Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 13:47:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7te9_25843/04_2023/7te9_25843.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7te9_25843/04_2023/7te9_25843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7te9_25843/04_2023/7te9_25843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7te9_25843/04_2023/7te9_25843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7te9_25843/04_2023/7te9_25843.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7te9_25843/04_2023/7te9_25843.pdb" } resolution = 3.92 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= 0.053 sd= 0.476 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: 4 Type Number sf(0) Gaussians S 174 5.16 5 C 17983 2.51 5 N 4715 2.21 5 O 5270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 219": "OD1" <-> "OD2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "B GLU 791": "OE1" <-> "OE2" Residue "C ASP 219": "OD1" <-> "OD2" Residue "C TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 543": "OE1" <-> "OE2" Residue "C GLU 682": "OE1" <-> "OE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 449": "OE1" <-> "OE2" Residue "D GLU 791": "OE1" <-> "OE2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "M GLU 89": "OE1" <-> "OE2" Residue "M PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 79": "OE1" <-> "OE2" Residue "N GLU 81": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 28142 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 6265 Classifications: {'peptide': 794} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 31, 'TRANS': 760} Chain breaks: 4 Chain: "B" Number of atoms: 6084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6084 Classifications: {'peptide': 784} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 26} Link IDs: {'PTRANS': 29, 'TRANS': 754} Chain breaks: 5 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "C" Number of atoms: 6265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 6265 Classifications: {'peptide': 794} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 31, 'TRANS': 760} Chain breaks: 4 Chain: "D" Number of atoms: 6084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6084 Classifications: {'peptide': 784} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 26} Link IDs: {'PTRANS': 29, 'TRANS': 754} Chain breaks: 5 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "H" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 905 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain breaks: 1 Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "M" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 899 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 1 Chain: "N" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Time building chain proxies: 14.44, per 1000 atoms: 0.51 Number of scatterers: 28142 At special positions: 0 Unit cell: (146.59, 223.31, 180.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 174 16.00 O 5270 8.00 N 4715 7.00 C 17983 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.04 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.04 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.03 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.04 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.04 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.04 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.04 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.03 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.04 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.04 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " 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 Time building additional restraints: 11.08 Conformation dependent library (CDL) restraints added in 4.3 seconds 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6678 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 45 sheets defined 34.5% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.929A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 77 Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 125 through 130 removed outlier: 4.418A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 removed outlier: 4.157A pdb=" N ARG A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 183 Processing helix chain 'A' and resid 184 through 188 removed outlier: 3.819A pdb=" N ARG A 187 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A 188 " --> pdb=" O GLU A 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 184 through 188' Processing helix chain 'A' and resid 225 through 234 removed outlier: 4.040A pdb=" N GLU A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 253 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 262 through 266 removed outlier: 4.438A pdb=" N GLY A 265 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR A 266 " --> pdb=" O GLY A 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 262 through 266' Processing helix chain 'A' and resid 297 through 318 removed outlier: 3.713A pdb=" N HIS A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 318 " --> pdb=" O HIS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 520 through 528 removed outlier: 3.712A pdb=" N GLY A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 547 removed outlier: 3.792A pdb=" N GLN A 546 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR A 547 " --> pdb=" O ARG A 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 543 through 547' Processing helix chain 'A' and resid 585 through 604 Processing helix chain 'A' and resid 626 through 636 removed outlier: 3.809A pdb=" N GLY A 633 " --> pdb=" O TRP A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 678 removed outlier: 3.503A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.553A pdb=" N ILE A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 726 Processing helix chain 'A' and resid 734 through 743 removed outlier: 3.838A pdb=" N ALA A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 743 " --> pdb=" O ILE A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 removed outlier: 4.926A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 791 removed outlier: 4.369A pdb=" N GLN A 791 " --> pdb=" O PRO A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 803 removed outlier: 3.773A pdb=" N ILE A 797 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU A 798 " --> pdb=" O SER A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 834 through 862 removed outlier: 4.454A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL A 841 " --> pdb=" O VAL A 837 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL A 846 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.611A pdb=" N ILE B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.993A pdb=" N ASP B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 120 removed outlier: 4.204A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 151 through 162 Processing helix chain 'B' and resid 179 through 187 removed outlier: 3.645A pdb=" N VAL B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN B 184 " --> pdb=" O GLN B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 219 Processing helix chain 'B' and resid 220 through 223 removed outlier: 3.537A pdb=" N LEU B 223 " --> pdb=" O LEU B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 220 through 223' Processing helix chain 'B' and resid 233 through 248 removed outlier: 4.259A pdb=" N GLU B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 243 " --> pdb=" O TYR B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 312 Processing helix chain 'B' and resid 331 through 340 removed outlier: 3.871A pdb=" N ILE B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 472 removed outlier: 3.583A pdb=" N LYS B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 removed outlier: 3.555A pdb=" N MET B 503 " --> pdb=" O GLY B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 521 removed outlier: 3.575A pdb=" N SER B 520 " --> pdb=" O ASN B 516 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 521' Processing helix chain 'B' and resid 557 through 567 removed outlier: 4.412A pdb=" N PHE B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 579 removed outlier: 3.851A pdb=" N PHE B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 612 removed outlier: 3.669A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY B 611 " --> pdb=" O TRP B 607 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 654 removed outlier: 4.344A pdb=" N VAL B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 644 " --> pdb=" O VAL B 640 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 696 removed outlier: 3.690A pdb=" N ARG B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.725A pdb=" N HIS B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 772 through 786 removed outlier: 3.501A pdb=" N VAL B 776 " --> pdb=" O TRP B 772 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 778 " --> pdb=" O ARG B 774 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU B 781 " --> pdb=" O ASP B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 793 through 796 Processing helix chain 'B' and resid 813 through 817 removed outlier: 3.989A pdb=" N ASP B 816 " --> pdb=" O LEU B 813 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN B 817 " --> pdb=" O ASP B 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 813 through 817' Processing helix chain 'B' and resid 818 through 838 removed outlier: 3.549A pdb=" N ALA B 827 " --> pdb=" O TYR B 823 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA B 828 " --> pdb=" O MET B 824 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 833 " --> pdb=" O MET B 829 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 836 " --> pdb=" O SER B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 841 No H-bonds generated for 'chain 'B' and resid 839 through 841' Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.930A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 106 through 111 Processing helix chain 'C' and resid 125 through 130 removed outlier: 4.417A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 159 removed outlier: 4.157A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 183 Processing helix chain 'C' and resid 184 through 188 removed outlier: 3.819A pdb=" N ARG C 187 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU C 188 " --> pdb=" O GLU C 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 184 through 188' Processing helix chain 'C' and resid 225 through 234 removed outlier: 4.040A pdb=" N GLU C 234 " --> pdb=" O MET C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 253 Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 262 through 266 removed outlier: 4.437A pdb=" N GLY C 265 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR C 266 " --> pdb=" O GLY C 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 262 through 266' Processing helix chain 'C' and resid 297 through 318 removed outlier: 3.712A pdb=" N HIS C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU C 318 " --> pdb=" O HIS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 478 through 492 Processing helix chain 'C' and resid 520 through 528 removed outlier: 3.712A pdb=" N GLY C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 525 " --> pdb=" O GLY C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 547 removed outlier: 3.791A pdb=" N GLN C 546 " --> pdb=" O GLU C 543 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR C 547 " --> pdb=" O ARG C 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 543 through 547' Processing helix chain 'C' and resid 585 through 604 Processing helix chain 'C' and resid 626 through 636 removed outlier: 3.808A pdb=" N GLY C 633 " --> pdb=" O TRP C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 678 removed outlier: 3.504A pdb=" N ARG C 651 " --> pdb=" O SER C 647 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 678 " --> pdb=" O ALA C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 717 removed outlier: 3.553A pdb=" N ILE C 712 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN C 717 " --> pdb=" O TYR C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 726 Processing helix chain 'C' and resid 734 through 743 removed outlier: 3.838A pdb=" N ALA C 738 " --> pdb=" O SER C 734 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG C 743 " --> pdb=" O ILE C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 764 removed outlier: 4.926A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER C 762 " --> pdb=" O GLU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 791 removed outlier: 4.369A pdb=" N GLN C 791 " --> pdb=" O PRO C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 803 removed outlier: 3.773A pdb=" N ILE C 797 " --> pdb=" O VAL C 793 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU C 798 " --> pdb=" O SER C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 834 through 862 removed outlier: 4.454A pdb=" N LEU C 840 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL C 841 " --> pdb=" O VAL C 837 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL C 846 " --> pdb=" O ALA C 842 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE C 849 " --> pdb=" O ILE C 845 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE C 850 " --> pdb=" O VAL C 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.611A pdb=" N ILE D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 removed outlier: 3.993A pdb=" N ASP D 87 " --> pdb=" O THR D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 120 removed outlier: 4.203A pdb=" N GLN D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'D' and resid 151 through 162 Processing helix chain 'D' and resid 179 through 187 removed outlier: 3.645A pdb=" N VAL D 183 " --> pdb=" O TYR D 179 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN D 184 " --> pdb=" O GLN D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'D' and resid 220 through 223 removed outlier: 3.537A pdb=" N LEU D 223 " --> pdb=" O LEU D 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 220 through 223' Processing helix chain 'D' and resid 233 through 248 removed outlier: 4.259A pdb=" N GLU D 242 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 243 " --> pdb=" O TYR D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 312 Processing helix chain 'D' and resid 331 through 340 removed outlier: 3.872A pdb=" N ILE D 340 " --> pdb=" O ASN D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 472 removed outlier: 3.582A pdb=" N LYS D 467 " --> pdb=" O ASP D 463 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 503 removed outlier: 3.555A pdb=" N MET D 503 " --> pdb=" O GLY D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 521 removed outlier: 3.574A pdb=" N SER D 520 " --> pdb=" O ASN D 516 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 516 through 521' Processing helix chain 'D' and resid 557 through 567 removed outlier: 4.412A pdb=" N PHE D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL D 564 " --> pdb=" O VAL D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 579 removed outlier: 3.851A pdb=" N PHE D 577 " --> pdb=" O ALA D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 612 removed outlier: 3.669A pdb=" N TRP D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY D 611 " --> pdb=" O TRP D 607 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 654 removed outlier: 4.344A pdb=" N VAL D 632 " --> pdb=" O SER D 628 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER D 633 " --> pdb=" O LYS D 629 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE D 641 " --> pdb=" O PHE D 637 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 644 " --> pdb=" O VAL D 640 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 648 " --> pdb=" O ALA D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 696 removed outlier: 3.689A pdb=" N ARG D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 removed outlier: 3.724A pdb=" N HIS D 703 " --> pdb=" O TYR D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 740 Processing helix chain 'D' and resid 772 through 786 removed outlier: 3.501A pdb=" N VAL D 776 " --> pdb=" O TRP D 772 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 778 " --> pdb=" O ARG D 774 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU D 781 " --> pdb=" O ASP D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 792 Processing helix chain 'D' and resid 793 through 796 Processing helix chain 'D' and resid 813 through 817 removed outlier: 3.989A pdb=" N ASP D 816 " --> pdb=" O LEU D 813 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN D 817 " --> pdb=" O ASP D 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 813 through 817' Processing helix chain 'D' and resid 818 through 838 removed outlier: 3.549A pdb=" N ALA D 827 " --> pdb=" O TYR D 823 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA D 828 " --> pdb=" O MET D 824 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU D 833 " --> pdb=" O MET D 829 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE D 836 " --> pdb=" O SER D 832 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 841 No H-bonds generated for 'chain 'D' and resid 839 through 841' Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.603A pdb=" N VAL A 27 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 11.670A pdb=" N ILE A 26 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 11.325A pdb=" N ALA A 89 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ASN A 28 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N LEU A 91 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY A 30 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 214 through 215 Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 290 Processing sheet with id=AA4, first strand: chain 'A' and resid 494 through 499 removed outlier: 3.693A pdb=" N THR A 423 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET A 533 " --> pdb=" O LYS A 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 433 through 434 Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 511 removed outlier: 3.699A pdb=" N GLU A 509 " --> pdb=" O GLU A 518 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 518 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS A 516 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 750 through 753 Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 73 removed outlier: 8.383A pdb=" N VAL B 71 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 39 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N MET B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE B 123 " --> pdb=" O PHE B 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 203 through 204 removed outlier: 3.585A pdb=" N LEU B 203 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE B 228 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 278 through 281 removed outlier: 5.013A pdb=" N SER B 279 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE B 365 " --> pdb=" O SER B 279 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 378 through 380 Processing sheet with id=AB3, first strand: chain 'B' and resid 408 through 410 removed outlier: 6.195A pdb=" N ILE B 408 " --> pdb=" O TYR B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AB5, first strand: chain 'B' and resid 488 through 490 removed outlier: 3.968A pdb=" N LYS B 488 " --> pdb=" O ASN B 495 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 524 through 525 removed outlier: 4.116A pdb=" N ASP B 524 " --> pdb=" O ILE B 766 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 766 " --> pdb=" O ASP B 524 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AB8, first strand: chain 'B' and resid 534 through 538 removed outlier: 3.630A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.602A pdb=" N VAL C 27 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 11.671A pdb=" N ILE C 26 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 11.323A pdb=" N ALA C 89 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASN C 28 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N LEU C 91 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY C 30 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 214 through 215 Processing sheet with id=AC2, first strand: chain 'C' and resid 288 through 290 Processing sheet with id=AC3, first strand: chain 'C' and resid 494 through 499 removed outlier: 3.694A pdb=" N THR C 423 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET C 533 " --> pdb=" O LYS C 420 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 433 through 434 Processing sheet with id=AC5, first strand: chain 'C' and resid 508 through 511 removed outlier: 3.699A pdb=" N GLU C 509 " --> pdb=" O GLU C 518 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU C 518 " --> pdb=" O GLU C 509 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS C 516 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 750 through 753 Processing sheet with id=AC7, first strand: chain 'D' and resid 70 through 73 removed outlier: 8.383A pdb=" N VAL D 71 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL D 39 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N MET D 73 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE D 123 " --> pdb=" O PHE D 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 203 through 204 removed outlier: 3.586A pdb=" N LEU D 203 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE D 228 " --> pdb=" O THR D 255 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 278 through 281 removed outlier: 5.014A pdb=" N SER D 279 " --> pdb=" O ILE D 365 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE D 365 " --> pdb=" O SER D 279 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 378 through 380 Processing sheet with id=AD2, first strand: chain 'D' and resid 408 through 410 removed outlier: 6.195A pdb=" N ILE D 408 " --> pdb=" O TYR D 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 418 through 420 Processing sheet with id=AD4, first strand: chain 'D' and resid 488 through 490 removed outlier: 3.967A pdb=" N LYS D 488 " --> pdb=" O ASN D 495 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 524 through 525 removed outlier: 4.115A pdb=" N ASP D 524 " --> pdb=" O ILE D 766 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 766 " --> pdb=" O ASP D 524 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 531 through 532 Processing sheet with id=AD7, first strand: chain 'D' and resid 534 through 538 removed outlier: 3.631A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.600A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS H 22 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.950A pdb=" N SER H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA H 97 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.950A pdb=" N SER H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA H 97 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 12 through 13 removed outlier: 3.757A pdb=" N ALA L 13 " --> pdb=" O GLU L 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AE4, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AE5, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.573A pdb=" N LEU M 18 " --> pdb=" O MET M 83 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU M 81 " --> pdb=" O LEU M 20 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N CYS M 22 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU M 79 " --> pdb=" O CYS M 22 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 45 through 47 removed outlier: 3.813A pdb=" N SER M 35 " --> pdb=" O ALA M 97 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA M 97 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET M 93 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 12 through 13 removed outlier: 3.758A pdb=" N ALA N 13 " --> pdb=" O GLU N 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'N' and resid 18 through 24 Processing sheet with id=AE9, first strand: chain 'N' and resid 45 through 46 852 hydrogen bonds defined for protein. 2424 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.88 Time building geometry restraints manager: 11.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6032 1.33 - 1.45: 6757 1.45 - 1.57: 15665 1.57 - 1.70: 2 1.70 - 1.82: 298 Bond restraints: 28754 Sorted by residual: bond pdb=" C SER D 63 " pdb=" N VAL D 64 " ideal model delta sigma weight residual 1.330 1.204 0.126 1.57e-02 4.06e+03 6.42e+01 bond pdb=" CA THR A 830 " pdb=" CB THR A 830 " ideal model delta sigma weight residual 1.530 1.573 -0.043 1.69e-02 3.50e+03 6.51e+00 bond pdb=" CA THR C 830 " pdb=" CB THR C 830 " ideal model delta sigma weight residual 1.530 1.573 -0.043 1.69e-02 3.50e+03 6.51e+00 bond pdb=" CB THR A 830 " pdb=" CG2 THR A 830 " ideal model delta sigma weight residual 1.521 1.601 -0.080 3.30e-02 9.18e+02 5.85e+00 bond pdb=" CB THR C 830 " pdb=" CG2 THR C 830 " ideal model delta sigma weight residual 1.521 1.600 -0.079 3.30e-02 9.18e+02 5.74e+00 ... (remaining 28749 not shown) Histogram of bond angle deviations from ideal: 96.92 - 105.98: 669 105.98 - 115.03: 17358 115.03 - 124.09: 20092 124.09 - 133.14: 753 133.14 - 142.20: 70 Bond angle restraints: 38942 Sorted by residual: angle pdb=" O SER D 63 " pdb=" C SER D 63 " pdb=" N VAL D 64 " ideal model delta sigma weight residual 122.23 97.18 25.05 1.30e+00 5.92e-01 3.71e+02 angle pdb=" O SER B 63 " pdb=" C SER B 63 " pdb=" N VAL B 64 " ideal model delta sigma weight residual 122.33 96.92 25.41 1.34e+00 5.57e-01 3.60e+02 angle pdb=" CA SER B 63 " pdb=" C SER B 63 " pdb=" N VAL B 64 " ideal model delta sigma weight residual 117.82 142.20 -24.38 1.42e+00 4.96e-01 2.95e+02 angle pdb=" CA SER D 63 " pdb=" C SER D 63 " pdb=" N VAL D 64 " ideal model delta sigma weight residual 117.48 140.42 -22.94 1.41e+00 5.03e-01 2.65e+02 angle pdb=" C SER B 63 " pdb=" N VAL B 64 " pdb=" CA VAL B 64 " ideal model delta sigma weight residual 122.67 140.41 -17.74 1.68e+00 3.54e-01 1.11e+02 ... (remaining 38937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 15096 17.92 - 35.84: 1679 35.84 - 53.76: 285 53.76 - 71.69: 97 71.69 - 89.61: 17 Dihedral angle restraints: 17174 sinusoidal: 6779 harmonic: 10395 Sorted by residual: dihedral pdb=" CA PHE A 113 " pdb=" C PHE A 113 " pdb=" N TYR A 114 " pdb=" CA TYR A 114 " ideal model delta harmonic sigma weight residual 180.00 103.89 76.11 0 5.00e+00 4.00e-02 2.32e+02 dihedral pdb=" CA PHE C 113 " pdb=" C PHE C 113 " pdb=" N TYR C 114 " pdb=" CA TYR C 114 " ideal model delta harmonic sigma weight residual 180.00 103.92 76.08 0 5.00e+00 4.00e-02 2.32e+02 dihedral pdb=" CA LEU D 367 " pdb=" C LEU D 367 " pdb=" N ASN D 368 " pdb=" CA ASN D 368 " ideal model delta harmonic sigma weight residual 180.00 116.08 63.92 0 5.00e+00 4.00e-02 1.63e+02 ... (remaining 17171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3301 0.060 - 0.120: 845 0.120 - 0.180: 174 0.180 - 0.240: 31 0.240 - 0.300: 4 Chirality restraints: 4355 Sorted by residual: chirality pdb=" CB ILE A 26 " pdb=" CA ILE A 26 " pdb=" CG1 ILE A 26 " pdb=" CG2 ILE A 26 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB ILE C 26 " pdb=" CA ILE C 26 " pdb=" CG1 ILE C 26 " pdb=" CG2 ILE C 26 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE D 630 " pdb=" CA ILE D 630 " pdb=" CG1 ILE D 630 " pdb=" CG2 ILE D 630 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 4352 not shown) Planarity restraints: 4945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 63 " 0.035 2.00e-02 2.50e+03 5.81e-02 3.37e+01 pdb=" C SER D 63 " -0.100 2.00e-02 2.50e+03 pdb=" O SER D 63 " 0.027 2.00e-02 2.50e+03 pdb=" N VAL D 64 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 63 " -0.027 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C SER B 63 " 0.076 2.00e-02 2.50e+03 pdb=" O SER B 63 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL B 64 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 567 " 0.059 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO C 568 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO C 568 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 568 " 0.049 5.00e-02 4.00e+02 ... (remaining 4942 not shown) Histogram of nonbonded interaction distances: 0.93 - 1.72: 2 1.72 - 2.52: 226 2.52 - 3.31: 31858 3.31 - 4.11: 66036 4.11 - 4.90: 115199 Warning: very small nonbonded interaction distances. Nonbonded interactions: 213321 Sorted by model distance: nonbonded pdb=" O PHE H 109 " pdb=" OH TYR L 36 " model vdw 0.928 2.440 nonbonded pdb=" O PHE M 109 " pdb=" OH TYR N 36 " model vdw 1.072 2.440 nonbonded pdb=" OD2 ASP B 58 " pdb=" OG SER M 52 " model vdw 1.782 2.440 nonbonded pdb=" OH TYR H 108 " pdb=" O ILE L 33 " model vdw 1.896 2.440 nonbonded pdb=" OH TYR H 108 " pdb=" C ILE L 33 " model vdw 1.922 3.270 ... (remaining 213316 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' selection = chain 'D' } ncs_group { reference = (chain 'H' and resid 2 through 120) selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 6.280 Check model and map are aligned: 0.410 Set scattering table: 0.230 Process input model: 69.740 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 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 : 0.006 0.126 28754 Z= 0.379 Angle : 1.061 25.410 38942 Z= 0.621 Chirality : 0.057 0.300 4355 Planarity : 0.008 0.090 4945 Dihedral : 15.479 89.606 10436 Min Nonbonded Distance : 0.928 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.79 % Favored : 89.59 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 9.86 % Twisted General : 1.49 % 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: -4.42 (0.11), residues: 3545 helix: -3.17 (0.10), residues: 1128 sheet: -1.85 (0.22), residues: 498 loop : -3.16 (0.12), residues: 1919 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 232 time to evaluate : 3.674 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 outliers start: 37 outliers final: 7 residues processed: 268 average time/residue: 0.4198 time to fit residues: 178.0868 Evaluate side-chains 181 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 174 time to evaluate : 3.814 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2417 time to fit residues: 7.9839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 0.4980 chunk 269 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 279 optimal weight: 7.9990 chunk 107 optimal weight: 30.0000 chunk 169 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 323 optimal weight: 50.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 GLN B 95 GLN B 359 HIS B 385 GLN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 ASN B 656 GLN ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 ASN B 711 GLN B 767 GLN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 HIS C 817 GLN D 95 GLN D 359 HIS D 385 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN D 656 GLN D 711 GLN D 767 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 28754 Z= 0.305 Angle : 0.763 12.715 38942 Z= 0.403 Chirality : 0.045 0.206 4355 Planarity : 0.006 0.090 4945 Dihedral : 8.073 74.446 3869 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.99 % Favored : 89.59 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 8.45 % Twisted General : 0.82 % 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: -3.39 (0.12), residues: 3545 helix: -1.44 (0.14), residues: 1220 sheet: -1.84 (0.21), residues: 516 loop : -3.02 (0.12), residues: 1809 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 178 time to evaluate : 3.576 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 outliers start: 48 outliers final: 19 residues processed: 218 average time/residue: 0.4120 time to fit residues: 145.8197 Evaluate side-chains 188 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 169 time to evaluate : 3.481 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2651 time to fit residues: 13.9998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 269 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 323 optimal weight: 50.0000 chunk 349 optimal weight: 10.0000 chunk 288 optimal weight: 6.9990 chunk 321 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 259 optimal weight: 0.0970 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN C 47 ASN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 698 ASN H 5 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 28754 Z= 0.255 Angle : 0.709 11.763 38942 Z= 0.371 Chirality : 0.044 0.174 4355 Planarity : 0.005 0.089 4945 Dihedral : 7.589 73.130 3869 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.63 % Favored : 89.00 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 8.45 % Twisted General : 0.61 % 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: -2.75 (0.13), residues: 3545 helix: -0.55 (0.15), residues: 1216 sheet: -1.77 (0.21), residues: 550 loop : -2.84 (0.13), residues: 1779 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 173 time to evaluate : 3.404 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 outliers start: 50 outliers final: 20 residues processed: 215 average time/residue: 0.4162 time to fit residues: 147.8952 Evaluate side-chains 186 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 3.798 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2844 time to fit residues: 15.5524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 0.8980 chunk 243 optimal weight: 0.0470 chunk 168 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 325 optimal weight: 8.9990 chunk 344 optimal weight: 20.0000 chunk 169 optimal weight: 9.9990 chunk 308 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 overall best weight: 2.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 GLN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN M 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 28754 Z= 0.189 Angle : 0.679 12.911 38942 Z= 0.351 Chirality : 0.044 0.184 4355 Planarity : 0.005 0.085 4945 Dihedral : 7.157 70.862 3869 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.01 % Favored : 89.68 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 6.34 % Twisted General : 0.58 % 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: -2.40 (0.14), residues: 3545 helix: -0.16 (0.15), residues: 1208 sheet: -1.55 (0.22), residues: 549 loop : -2.71 (0.13), residues: 1788 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 177 time to evaluate : 3.655 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: 34 outliers final: 13 residues processed: 205 average time/residue: 0.4163 time to fit residues: 137.4739 Evaluate side-chains 177 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 164 time to evaluate : 3.528 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3080 time to fit residues: 12.6588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 256 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 293 optimal weight: 0.7980 chunk 237 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 175 optimal weight: 4.9990 chunk 308 optimal weight: 0.9980 chunk 86 optimal weight: 0.0670 overall best weight: 2.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 GLN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 28754 Z= 0.194 Angle : 0.680 12.963 38942 Z= 0.347 Chirality : 0.043 0.156 4355 Planarity : 0.005 0.082 4945 Dihedral : 6.954 69.799 3869 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.66 % Favored : 89.06 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 5.63 % Twisted General : 0.52 % 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: -2.17 (0.14), residues: 3545 helix: 0.12 (0.15), residues: 1220 sheet: -1.32 (0.23), residues: 511 loop : -2.68 (0.13), residues: 1814 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 3.479 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: 25 outliers final: 14 residues processed: 189 average time/residue: 0.3974 time to fit residues: 123.4300 Evaluate side-chains 177 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 163 time to evaluate : 3.384 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2695 time to fit residues: 11.5486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 0.0670 chunk 309 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 202 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 344 optimal weight: 30.0000 chunk 285 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN H 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 28754 Z= 0.260 Angle : 0.714 12.830 38942 Z= 0.364 Chirality : 0.044 0.256 4355 Planarity : 0.005 0.082 4945 Dihedral : 6.917 70.143 3869 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.94 % Favored : 88.77 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 6.34 % Twisted General : 0.52 % 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: -2.10 (0.14), residues: 3545 helix: 0.24 (0.16), residues: 1224 sheet: -1.42 (0.22), residues: 557 loop : -2.67 (0.14), residues: 1764 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 3.307 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: 31 outliers final: 12 residues processed: 187 average time/residue: 0.4163 time to fit residues: 125.7894 Evaluate side-chains 172 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 160 time to evaluate : 3.470 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2875 time to fit residues: 10.5211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 30.0000 chunk 38 optimal weight: 7.9990 chunk 196 optimal weight: 7.9990 chunk 251 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 289 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 343 optimal weight: 50.0000 chunk 214 optimal weight: 0.4980 chunk 209 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 HIS ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 GLN D 152 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 28754 Z= 0.202 Angle : 0.691 13.307 38942 Z= 0.350 Chirality : 0.044 0.205 4355 Planarity : 0.004 0.080 4945 Dihedral : 6.764 68.815 3869 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.58 % Favored : 89.14 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 5.63 % Twisted General : 0.52 % 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: -1.98 (0.14), residues: 3545 helix: 0.39 (0.16), residues: 1224 sheet: -1.43 (0.22), residues: 551 loop : -2.61 (0.14), residues: 1770 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 167 time to evaluate : 3.336 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: 33 outliers final: 7 residues processed: 194 average time/residue: 0.4061 time to fit residues: 128.3678 Evaluate side-chains 168 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 161 time to evaluate : 3.432 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2774 time to fit residues: 8.2165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 30.0000 chunk 137 optimal weight: 7.9990 chunk 204 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 269 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN ** A 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 HIS B 159 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 GLN C 61 GLN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN M 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 28754 Z= 0.304 Angle : 0.783 14.204 38942 Z= 0.392 Chirality : 0.045 0.236 4355 Planarity : 0.005 0.082 4945 Dihedral : 6.885 69.801 3869 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.57 % Favored : 88.10 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 6.34 % Twisted General : 0.52 % 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: -2.06 (0.14), residues: 3545 helix: 0.34 (0.16), residues: 1222 sheet: -1.52 (0.21), residues: 573 loop : -2.65 (0.14), residues: 1750 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 163 time to evaluate : 3.749 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: 20 outliers final: 6 residues processed: 179 average time/residue: 0.4092 time to fit residues: 120.9982 Evaluate side-chains 164 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 3.436 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2625 time to fit residues: 7.6658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 7.9990 chunk 328 optimal weight: 7.9990 chunk 299 optimal weight: 0.9990 chunk 319 optimal weight: 50.0000 chunk 192 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 251 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 288 optimal weight: 4.9990 chunk 302 optimal weight: 0.7980 chunk 318 optimal weight: 9.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 HIS D 159 ASN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 28754 Z= 0.218 Angle : 0.747 13.810 38942 Z= 0.372 Chirality : 0.045 0.189 4355 Planarity : 0.004 0.081 4945 Dihedral : 6.745 68.206 3869 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.80 % Favored : 88.89 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 5.63 % Twisted General : 0.52 % 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: -1.94 (0.14), residues: 3545 helix: 0.49 (0.16), residues: 1222 sheet: -1.47 (0.22), residues: 545 loop : -2.62 (0.14), residues: 1778 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 3.446 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: 12 outliers final: 3 residues processed: 171 average time/residue: 0.4138 time to fit residues: 117.0509 Evaluate side-chains 162 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 159 time to evaluate : 3.450 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3066 time to fit residues: 6.3028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 0.0980 chunk 338 optimal weight: 10.0000 chunk 206 optimal weight: 7.9990 chunk 160 optimal weight: 8.9990 chunk 235 optimal weight: 5.9990 chunk 354 optimal weight: 20.0000 chunk 326 optimal weight: 50.0000 chunk 282 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 173 optimal weight: 0.3980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN M 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 28754 Z= 0.184 Angle : 0.749 15.232 38942 Z= 0.369 Chirality : 0.045 0.227 4355 Planarity : 0.004 0.080 4945 Dihedral : 6.590 66.754 3869 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.52 % Favored : 89.20 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 5.63 % Twisted General : 0.52 % 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: -1.82 (0.14), residues: 3545 helix: 0.60 (0.16), residues: 1220 sheet: -1.51 (0.22), residues: 553 loop : -2.51 (0.14), residues: 1772 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 166 time to evaluate : 4.851 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: 8 outliers final: 0 residues processed: 174 average time/residue: 0.4397 time to fit residues: 126.3439 Evaluate side-chains 160 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 3.434 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 10.0000 chunk 300 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 260 optimal weight: 9.9990 chunk 41 optimal weight: 0.1980 chunk 78 optimal weight: 9.9990 chunk 282 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 290 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 GLN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN H 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.048864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.036693 restraints weight = 309723.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.036758 restraints weight = 184338.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.037267 restraints weight = 125194.342| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 28754 Z= 0.171 Angle : 0.741 14.725 38942 Z= 0.365 Chirality : 0.045 0.171 4355 Planarity : 0.004 0.079 4945 Dihedral : 6.396 65.591 3869 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.99 % Favored : 89.68 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 5.63 % Twisted General : 0.50 % 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: -1.72 (0.14), residues: 3545 helix: 0.65 (0.16), residues: 1230 sheet: -1.26 (0.23), residues: 501 loop : -2.49 (0.14), residues: 1814 =============================================================================== Job complete usr+sys time: 4552.09 seconds wall clock time: 85 minutes 4.68 seconds (5104.68 seconds total)