : 0.004 0.052 4206 Dihedral : 6.086 110.884 3332 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer Outliers : 1.49 % 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: -0.51 (0.16), residues: 2980 helix: 1.06 (0.15), residues: 1194 sheet: -1.06 (0.26), residues: 430 loop : -1.36 (0.17), residues: 1356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 222 time to evaluate : 2.787 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: 39 outliers final: 26 residues processed: 242 average time/residue: 0.3510 time to fit residues: 136.4074 Evaluate side-chains 234 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 2.827 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2503 time to fit residues: 15.3876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 98 optimal weight: 7.9990 chunk 262 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 72 optimal weight: 30.0000 chunk 292 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 HIS ** C 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 HIS ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 24758 Z= 0.337 Angle : 0.681 11.289 33566 Z= 0.345 Chirality : 0.046 0.331 3826 Planarity : 0.004 0.089 4206 Dihedral : 6.334 111.625 3332 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 1.52 % 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: -0.83 (0.15), residues: 2980 helix: 0.84 (0.15), residues: 1182 sheet: -1.38 (0.24), residues: 466 loop : -1.49 (0.17), residues: 1332 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 214 time to evaluate : 2.777 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: 40 outliers final: 25 residues processed: 242 average time/residue: 0.3747 time to fit residues: 143.8147 Evaluate side-chains 224 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 199 time to evaluate : 2.993 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2572 time to fit residues: 15.4264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 281 optimal weight: 50.0000 chunk 32 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 165 optimal weight: 8.9990 chunk 245 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 291 optimal weight: 2.9990 chunk 182 optimal weight: 0.0670 chunk 177 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 24758 Z= 0.170 Angle : 0.629 11.934 33566 Z= 0.310 Chirality : 0.045 0.347 3826 Planarity : 0.004 0.044 4206 Dihedral : 6.089 110.994 3332 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.57 % 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: -0.58 (0.16), residues: 2980 helix: 0.98 (0.15), residues: 1172 sheet: -1.09 (0.24), residues: 460 loop : -1.33 (0.17), residues: 1348 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 227 time to evaluate : 3.241 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: 15 outliers final: 8 residues processed: 234 average time/residue: 0.4033 time to fit residues: 147.7603 Evaluate side-chains 219 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 211 time to evaluate : 3.193 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2848 time to fit residues: 7.9319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 180 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 185 optimal weight: 0.5980 chunk 198 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 228 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 24758 Z= 0.202 Angle : 0.641 11.434 33566 Z= 0.313 Chirality : 0.044 0.345 3826 Planarity : 0.004 0.044 4206 Dihedral : 6.069 111.540 3332 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2980 helix: 0.91 (0.15), residues: 1186 sheet: -1.17 (0.25), residues: 422 loop : -1.25 (0.17), residues: 1372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 219 time to evaluate : 2.810 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: 16 outliers final: 3 residues processed: 229 average time/residue: 0.3904 time to fit residues: 141.2184 Evaluate side-chains 214 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 211 time to evaluate : 2.907 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2725 time to fit residues: 5.3368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 264 optimal weight: 10.0000 chunk 278 optimal weight: 9.9990 chunk 254 optimal weight: 0.0980 chunk 271 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 245 optimal weight: 10.0000 chunk 256 optimal weight: 7.9990 chunk 270 optimal weight: 8.9990 overall best weight: 6.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN ** C 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN ** D 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.6149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.061 24758 Z= 0.449 Angle : 0.784 12.053 33566 Z= 0.395 Chirality : 0.047 0.336 3826 Planarity : 0.005 0.054 4206 Dihedral : 6.604 112.292 3332 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.15), residues: 2980 helix: 0.46 (0.15), residues: 1196 sheet: -1.78 (0.26), residues: 392 loop : -1.57 (0.17), residues: 1392 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 199 time to evaluate : 3.031 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: 22 outliers final: 10 residues processed: 211 average time/residue: 0.4008 time to fit residues: 131.8626 Evaluate side-chains 200 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 190 time to evaluate : 2.717 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3286 time to fit residues: 9.8838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 178 optimal weight: 9.9990 chunk 286 optimal weight: 0.0970 chunk 175 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 chunk 300 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 chunk 239 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 146 optimal weight: 0.4980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN B 146 HIS B 177 GLN B 427 ASN B 705 HIS ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN C 736 ASN D 146 HIS ** D 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 427 ASN ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 24758 Z= 0.181 Angle : 0.676 12.277 33566 Z= 0.332 Chirality : 0.045 0.361 3826 Planarity : 0.004 0.045 4206 Dihedral : 6.265 111.596 3332 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.16), residues: 2980 helix: 0.73 (0.15), residues: 1182 sheet: -1.39 (0.24), residues: 450 loop : -1.33 (0.17), residues: 1348 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 213 time to evaluate : 2.872 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: 6 outliers final: 2 residues processed: 217 average time/residue: 0.3846 time to fit residues: 131.2115 Evaluate side-chains 200 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 198 time to evaluate : 3.013 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2515 time to fit residues: 4.9490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 190 optimal weight: 10.0000 chunk 255 optimal weight: 7.9990 chunk 73 optimal weight: 50.0000 chunk 220 optimal weight: 0.0170 chunk 35 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 239 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 246 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.086481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.062395 restraints weight = 114867.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.064151 restraints weight = 63994.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.065475 restraints weight = 44152.130| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.6120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 24758 Z= 0.265 Angle : 0.697 13.696 33566 Z= 0.341 Chirality : 0.045 0.352 3826 Planarity : 0.004 0.046 4206 Dihedral : 6.268 112.091 3332 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.91 (0.16), residues: 2980 helix: 0.62 (0.15), residues: 1196 sheet: -1.45 (0.25), residues: 428 loop : -1.39 (0.17), residues: 1356 =============================================================================== Job complete usr+sys time: 4388.45 seconds wall clock time: 82 minutes 2.28 seconds (4922.28 seconds total)