Starting phenix.real_space_refine on Fri Mar 6 10:52:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wkr_21707/03_2026/6wkr_21707.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wkr_21707/03_2026/6wkr_21707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wkr_21707/03_2026/6wkr_21707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wkr_21707/03_2026/6wkr_21707.map" model { file = "/net/cci-nas-00/data/ceres_data/6wkr_21707/03_2026/6wkr_21707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wkr_21707/03_2026/6wkr_21707.cif" } resolution = 3.5 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1328 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 314 5.49 5 Mg 1 5.21 5 S 116 5.16 5 C 17488 2.51 5 N 5363 2.21 5 O 6013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29296 Number of models: 1 Model: "" Number of chains: 21 Chain: "T" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 604 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3340 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 19, 'TRANS': 419} Chain breaks: 7 Unresolved non-hydrogen bonds: 294 Unresolved non-hydrogen angles: 356 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 16, 'GLN:plan1': 9, 'ASN:plan1': 9, 'HIS:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 184 Chain: "L" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2874 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 349} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "N" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3080 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 22, 'TRANS': 372} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 4278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4278 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 33, 'TRANS': 572} Chain breaks: 2 Unresolved non-hydrogen bonds: 604 Unresolved non-hydrogen angles: 753 Unresolved non-hydrogen dihedrals: 486 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'ARG:plan': 16, 'GLU:plan': 27, 'TYR:plan': 5, 'GLN:plan1': 10, 'PHE:plan': 6, 'ASP:plan': 15, 'ASN:plan1': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 372 Chain: "B" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 290 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'M3L:plan-1': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "P" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1346 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 1 Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASN:plan1': 5, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 7, 'GLN:plan1': 5, 'PHE:plan': 2, 'HIS:plan': 3, 'ARG:plan': 7, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 154 Chain: "H" Number of atoms: 6439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 6439 Classifications: {'DNA': 314} Link IDs: {'rna3p': 313} Chain breaks: 1 Chain: "I" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 935 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "K" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "Q" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 667 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "S" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 203 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 34} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N LEU T 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU T 73 " occ=0.45 residue: pdb=" N ARG T 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG T 74 " occ=0.45 residue: pdb=" N GLY T 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY T 75 " occ=0.25 Time building chain proxies: 5.69, per 1000 atoms: 0.19 Number of scatterers: 29296 At special positions: 0 Unit cell: (167.783, 203.408, 171.231, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 116 16.00 P 314 15.00 Mg 1 11.99 O 6013 8.00 N 5363 7.00 C 17488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 429 " distance=2.04 Simple disulfide: pdb=" SG CYS C 286 " - pdb=" SG CYS C 294 " distance=2.02 Simple disulfide: pdb=" SG CYS C 523 " - pdb=" SG CYS C 536 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 549 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 553 " distance=2.03 Simple disulfide: pdb=" SG CYS C 549 " - pdb=" SG CYS C 553 " distance=2.87 Simple disulfide: pdb=" SG CYS C 560 " - pdb=" SG CYS C 573 " distance=2.01 Simple disulfide: pdb=" SG CYS C 560 " - pdb=" SG CYS C 580 " distance=2.03 Simple disulfide: pdb=" SG CYS C 562 " - pdb=" SG CYS C 571 " distance=2.02 Simple disulfide: pdb=" SG CYS C 566 " - pdb=" SG CYS C 585 " distance=3.00 Simple disulfide: pdb=" SG CYS C 566 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 573 " - pdb=" SG CYS C 580 " distance=2.84 Simple disulfide: pdb=" SG CYS C 585 " - pdb=" SG CYS C 588 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN P 301 " pdb="ZN ZN P 301 " - pdb=" NE2 HIS P 110 " 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5726 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 35 sheets defined 37.3% alpha, 14.3% beta 147 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'T' and resid 22 through 35 Processing helix chain 'T' and resid 37 through 39 No H-bonds generated for 'chain 'T' and resid 37 through 39' Processing helix chain 'T' and resid 55 through 60 removed outlier: 3.583A pdb=" N TYR T 59 " --> pdb=" O THR T 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 107 Proline residue: A 93 - end of helix removed outlier: 4.107A pdb=" N ILE A 96 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 134 through 147 removed outlier: 3.997A pdb=" N MET A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 459 through 470 Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 539 through 543 Processing helix chain 'A' and resid 589 through 602 removed outlier: 3.522A pdb=" N ARG A 593 " --> pdb=" O PRO A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 625 removed outlier: 4.891A pdb=" N VAL A 613 " --> pdb=" O GLY A 609 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS A 620 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A 624 " --> pdb=" O HIS A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 630 No H-bonds generated for 'chain 'A' and resid 628 through 630' Processing helix chain 'A' and resid 631 through 651 removed outlier: 6.606A pdb=" N GLN A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LYS A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 Processing helix chain 'A' and resid 670 through 682 removed outlier: 3.593A pdb=" N ILE A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP A 675 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS A 676 " --> pdb=" O MET A 672 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 682 " --> pdb=" O VAL A 678 " (cutoff:3.500A) Processing helix chain 'L' and resid 267 through 278 Processing helix chain 'N' and resid 5 through 28 Processing helix chain 'N' and resid 153 through 157 Processing helix chain 'N' and resid 355 through 362 Processing helix chain 'C' and resid 18 through 61 removed outlier: 4.266A pdb=" N LEU C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 143 through 153 removed outlier: 4.280A pdb=" N GLU C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 178 Processing helix chain 'C' and resid 221 through 231 Processing helix chain 'C' and resid 236 through 250 removed outlier: 3.855A pdb=" N LEU C 240 " --> pdb=" O THR C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 removed outlier: 4.757A pdb=" N SER C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N PHE C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 338 removed outlier: 4.541A pdb=" N ALA C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 448 removed outlier: 4.197A pdb=" N GLY C 445 " --> pdb=" O ARG C 441 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR C 446 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 447 " --> pdb=" O LEU C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 458 removed outlier: 3.581A pdb=" N ARG C 456 " --> pdb=" O CYS C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 473 Processing helix chain 'C' and resid 474 through 477 Processing helix chain 'C' and resid 491 through 496 removed outlier: 4.217A pdb=" N LYS C 495 " --> pdb=" O LYS C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.558A pdb=" N LYS C 510 " --> pdb=" O ILE C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 534 through 539 Processing helix chain 'C' and resid 571 through 576 Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'C' and resid 648 through 662 removed outlier: 3.507A pdb=" N ARG C 653 " --> pdb=" O ASP C 649 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 656 " --> pdb=" O ASP C 652 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 657 " --> pdb=" O ARG C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 687 Processing helix chain 'C' and resid 729 through 737 Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.696A pdb=" N GLN B 112 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.649A pdb=" N ARG B 164 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 78 Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.524A pdb=" N ARG P 83 " --> pdb=" O ASP P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 116 removed outlier: 3.571A pdb=" N GLY P 116 " --> pdb=" O LEU P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 210 removed outlier: 4.422A pdb=" N ALA P 197 " --> pdb=" O GLN P 193 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE P 198 " --> pdb=" O THR P 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 259 No H-bonds generated for 'chain 'P' and resid 257 through 259' Processing helix chain 'P' and resid 270 through 272 No H-bonds generated for 'chain 'P' and resid 270 through 272' Processing helix chain 'P' and resid 274 through 285 removed outlier: 3.819A pdb=" N LEU P 278 " --> pdb=" O ASP P 275 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU P 279 " --> pdb=" O THR P 276 " (cutoff:3.500A) Proline residue: P 282 - end of helix Processing helix chain 'I' and resid 44 through 55 removed outlier: 4.292A pdb=" N LEU I 48 " --> pdb=" O GLY I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 75 removed outlier: 3.528A pdb=" N PHE I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 114 removed outlier: 3.774A pdb=" N VAL I 89 " --> pdb=" O GLN I 85 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET I 90 " --> pdb=" O SER I 86 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU I 100 " --> pdb=" O SER I 96 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA I 114 " --> pdb=" O CYS I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 132 removed outlier: 3.766A pdb=" N ILE I 124 " --> pdb=" O MET I 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 29 Processing helix chain 'J' and resid 30 through 42 Processing helix chain 'J' and resid 49 through 76 removed outlier: 3.925A pdb=" N GLU J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS J 59 " --> pdb=" O ARG J 55 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL J 65 " --> pdb=" O PHE J 61 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASP J 68 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 94 removed outlier: 3.641A pdb=" N VAL J 86 " --> pdb=" O THR J 82 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY J 94 " --> pdb=" O LEU J 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 22 Processing helix chain 'K' and resid 26 through 37 removed outlier: 3.604A pdb=" N ARG K 35 " --> pdb=" O HIS K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 73 removed outlier: 4.632A pdb=" N VAL K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN K 73 " --> pdb=" O ALA K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 88 removed outlier: 3.573A pdb=" N LEU K 83 " --> pdb=" O ILE K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 97 removed outlier: 3.880A pdb=" N LEU K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 44 Processing helix chain 'M' and resid 53 through 81 removed outlier: 3.951A pdb=" N MET M 59 " --> pdb=" O ALA M 55 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL M 63 " --> pdb=" O MET M 59 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU M 68 " --> pdb=" O ASN M 64 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU M 73 " --> pdb=" O ARG M 69 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 99 removed outlier: 3.946A pdb=" N ILE M 91 " --> pdb=" O THR M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 121 removed outlier: 3.707A pdb=" N SER M 109 " --> pdb=" O LYS M 105 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR M 118 " --> pdb=" O ALA M 114 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER M 120 " --> pdb=" O THR M 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 55 removed outlier: 3.979A pdb=" N LEU O 48 " --> pdb=" O GLY O 44 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG O 49 " --> pdb=" O THR O 45 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG O 52 " --> pdb=" O LEU O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 76 removed outlier: 3.806A pdb=" N PHE O 67 " --> pdb=" O ARG O 63 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN O 76 " --> pdb=" O ARG O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 removed outlier: 4.026A pdb=" N VAL O 89 " --> pdb=" O GLN O 85 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP O 106 " --> pdb=" O GLY O 102 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA O 114 " --> pdb=" O CYS O 110 " (cutoff:3.500A) Processing helix chain 'O' and resid 120 through 131 removed outlier: 3.638A pdb=" N ARG O 129 " --> pdb=" O GLN O 125 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 29 Processing helix chain 'Q' and resid 30 through 42 Processing helix chain 'Q' and resid 49 through 77 removed outlier: 3.732A pdb=" N GLU Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG Q 55 " --> pdb=" O TYR Q 51 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS Q 59 " --> pdb=" O ARG Q 55 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP Q 68 " --> pdb=" O ASN Q 64 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 93 removed outlier: 4.046A pdb=" N VAL Q 86 " --> pdb=" O THR Q 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 22 removed outlier: 3.630A pdb=" N ARG R 20 " --> pdb=" O THR R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 36 Processing helix chain 'R' and resid 45 through 73 removed outlier: 4.621A pdb=" N VAL R 49 " --> pdb=" O ALA R 45 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN R 73 " --> pdb=" O ALA R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 88 Processing helix chain 'R' and resid 90 through 97 Processing helix chain 'S' and resid 34 through 44 removed outlier: 3.595A pdb=" N GLN S 44 " --> pdb=" O LYS S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 82 removed outlier: 3.758A pdb=" N ASN S 81 " --> pdb=" O LEU S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 97 Processing helix chain 'S' and resid 101 through 121 removed outlier: 3.577A pdb=" N TYR S 118 " --> pdb=" O ALA S 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 35 Processing helix chain 'E' and resid 24 through 36 Processing helix chain 'E' and resid 46 through 51 removed outlier: 4.034A pdb=" N GLU E 50 " --> pdb=" O ARG E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 56 removed outlier: 3.861A pdb=" N SER E 55 " --> pdb=" O GLY E 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'T' and resid 12 through 16 removed outlier: 3.645A pdb=" N LEU T 15 " --> pdb=" O ILE T 3 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE T 3 " --> pdb=" O LEU T 15 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N LEU T 67 " --> pdb=" O GLN T 2 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE T 4 " --> pdb=" O LEU T 67 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU T 69 " --> pdb=" O PHE T 4 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS T 6 " --> pdb=" O LEU T 69 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N LEU T 71 " --> pdb=" O LYS T 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 160 Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 165 removed outlier: 4.774A pdb=" N ALA A 318 " --> pdb=" O ILE P 227 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N ILE P 227 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU P 240 " --> pdb=" O ILE P 227 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LYS P 229 " --> pdb=" O LYS P 238 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LYS P 238 " --> pdb=" O LYS P 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 164 through 165 removed outlier: 4.774A pdb=" N ALA A 318 " --> pdb=" O ILE P 227 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N ILE P 227 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 203 through 211 removed outlier: 4.431A pdb=" N THR A 208 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N VAL A 186 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LYS A 210 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU A 184 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 439 through 444 removed outlier: 4.292A pdb=" N ILE A 428 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ARG A 427 " --> pdb=" O ALA A 485 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ILE A 487 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE A 429 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL A 489 " --> pdb=" O PHE A 429 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN A 431 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE A 491 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N LEU A 433 " --> pdb=" O ILE A 491 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 525 through 528 removed outlier: 5.253A pdb=" N GLN N 403 " --> pdb=" O ASP N 33 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL N 35 " --> pdb=" O VAL N 401 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL N 401 " --> pdb=" O VAL N 35 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR N 37 " --> pdb=" O MET N 399 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET N 399 " --> pdb=" O THR N 37 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE N 398 " --> pdb=" O SER N 394 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP N 402 " --> pdb=" O ILE N 390 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE N 390 " --> pdb=" O TRP N 402 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 413 through 418 removed outlier: 6.967A pdb=" N VAL L 428 " --> pdb=" O ARG L 414 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR L 416 " --> pdb=" O ILE L 426 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE L 426 " --> pdb=" O THR L 416 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N PHE L 418 " --> pdb=" O ILE L 424 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ILE L 424 " --> pdb=" O PHE L 418 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA L 427 " --> pdb=" O TRP L 435 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER L 433 " --> pdb=" O CYS L 429 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE L 434 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER L 87 " --> pdb=" O ILE L 434 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ARG L 436 " --> pdb=" O VAL L 85 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL L 85 " --> pdb=" O ARG L 436 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 100 through 101 removed outlier: 4.509A pdb=" N LEU L 111 " --> pdb=" O CYS L 126 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU L 123 " --> pdb=" O LEU L 135 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 138 through 139 Processing sheet with id=AB2, first strand: chain 'L' and resid 149 through 154 removed outlier: 3.522A pdb=" N THR L 149 " --> pdb=" O ALA L 166 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA L 166 " --> pdb=" O THR L 149 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU L 163 " --> pdb=" O ILE L 175 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE L 172 " --> pdb=" O HIS L 185 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS L 185 " --> pdb=" O ILE L 172 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE L 174 " --> pdb=" O ILE L 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 193 through 198 removed outlier: 6.801A pdb=" N VAL L 209 " --> pdb=" O ASN L 194 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU L 196 " --> pdb=" O LEU L 207 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU L 207 " --> pdb=" O LEU L 196 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE L 198 " --> pdb=" O LEU L 205 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LEU L 205 " --> pdb=" O PHE L 198 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU L 215 " --> pdb=" O ILE L 228 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE L 228 " --> pdb=" O LEU L 215 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU L 217 " --> pdb=" O VAL L 226 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR L 224 " --> pdb=" O ASN L 219 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N GLN L 292 " --> pdb=" O THR L 224 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL L 226 " --> pdb=" O GLN L 292 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE L 294 " --> pdb=" O VAL L 226 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE L 228 " --> pdb=" O ILE L 294 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 239 through 244 removed outlier: 6.697A pdb=" N CYS L 254 " --> pdb=" O LEU L 240 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA L 242 " --> pdb=" O MET L 252 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET L 252 " --> pdb=" O ALA L 242 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TYR L 244 " --> pdb=" O LYS L 250 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LYS L 250 " --> pdb=" O TYR L 244 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE L 299 " --> pdb=" O LEU L 262 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 309 through 315 removed outlier: 4.581A pdb=" N CYS L 311 " --> pdb=" O LYS L 322 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER L 323 " --> pdb=" O ALA L 327 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ALA L 327 " --> pdb=" O SER L 323 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE L 328 " --> pdb=" O ARG L 355 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ARG L 355 " --> pdb=" O ILE L 328 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N CYS L 330 " --> pdb=" O LEU L 353 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 368 through 370 Processing sheet with id=AB7, first strand: chain 'N' and resid 48 through 54 removed outlier: 5.405A pdb=" N ARG N 65 " --> pdb=" O LEU N 50 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ASP N 52 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ILE N 63 " --> pdb=" O ASP N 52 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ASN N 77 " --> pdb=" O ASN N 122 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASN N 122 " --> pdb=" O ASN N 77 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU N 79 " --> pdb=" O LYS N 120 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS N 120 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE N 81 " --> pdb=" O GLU N 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 140 through 143 Processing sheet with id=AB9, first strand: chain 'N' and resid 180 through 185 removed outlier: 3.976A pdb=" N ALA N 196 " --> pdb=" O GLY N 182 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 230 through 232 removed outlier: 6.834A pdb=" N VAL N 246 " --> pdb=" O GLU N 231 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA N 247 " --> pdb=" O LYS N 251 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LYS N 251 " --> pdb=" O ALA N 247 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 276 through 281 Processing sheet with id=AC3, first strand: chain 'N' and resid 320 through 323 removed outlier: 3.519A pdb=" N GLN N 322 " --> pdb=" O SER N 336 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU N 342 " --> pdb=" O HIS N 370 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 82 through 84 Processing sheet with id=AC5, first strand: chain 'C' and resid 114 through 115 removed outlier: 6.029A pdb=" N SER C 114 " --> pdb=" O GLY C 681 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 120 through 121 removed outlier: 6.524A pdb=" N PHE C 120 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N SER C 647 " --> pdb=" O PHE C 120 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AC8, first strand: chain 'C' and resid 614 through 618 removed outlier: 3.760A pdb=" N ALA C 617 " --> pdb=" O GLY C 625 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 637 through 640 removed outlier: 7.275A pdb=" N PHE C 637 " --> pdb=" O ALA C 712 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA C 712 " --> pdb=" O PHE C 637 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER C 639 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C 709 " --> pdb=" O LYS C 698 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 53 through 54 Processing sheet with id=AD2, first strand: chain 'I' and resid 83 through 84 removed outlier: 7.621A pdb=" N ARG I 83 " --> pdb=" O VAL J 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'I' and resid 118 through 119 removed outlier: 4.182A pdb=" N ILE I 119 " --> pdb=" O ARG J 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'K' and resid 42 through 43 removed outlier: 7.305A pdb=" N ARG K 42 " --> pdb=" O ILE M 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'K' and resid 101 through 102 removed outlier: 6.617A pdb=" N THR K 101 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'R' and resid 42 through 43 removed outlier: 7.278A pdb=" N ARG R 42 " --> pdb=" O ILE S 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'R' and resid 77 through 78 Processing sheet with id=AD8, first strand: chain 'F' and resid 12 through 16 removed outlier: 4.106A pdb=" N SER F 65 " --> pdb=" O GLN F 2 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU F 69 " --> pdb=" O LYS F 6 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS F 68 " --> pdb=" O ILE F 44 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE F 45 " --> pdb=" O LYS F 48 " (cutoff:3.500A) 911 hydrogen bonds defined for protein. 2562 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 7.43 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7790 1.33 - 1.46: 8543 1.46 - 1.58: 13418 1.58 - 1.70: 625 1.70 - 1.83: 165 Bond restraints: 30541 Sorted by residual: bond pdb=" C GLN R 24 " pdb=" N PHE R 25 " ideal model delta sigma weight residual 1.333 1.232 0.101 1.59e-02 3.96e+03 4.03e+01 bond pdb=" CA ARG I 69 " pdb=" C ARG I 69 " ideal model delta sigma weight residual 1.522 1.461 0.061 1.36e-02 5.41e+03 2.03e+01 bond pdb=" CA ALA I 75 " pdb=" C ALA I 75 " ideal model delta sigma weight residual 1.522 1.446 0.076 1.72e-02 3.38e+03 1.96e+01 bond pdb=" C GLN K 24 " pdb=" N PHE K 25 " ideal model delta sigma weight residual 1.333 1.250 0.082 2.74e-02 1.33e+03 9.06e+00 bond pdb=" N VAL E 29 " pdb=" CA VAL E 29 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.52e+00 ... (remaining 30536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 42090 2.77 - 5.55: 609 5.55 - 8.32: 58 8.32 - 11.09: 10 11.09 - 13.87: 3 Bond angle restraints: 42770 Sorted by residual: angle pdb=" N VAL L 85 " pdb=" CA VAL L 85 " pdb=" C VAL L 85 " ideal model delta sigma weight residual 112.90 108.04 4.86 9.60e-01 1.09e+00 2.56e+01 angle pdb=" N VAL O 117 " pdb=" CA VAL O 117 " pdb=" C VAL O 117 " ideal model delta sigma weight residual 113.71 109.30 4.41 9.50e-01 1.11e+00 2.16e+01 angle pdb=" N ILE L 265 " pdb=" CA ILE L 265 " pdb=" C ILE L 265 " ideal model delta sigma weight residual 113.71 109.33 4.38 9.50e-01 1.11e+00 2.13e+01 angle pdb=" CB GLU E 25 " pdb=" CG GLU E 25 " pdb=" CD GLU E 25 " ideal model delta sigma weight residual 112.60 119.84 -7.24 1.70e+00 3.46e-01 1.82e+01 angle pdb=" N GLN B 143 " pdb=" CA GLN B 143 " pdb=" C GLN B 143 " ideal model delta sigma weight residual 107.73 113.34 -5.61 1.34e+00 5.57e-01 1.75e+01 ... (remaining 42765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 15796 35.98 - 71.96: 1609 71.96 - 107.94: 62 107.94 - 143.92: 4 143.92 - 179.90: 28 Dihedral angle restraints: 17499 sinusoidal: 8700 harmonic: 8799 Sorted by residual: dihedral pdb=" CB CYS C 560 " pdb=" SG CYS C 560 " pdb=" SG CYS C 573 " pdb=" CB CYS C 573 " ideal model delta sinusoidal sigma weight residual 93.00 172.62 -79.62 1 1.00e+01 1.00e-02 7.87e+01 dihedral pdb=" CB CYS C 530 " pdb=" SG CYS C 530 " pdb=" SG CYS C 549 " pdb=" CB CYS C 549 " ideal model delta sinusoidal sigma weight residual -86.00 -164.28 78.28 1 1.00e+01 1.00e-02 7.65e+01 dihedral pdb=" CB CYS C 549 " pdb=" SG CYS C 549 " pdb=" SG CYS C 553 " pdb=" CB CYS C 553 " ideal model delta sinusoidal sigma weight residual 93.00 31.89 61.11 1 1.00e+01 1.00e-02 4.96e+01 ... (remaining 17496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3613 0.053 - 0.106: 1070 0.106 - 0.159: 154 0.159 - 0.212: 10 0.212 - 0.265: 3 Chirality restraints: 4850 Sorted by residual: chirality pdb=" CA GLU E 25 " pdb=" N GLU E 25 " pdb=" C GLU E 25 " pdb=" CB GLU E 25 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB VAL E 28 " pdb=" CA VAL E 28 " pdb=" CG1 VAL E 28 " pdb=" CG2 VAL E 28 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA LYS B 151 " pdb=" N LYS B 151 " pdb=" C LYS B 151 " pdb=" CB LYS B 151 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 4847 not shown) Planarity restraints: 4397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG H 121 " 0.034 2.00e-02 2.50e+03 1.41e-02 5.96e+00 pdb=" N9 DG H 121 " -0.029 2.00e-02 2.50e+03 pdb=" C8 DG H 121 " -0.007 2.00e-02 2.50e+03 pdb=" N7 DG H 121 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG H 121 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DG H 121 " 0.001 2.00e-02 2.50e+03 pdb=" O6 DG H 121 " 0.016 2.00e-02 2.50e+03 pdb=" N1 DG H 121 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG H 121 " -0.004 2.00e-02 2.50e+03 pdb=" N2 DG H 121 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG H 121 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG H 121 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA H 299 " 0.030 2.00e-02 2.50e+03 1.37e-02 5.17e+00 pdb=" N9 DA H 299 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DA H 299 " -0.020 2.00e-02 2.50e+03 pdb=" N7 DA H 299 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DA H 299 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA H 299 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA H 299 " 0.017 2.00e-02 2.50e+03 pdb=" N1 DA H 299 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DA H 299 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA H 299 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA H 299 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC H 215 " 0.025 2.00e-02 2.50e+03 1.51e-02 5.11e+00 pdb=" N1 DC H 215 " -0.018 2.00e-02 2.50e+03 pdb=" C2 DC H 215 " -0.018 2.00e-02 2.50e+03 pdb=" O2 DC H 215 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DC H 215 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC H 215 " -0.012 2.00e-02 2.50e+03 pdb=" N4 DC H 215 " 0.023 2.00e-02 2.50e+03 pdb=" C5 DC H 215 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DC H 215 " 0.002 2.00e-02 2.50e+03 ... (remaining 4394 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 392 2.52 - 3.11: 24907 3.11 - 3.71: 51501 3.71 - 4.30: 66684 4.30 - 4.90: 100508 Nonbonded interactions: 243992 Sorted by model distance: nonbonded pdb=" O2 DC H 103 " pdb=" N2 DG H 212 " model vdw 1.921 3.120 nonbonded pdb=" O2 DC H 110 " pdb=" N2 DG H 205 " model vdw 1.938 2.496 nonbonded pdb=" O2 DC H 154 " pdb=" N2 DG H 161 " model vdw 1.956 2.496 nonbonded pdb=" O2 DC H 53 " pdb=" N2 DG H 262 " model vdw 1.981 2.496 nonbonded pdb=" N2 DG H 137 " pdb=" O2 DC H 178 " model vdw 2.004 2.496 ... (remaining 243987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'F' selection = (chain 'T' and (resid 1 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB or name SG )))) } ncs_group { reference = (chain 'J' and ((resid 20 through 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 102)) selection = (chain 'Q' and resid 20 through 102) } ncs_group { reference = chain 'K' selection = (chain 'R' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 119)) } ncs_group { reference = chain 'M' selection = (chain 'S' and resid 28 through 122) } 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=0.25 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: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 33.090 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 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 : 0.015 0.967 30556 Z= 0.842 Angle : 0.972 40.543 42796 Z= 0.556 Chirality : 0.048 0.265 4850 Planarity : 0.004 0.052 4397 Dihedral : 24.154 179.905 11734 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 28.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 0.31 % Allowed : 7.41 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.79 (0.12), residues: 2956 helix: -3.23 (0.12), residues: 982 sheet: -2.47 (0.21), residues: 436 loop : -3.40 (0.13), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 685 TYR 0.021 0.002 TYR M 39 PHE 0.017 0.002 PHE A 237 TRP 0.015 0.002 TRP L 364 HIS 0.008 0.002 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.01027 (30541) covalent geometry : angle 0.92864 (42770) SS BOND : bond 0.42091 ( 13) SS BOND : angle 11.62864 ( 26) hydrogen bonds : bond 0.22413 ( 1279) hydrogen bonds : angle 8.62521 ( 3270) metal coordination : bond 0.65385 ( 1) Misc. bond : bond 0.90126 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 174 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 612 GLU cc_start: 0.9298 (tp30) cc_final: 0.9022 (tp30) REVERT: L 181 GLN cc_start: 0.9115 (mt0) cc_final: 0.8563 (mp10) REVERT: L 252 MET cc_start: 0.8723 (tpp) cc_final: 0.8444 (mmm) REVERT: L 271 MET cc_start: 0.9234 (mtm) cc_final: 0.8864 (mtm) REVERT: L 376 MET cc_start: 0.9523 (ttp) cc_final: 0.9015 (tmm) REVERT: B 151 LYS cc_start: 0.9242 (pttm) cc_final: 0.9030 (pttm) REVERT: I 50 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8787 (mt-10) REVERT: I 105 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8523 (tm-30) REVERT: J 53 GLU cc_start: 0.9248 (mm-30) cc_final: 0.9005 (mp0) REVERT: J 84 MET cc_start: 0.8346 (mmm) cc_final: 0.8015 (mmm) REVERT: K 56 GLU cc_start: 0.8500 (tt0) cc_final: 0.8180 (mt-10) REVERT: K 118 LYS cc_start: 0.9257 (mtpt) cc_final: 0.8763 (tptp) REVERT: M 110 GLU cc_start: 0.9324 (mm-30) cc_final: 0.9063 (tm-30) REVERT: R 56 GLU cc_start: 0.8489 (tt0) cc_final: 0.8269 (tt0) REVERT: S 56 MET cc_start: 0.9011 (tpp) cc_final: 0.8797 (tpp) outliers start: 7 outliers final: 4 residues processed: 180 average time/residue: 0.2372 time to fit residues: 63.9283 Evaluate side-chains 126 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain M residue 48 ASP Chi-restraints excluded: chain Q residue 68 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.0970 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.0570 chunk 298 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN A 235 ASN A 241 ASN A 243 HIS A 431 GLN A 504 GLN L 94 GLN ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 GLN L 382 GLN N 123 HIS N 157 HIS N 188 ASN N 239 HIS N 329 ASN N 343 ASN N 397 ASN C 94 GLN C 117 GLN C 507 GLN ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 ASN P 268 HIS I 68 GLN I 85 GLN J 25 ASN M 92 GLN O 39 HIS O 68 GLN R 31 HIS S 46 HIS F 40 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.052209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.030780 restraints weight = 221394.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.031100 restraints weight = 119274.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.031518 restraints weight = 85697.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.031616 restraints weight = 73071.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.031705 restraints weight = 68831.009| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30556 Z= 0.166 Angle : 0.718 26.147 42796 Z= 0.392 Chirality : 0.044 0.202 4850 Planarity : 0.004 0.046 4397 Dihedral : 28.528 179.917 6658 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.93 % Allowed : 9.84 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.14), residues: 2956 helix: -0.40 (0.15), residues: 1044 sheet: -2.00 (0.22), residues: 442 loop : -2.65 (0.14), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 593 TYR 0.014 0.001 TYR K 39 PHE 0.014 0.001 PHE C 440 TRP 0.033 0.002 TRP P 106 HIS 0.008 0.001 HIS P 110 Details of bonding type rmsd covalent geometry : bond 0.00349 (30541) covalent geometry : angle 0.69456 (42770) SS BOND : bond 0.02263 ( 13) SS BOND : angle 7.40739 ( 26) hydrogen bonds : bond 0.07773 ( 1279) hydrogen bonds : angle 5.29992 ( 3270) metal coordination : bond 0.02393 ( 1) Misc. bond : bond 0.00222 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.811 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: T 1 MET cc_start: 0.7568 (tmm) cc_final: 0.7304 (ppp) REVERT: A 118 MET cc_start: 0.9422 (mmm) cc_final: 0.9221 (mmm) REVERT: A 310 LEU cc_start: 0.9460 (mp) cc_final: 0.9163 (mp) REVERT: A 612 GLU cc_start: 0.9428 (tp30) cc_final: 0.9141 (tp30) REVERT: A 614 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.9026 (mtt) REVERT: A 657 MET cc_start: 0.9510 (mtp) cc_final: 0.9297 (mmt) REVERT: L 181 GLN cc_start: 0.8954 (mt0) cc_final: 0.8484 (mp10) REVERT: L 252 MET cc_start: 0.8556 (tpp) cc_final: 0.8177 (mmm) REVERT: L 376 MET cc_start: 0.9438 (ttp) cc_final: 0.9174 (tmm) REVERT: N 133 MET cc_start: 0.9138 (ttt) cc_final: 0.8911 (tmm) REVERT: N 253 MET cc_start: 0.8779 (mtt) cc_final: 0.8561 (mtp) REVERT: N 404 MET cc_start: 0.8541 (pmm) cc_final: 0.8281 (pmm) REVERT: C 41 MET cc_start: 0.9617 (mmm) cc_final: 0.9405 (mmm) REVERT: C 121 MET cc_start: 0.8250 (mtm) cc_final: 0.7589 (mtp) REVERT: P 188 ASP cc_start: 0.9284 (p0) cc_final: 0.9030 (t0) REVERT: P 275 ASP cc_start: 0.9685 (p0) cc_final: 0.9342 (p0) REVERT: P 288 MET cc_start: 0.8663 (mmm) cc_final: 0.8410 (tpp) REVERT: I 105 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8575 (tm-30) REVERT: I 106 ASP cc_start: 0.9271 (m-30) cc_final: 0.8715 (m-30) REVERT: J 53 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8985 (mp0) REVERT: J 59 LYS cc_start: 0.9385 (ttmm) cc_final: 0.8618 (ttpp) REVERT: J 63 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8375 (mp0) REVERT: J 84 MET cc_start: 0.8459 (mmm) cc_final: 0.7818 (mmm) REVERT: K 39 TYR cc_start: 0.9211 (m-80) cc_final: 0.8293 (m-80) REVERT: K 56 GLU cc_start: 0.8681 (tt0) cc_final: 0.8209 (mt-10) REVERT: K 118 LYS cc_start: 0.9271 (mtpt) cc_final: 0.8844 (tptt) REVERT: M 31 LYS cc_start: 0.8862 (mmmm) cc_final: 0.8598 (mmtt) REVERT: M 68 GLU cc_start: 0.8860 (tt0) cc_final: 0.8489 (tp30) REVERT: M 110 GLU cc_start: 0.9387 (mm-30) cc_final: 0.9183 (tm-30) REVERT: O 50 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8528 (mm-30) REVERT: O 105 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8190 (pp20) REVERT: Q 59 LYS cc_start: 0.9398 (OUTLIER) cc_final: 0.9121 (tptm) REVERT: R 56 GLU cc_start: 0.8836 (tt0) cc_final: 0.8389 (tt0) outliers start: 21 outliers final: 10 residues processed: 197 average time/residue: 0.2030 time to fit residues: 62.5700 Evaluate side-chains 152 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain P residue 203 ILE Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain Q residue 59 LYS Chi-restraints excluded: chain E residue 25 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 196 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 141 optimal weight: 40.0000 chunk 165 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 256 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 HIS A 504 GLN A 507 HIS ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 360 GLN ** N 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 343 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 283 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.049959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.029009 restraints weight = 232074.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.029202 restraints weight = 129546.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.029403 restraints weight = 94307.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.029667 restraints weight = 82107.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.029667 restraints weight = 75437.433| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 30556 Z= 0.413 Angle : 0.809 22.919 42796 Z= 0.436 Chirality : 0.046 0.202 4850 Planarity : 0.005 0.042 4397 Dihedral : 28.279 179.658 6650 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 2.34 % Allowed : 13.11 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.14), residues: 2956 helix: -0.25 (0.15), residues: 1038 sheet: -1.93 (0.22), residues: 449 loop : -2.51 (0.15), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 304 TYR 0.021 0.002 TYR R 39 PHE 0.017 0.002 PHE A 86 TRP 0.017 0.002 TRP P 106 HIS 0.007 0.002 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00903 (30541) covalent geometry : angle 0.79358 (42770) SS BOND : bond 0.01389 ( 13) SS BOND : angle 6.50060 ( 26) hydrogen bonds : bond 0.10388 ( 1279) hydrogen bonds : angle 5.66642 ( 3270) metal coordination : bond 0.00025 ( 1) Misc. bond : bond 0.00116 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 131 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 1 MET cc_start: 0.7390 (tmm) cc_final: 0.7089 (ppp) REVERT: A 612 GLU cc_start: 0.9480 (tp30) cc_final: 0.9214 (tp30) REVERT: L 181 GLN cc_start: 0.9041 (mt0) cc_final: 0.8413 (mm110) REVERT: L 370 MET cc_start: 0.8614 (mmm) cc_final: 0.8404 (mmm) REVERT: N 253 MET cc_start: 0.8777 (mtt) cc_final: 0.8557 (mtp) REVERT: N 404 MET cc_start: 0.8627 (pmm) cc_final: 0.8132 (pmm) REVERT: C 121 MET cc_start: 0.8213 (mtm) cc_final: 0.7870 (mtt) REVERT: C 530 CYS cc_start: 0.8751 (OUTLIER) cc_final: 0.7800 (t) REVERT: I 105 GLU cc_start: 0.9264 (tm-30) cc_final: 0.8772 (tm-30) REVERT: J 53 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9072 (mp0) REVERT: J 59 LYS cc_start: 0.9452 (ttmm) cc_final: 0.9148 (tppp) REVERT: J 84 MET cc_start: 0.8564 (mmm) cc_final: 0.7897 (mmm) REVERT: K 56 GLU cc_start: 0.8750 (tt0) cc_final: 0.8267 (mt-10) REVERT: K 110 ASN cc_start: 0.9603 (t0) cc_final: 0.9371 (t0) REVERT: K 118 LYS cc_start: 0.9242 (mtpt) cc_final: 0.8779 (tptt) REVERT: M 110 GLU cc_start: 0.9451 (mm-30) cc_final: 0.9196 (tm-30) REVERT: O 50 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8655 (mm-30) REVERT: O 90 MET cc_start: 0.8774 (mmm) cc_final: 0.8562 (mmm) REVERT: O 105 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8453 (tm-30) REVERT: O 106 ASP cc_start: 0.9076 (m-30) cc_final: 0.8742 (m-30) REVERT: O 120 MET cc_start: 0.8763 (mmm) cc_final: 0.8414 (mmm) REVERT: Q 59 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.9076 (tptm) REVERT: R 56 GLU cc_start: 0.8901 (tt0) cc_final: 0.8415 (tt0) outliers start: 53 outliers final: 32 residues processed: 175 average time/residue: 0.1844 time to fit residues: 52.4759 Evaluate side-chains 156 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 256 MET Chi-restraints excluded: chain L residue 269 ARG Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain P residue 98 ASN Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 104 PHE Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain Q residue 59 LYS Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 99 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 309 optimal weight: 1.9990 chunk 15 optimal weight: 30.0000 chunk 116 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 257 optimal weight: 0.7980 chunk 176 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 277 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 235 HIS ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.051470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.029632 restraints weight = 224058.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.030257 restraints weight = 122277.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.030643 restraints weight = 90188.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.030749 restraints weight = 76740.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.030972 restraints weight = 72544.856| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30556 Z= 0.181 Angle : 0.672 20.225 42796 Z= 0.365 Chirality : 0.042 0.192 4850 Planarity : 0.004 0.041 4397 Dihedral : 28.256 179.326 6650 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.90 % Allowed : 14.30 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.15), residues: 2956 helix: 0.53 (0.16), residues: 1035 sheet: -1.63 (0.22), residues: 456 loop : -2.30 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 55 TYR 0.015 0.001 TYR R 39 PHE 0.013 0.001 PHE A 86 TRP 0.014 0.001 TRP N 205 HIS 0.004 0.001 HIS C 613 Details of bonding type rmsd covalent geometry : bond 0.00396 (30541) covalent geometry : angle 0.65737 (42770) SS BOND : bond 0.00957 ( 13) SS BOND : angle 5.73939 ( 26) hydrogen bonds : bond 0.07507 ( 1279) hydrogen bonds : angle 4.92389 ( 3270) metal coordination : bond 0.00152 ( 1) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 1 MET cc_start: 0.7289 (tmm) cc_final: 0.6989 (ppp) REVERT: A 612 GLU cc_start: 0.9440 (tp30) cc_final: 0.9117 (tp30) REVERT: L 252 MET cc_start: 0.8666 (mmm) cc_final: 0.8165 (mmm) REVERT: N 246 VAL cc_start: 0.7498 (OUTLIER) cc_final: 0.7297 (p) REVERT: N 253 MET cc_start: 0.8838 (mtt) cc_final: 0.8569 (mtp) REVERT: N 318 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7172 (m-30) REVERT: N 404 MET cc_start: 0.8577 (pmm) cc_final: 0.8140 (pmm) REVERT: C 121 MET cc_start: 0.8370 (mtm) cc_final: 0.8057 (mtt) REVERT: P 275 ASP cc_start: 0.9633 (p0) cc_final: 0.9386 (p0) REVERT: I 105 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8677 (tm-30) REVERT: J 53 GLU cc_start: 0.9364 (mm-30) cc_final: 0.8964 (mp0) REVERT: J 59 LYS cc_start: 0.9372 (ttmm) cc_final: 0.9094 (tppp) REVERT: J 63 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8358 (mt-10) REVERT: J 84 MET cc_start: 0.8493 (mmm) cc_final: 0.7886 (mmm) REVERT: K 39 TYR cc_start: 0.9189 (m-80) cc_final: 0.8237 (m-80) REVERT: K 56 GLU cc_start: 0.8747 (tt0) cc_final: 0.8249 (mt-10) REVERT: K 118 LYS cc_start: 0.9308 (mtpt) cc_final: 0.8872 (tptt) REVERT: M 68 GLU cc_start: 0.8725 (tt0) cc_final: 0.8381 (tp30) REVERT: O 50 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8545 (mm-30) REVERT: O 90 MET cc_start: 0.8833 (mmm) cc_final: 0.8516 (mmm) REVERT: O 105 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8334 (tm-30) REVERT: O 106 ASP cc_start: 0.9009 (m-30) cc_final: 0.8505 (m-30) REVERT: O 120 MET cc_start: 0.8813 (mmm) cc_final: 0.8390 (mmm) REVERT: Q 59 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8921 (tptm) REVERT: R 56 GLU cc_start: 0.8841 (tt0) cc_final: 0.8408 (tt0) outliers start: 43 outliers final: 27 residues processed: 175 average time/residue: 0.2055 time to fit residues: 56.4938 Evaluate side-chains 155 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 269 ARG Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 318 ASP Chi-restraints excluded: chain N residue 385 ASN Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 259 ARG Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain Q residue 59 LYS Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 79 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 273 optimal weight: 3.9990 chunk 105 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 12 optimal weight: 0.0010 chunk 139 optimal weight: 20.0000 chunk 73 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 205 optimal weight: 10.0000 chunk 189 optimal weight: 50.0000 chunk 196 optimal weight: 30.0000 overall best weight: 5.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.050165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.028518 restraints weight = 231818.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.029196 restraints weight = 127812.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.029561 restraints weight = 94417.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.029657 restraints weight = 81044.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.029788 restraints weight = 76767.028| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 30556 Z= 0.376 Angle : 0.788 18.836 42796 Z= 0.422 Chirality : 0.045 0.191 4850 Planarity : 0.004 0.041 4397 Dihedral : 28.120 179.824 6650 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.82 % Allowed : 16.06 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.15), residues: 2956 helix: 0.37 (0.16), residues: 1032 sheet: -1.49 (0.23), residues: 445 loop : -2.31 (0.15), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 96 TYR 0.020 0.002 TYR M 39 PHE 0.017 0.002 PHE Q 61 TRP 0.011 0.002 TRP P 106 HIS 0.006 0.001 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00826 (30541) covalent geometry : angle 0.76745 (42770) SS BOND : bond 0.01073 ( 13) SS BOND : angle 7.25433 ( 26) hydrogen bonds : bond 0.09821 ( 1279) hydrogen bonds : angle 5.28997 ( 3270) metal coordination : bond 0.00105 ( 1) Misc. bond : bond 0.00127 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 123 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 1 MET cc_start: 0.7481 (tmm) cc_final: 0.7211 (ppp) REVERT: A 612 GLU cc_start: 0.9468 (tp30) cc_final: 0.9197 (tp30) REVERT: L 181 GLN cc_start: 0.9072 (mt0) cc_final: 0.8562 (mt0) REVERT: L 252 MET cc_start: 0.8733 (mmm) cc_final: 0.8294 (mmm) REVERT: N 318 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: N 404 MET cc_start: 0.8662 (pmm) cc_final: 0.7824 (pmm) REVERT: C 121 MET cc_start: 0.8272 (mtm) cc_final: 0.7877 (mtt) REVERT: P 288 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8059 (tpp) REVERT: I 105 GLU cc_start: 0.9256 (tm-30) cc_final: 0.8740 (tm-30) REVERT: J 53 GLU cc_start: 0.9423 (mm-30) cc_final: 0.9064 (mp0) REVERT: J 84 MET cc_start: 0.8595 (mmm) cc_final: 0.8002 (mmm) REVERT: K 39 TYR cc_start: 0.9258 (m-80) cc_final: 0.8308 (m-80) REVERT: K 56 GLU cc_start: 0.8797 (tt0) cc_final: 0.8280 (mt-10) REVERT: K 118 LYS cc_start: 0.9272 (mtpt) cc_final: 0.8792 (tptt) REVERT: M 30 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8861 (ptm160) REVERT: M 68 GLU cc_start: 0.8766 (tt0) cc_final: 0.8445 (tp30) REVERT: O 50 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8617 (mm-30) REVERT: O 90 MET cc_start: 0.8884 (mmm) cc_final: 0.8547 (mmm) REVERT: O 105 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8274 (tm-30) REVERT: O 106 ASP cc_start: 0.9098 (m-30) cc_final: 0.8539 (m-30) REVERT: Q 59 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.9044 (tptm) REVERT: R 56 GLU cc_start: 0.8886 (tt0) cc_final: 0.8399 (tt0) REVERT: S 31 LYS cc_start: 0.8896 (mmmm) cc_final: 0.8385 (mmmm) outliers start: 64 outliers final: 40 residues processed: 180 average time/residue: 0.1921 time to fit residues: 55.1525 Evaluate side-chains 161 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 117 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 256 MET Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain N residue 318 ASP Chi-restraints excluded: chain N residue 385 ASN Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain P residue 98 ASN Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 259 ARG Chi-restraints excluded: chain P residue 288 MET Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 97 GLU Chi-restraints excluded: chain O residue 104 PHE Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain Q residue 59 LYS Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain S residue 99 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 47 optimal weight: 0.6980 chunk 314 optimal weight: 20.0000 chunk 232 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 264 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 309 optimal weight: 0.9990 chunk 281 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.051564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.030024 restraints weight = 221335.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.030658 restraints weight = 123068.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.031048 restraints weight = 89819.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.031319 restraints weight = 76841.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.031416 restraints weight = 71113.638| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30556 Z= 0.175 Angle : 0.677 17.641 42796 Z= 0.364 Chirality : 0.042 0.180 4850 Planarity : 0.004 0.041 4397 Dihedral : 28.083 179.243 6650 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.38 % Allowed : 16.99 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.15), residues: 2956 helix: 0.93 (0.16), residues: 1035 sheet: -1.29 (0.23), residues: 444 loop : -2.19 (0.15), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 96 TYR 0.013 0.001 TYR A 461 PHE 0.011 0.001 PHE A 86 TRP 0.015 0.001 TRP N 205 HIS 0.004 0.001 HIS N 272 Details of bonding type rmsd covalent geometry : bond 0.00384 (30541) covalent geometry : angle 0.65886 (42770) SS BOND : bond 0.00918 ( 13) SS BOND : angle 6.30319 ( 26) hydrogen bonds : bond 0.06998 ( 1279) hydrogen bonds : angle 4.66596 ( 3270) metal coordination : bond 0.00061 ( 1) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 131 time to evaluate : 1.104 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: T 1 MET cc_start: 0.7305 (tmm) cc_final: 0.7017 (ppp) REVERT: A 612 GLU cc_start: 0.9431 (tp30) cc_final: 0.9091 (tp30) REVERT: L 179 THR cc_start: 0.9429 (OUTLIER) cc_final: 0.8923 (p) REVERT: L 181 GLN cc_start: 0.9034 (mt0) cc_final: 0.8596 (mt0) REVERT: L 252 MET cc_start: 0.8769 (mmm) cc_final: 0.8343 (mmm) REVERT: N 318 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: N 399 MET cc_start: 0.9406 (ppp) cc_final: 0.9199 (ppp) REVERT: N 404 MET cc_start: 0.8645 (pmm) cc_final: 0.7996 (pmm) REVERT: C 121 MET cc_start: 0.8384 (mtm) cc_final: 0.8015 (mtt) REVERT: P 288 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8053 (tpp) REVERT: I 105 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8681 (tm-30) REVERT: I 134 ARG cc_start: 0.7731 (ttp80) cc_final: 0.7424 (ttp80) REVERT: J 53 GLU cc_start: 0.9345 (mm-30) cc_final: 0.8967 (mp0) REVERT: J 84 MET cc_start: 0.8479 (mmm) cc_final: 0.7917 (mmm) REVERT: K 36 LYS cc_start: 0.9570 (mmmm) cc_final: 0.9329 (mmtt) REVERT: K 56 GLU cc_start: 0.8777 (tt0) cc_final: 0.8266 (mt-10) REVERT: M 30 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8935 (ptm160) REVERT: O 50 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8563 (mm-30) REVERT: O 90 MET cc_start: 0.8956 (mmm) cc_final: 0.8538 (mmm) REVERT: O 105 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8294 (tm-30) REVERT: O 106 ASP cc_start: 0.9034 (m-30) cc_final: 0.8573 (m-30) REVERT: O 120 MET cc_start: 0.8683 (mmm) cc_final: 0.8457 (mmm) REVERT: Q 59 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.8977 (tptm) REVERT: R 56 GLU cc_start: 0.8851 (tt0) cc_final: 0.8429 (tt0) REVERT: S 31 LYS cc_start: 0.8876 (mmmm) cc_final: 0.8402 (mmmm) outliers start: 54 outliers final: 37 residues processed: 178 average time/residue: 0.1812 time to fit residues: 52.6284 Evaluate side-chains 164 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 318 ASP Chi-restraints excluded: chain N residue 385 ASN Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 606 ILE Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 259 ARG Chi-restraints excluded: chain P residue 288 MET Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 104 PHE Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain Q residue 59 LYS Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain S residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 299 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 219 optimal weight: 5.9990 chunk 313 optimal weight: 50.0000 chunk 250 optimal weight: 0.0040 chunk 287 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 chunk 145 optimal weight: 30.0000 overall best weight: 2.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.051102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.029407 restraints weight = 227181.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.030160 restraints weight = 125013.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.030369 restraints weight = 91532.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.030653 restraints weight = 80744.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.030829 restraints weight = 74499.124| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 30556 Z= 0.226 Angle : 0.688 16.680 42796 Z= 0.368 Chirality : 0.041 0.176 4850 Planarity : 0.004 0.041 4397 Dihedral : 27.938 179.533 6650 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.60 % Allowed : 17.43 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.15), residues: 2956 helix: 0.96 (0.16), residues: 1041 sheet: -1.21 (0.23), residues: 446 loop : -2.15 (0.15), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 96 TYR 0.017 0.001 TYR K 39 PHE 0.012 0.001 PHE A 86 TRP 0.013 0.001 TRP N 205 HIS 0.004 0.001 HIS Q 75 Details of bonding type rmsd covalent geometry : bond 0.00497 (30541) covalent geometry : angle 0.67310 (42770) SS BOND : bond 0.00737 ( 13) SS BOND : angle 5.79701 ( 26) hydrogen bonds : bond 0.07589 ( 1279) hydrogen bonds : angle 4.67739 ( 3270) metal coordination : bond 0.00162 ( 1) Misc. bond : bond 0.00052 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 123 time to evaluate : 0.999 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: T 1 MET cc_start: 0.7271 (tmm) cc_final: 0.6984 (ppp) REVERT: A 612 GLU cc_start: 0.9444 (tp30) cc_final: 0.9110 (tp30) REVERT: L 179 THR cc_start: 0.9500 (OUTLIER) cc_final: 0.9022 (p) REVERT: L 181 GLN cc_start: 0.9083 (mt0) cc_final: 0.8621 (mt0) REVERT: L 252 MET cc_start: 0.8758 (mmm) cc_final: 0.8363 (mmm) REVERT: L 270 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8701 (ppp) REVERT: N 318 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7277 (m-30) REVERT: N 399 MET cc_start: 0.9419 (ppp) cc_final: 0.9157 (ppp) REVERT: N 404 MET cc_start: 0.8639 (pmm) cc_final: 0.7979 (pmm) REVERT: C 121 MET cc_start: 0.8337 (mtm) cc_final: 0.7827 (mtt) REVERT: P 288 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.8023 (tpp) REVERT: I 105 GLU cc_start: 0.9239 (tm-30) cc_final: 0.8702 (tm-30) REVERT: J 53 GLU cc_start: 0.9355 (mm-30) cc_final: 0.9028 (mp0) REVERT: J 84 MET cc_start: 0.8500 (mmm) cc_final: 0.7849 (mmm) REVERT: K 56 GLU cc_start: 0.8787 (tt0) cc_final: 0.8263 (mt-10) REVERT: M 30 ARG cc_start: 0.9239 (OUTLIER) cc_final: 0.8947 (ptm160) REVERT: M 68 GLU cc_start: 0.8740 (tt0) cc_final: 0.8423 (tp30) REVERT: O 50 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8576 (mm-30) REVERT: O 90 MET cc_start: 0.8978 (mmm) cc_final: 0.8582 (mmm) REVERT: O 105 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8286 (tm-30) REVERT: O 106 ASP cc_start: 0.9144 (m-30) cc_final: 0.8538 (m-30) REVERT: O 120 MET cc_start: 0.8686 (mmm) cc_final: 0.8468 (mmm) REVERT: Q 59 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.9067 (tptm) REVERT: R 56 GLU cc_start: 0.8835 (tt0) cc_final: 0.8422 (tt0) REVERT: R 61 GLU cc_start: 0.8992 (tp30) cc_final: 0.8744 (mm-30) REVERT: S 31 LYS cc_start: 0.8944 (mmmm) cc_final: 0.8479 (mmmm) outliers start: 59 outliers final: 44 residues processed: 173 average time/residue: 0.1891 time to fit residues: 52.8174 Evaluate side-chains 169 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 270 MET Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 318 ASP Chi-restraints excluded: chain N residue 385 ASN Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain C residue 553 CYS Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 606 ILE Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 259 ARG Chi-restraints excluded: chain P residue 288 MET Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 104 PHE Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain Q residue 59 LYS Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 99 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 35 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 286 optimal weight: 20.0000 chunk 198 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 203 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 189 optimal weight: 50.0000 chunk 150 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.050359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.029742 restraints weight = 231440.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.030468 restraints weight = 139538.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.030306 restraints weight = 97887.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.030356 restraints weight = 91798.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.030427 restraints weight = 87105.185| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 30556 Z= 0.345 Angle : 0.769 16.431 42796 Z= 0.408 Chirality : 0.044 0.185 4850 Planarity : 0.004 0.040 4397 Dihedral : 27.961 179.811 6650 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 2.87 % Allowed : 17.65 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.15), residues: 2956 helix: 0.74 (0.16), residues: 1026 sheet: -1.21 (0.23), residues: 440 loop : -2.18 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 134 TYR 0.026 0.002 TYR K 39 PHE 0.016 0.002 PHE Q 61 TRP 0.011 0.002 TRP L 218 HIS 0.006 0.001 HIS Q 75 Details of bonding type rmsd covalent geometry : bond 0.00757 (30541) covalent geometry : angle 0.75565 (42770) SS BOND : bond 0.00658 ( 13) SS BOND : angle 5.78732 ( 26) hydrogen bonds : bond 0.09063 ( 1279) hydrogen bonds : angle 5.01270 ( 3270) metal coordination : bond 0.00372 ( 1) Misc. bond : bond 0.00126 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 114 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 1 MET cc_start: 0.7264 (tmm) cc_final: 0.6985 (ppp) REVERT: A 612 GLU cc_start: 0.9449 (tp30) cc_final: 0.9150 (tp30) REVERT: L 181 GLN cc_start: 0.9090 (mt0) cc_final: 0.8432 (mt0) REVERT: L 252 MET cc_start: 0.8753 (mmm) cc_final: 0.8441 (mmm) REVERT: L 270 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8813 (ppp) REVERT: N 318 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7228 (m-30) REVERT: N 399 MET cc_start: 0.9457 (ppp) cc_final: 0.9179 (ppp) REVERT: N 404 MET cc_start: 0.8805 (pmm) cc_final: 0.8157 (pmm) REVERT: C 121 MET cc_start: 0.8278 (mtm) cc_final: 0.7798 (mtp) REVERT: P 288 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8165 (tpp) REVERT: I 105 GLU cc_start: 0.9244 (tm-30) cc_final: 0.8729 (tm-30) REVERT: J 53 GLU cc_start: 0.9395 (mm-30) cc_final: 0.8970 (mp0) REVERT: J 84 MET cc_start: 0.8561 (mmm) cc_final: 0.8012 (mmm) REVERT: K 56 GLU cc_start: 0.8774 (tt0) cc_final: 0.8264 (mt-10) REVERT: M 30 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8872 (ptm160) REVERT: M 68 GLU cc_start: 0.8723 (tt0) cc_final: 0.8423 (tp30) REVERT: O 90 MET cc_start: 0.8930 (mmm) cc_final: 0.8545 (mmm) REVERT: O 105 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8341 (tm-30) REVERT: O 120 MET cc_start: 0.8718 (mmm) cc_final: 0.8502 (mmm) REVERT: Q 59 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.9021 (tptm) REVERT: R 56 GLU cc_start: 0.8834 (tt0) cc_final: 0.8369 (tt0) REVERT: S 31 LYS cc_start: 0.9016 (mmmm) cc_final: 0.8543 (mmmm) outliers start: 65 outliers final: 49 residues processed: 171 average time/residue: 0.1923 time to fit residues: 53.6101 Evaluate side-chains 165 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 111 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 256 MET Chi-restraints excluded: chain L residue 270 MET Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 318 ASP Chi-restraints excluded: chain N residue 385 ASN Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain C residue 553 CYS Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 606 ILE Chi-restraints excluded: chain P residue 98 ASN Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 259 ARG Chi-restraints excluded: chain P residue 288 MET Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 104 PHE Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain Q residue 59 LYS Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain S residue 99 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 108 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 0 optimal weight: 80.0000 chunk 65 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 19 optimal weight: 50.0000 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 246 optimal weight: 0.9990 chunk 254 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** 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 = 0.3544 r_free = 0.3544 target = 0.051168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.031255 restraints weight = 226145.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.031970 restraints weight = 129100.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.031081 restraints weight = 95802.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.031202 restraints weight = 85524.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.031318 restraints weight = 76190.757| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 30556 Z= 0.212 Angle : 0.697 16.227 42796 Z= 0.371 Chirality : 0.041 0.170 4850 Planarity : 0.004 0.041 4397 Dihedral : 27.975 179.669 6650 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.38 % Allowed : 18.31 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.15), residues: 2956 helix: 1.05 (0.17), residues: 1020 sheet: -1.14 (0.23), residues: 451 loop : -2.05 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG I 134 TYR 0.022 0.001 TYR K 39 PHE 0.012 0.001 PHE A 86 TRP 0.014 0.001 TRP N 205 HIS 0.005 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00468 (30541) covalent geometry : angle 0.68427 (42770) SS BOND : bond 0.00610 ( 13) SS BOND : angle 5.46703 ( 26) hydrogen bonds : bond 0.07251 ( 1279) hydrogen bonds : angle 4.63471 ( 3270) metal coordination : bond 0.00043 ( 1) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 121 time to evaluate : 0.923 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: T 1 MET cc_start: 0.7453 (tmm) cc_final: 0.7141 (ppp) REVERT: A 319 MET cc_start: 0.9073 (tmm) cc_final: 0.8717 (tpp) REVERT: A 612 GLU cc_start: 0.9384 (tp30) cc_final: 0.9069 (tp30) REVERT: L 179 THR cc_start: 0.9440 (OUTLIER) cc_final: 0.8937 (p) REVERT: L 181 GLN cc_start: 0.9011 (mt0) cc_final: 0.8636 (mt0) REVERT: L 252 MET cc_start: 0.8761 (mmm) cc_final: 0.8480 (mmm) REVERT: N 318 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7271 (m-30) REVERT: N 404 MET cc_start: 0.8656 (pmm) cc_final: 0.7962 (pmm) REVERT: C 121 MET cc_start: 0.8347 (mtm) cc_final: 0.7859 (mtp) REVERT: C 296 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9166 (pp) REVERT: P 288 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8073 (tpp) REVERT: I 105 GLU cc_start: 0.9253 (tm-30) cc_final: 0.8715 (tm-30) REVERT: J 53 GLU cc_start: 0.9341 (mm-30) cc_final: 0.9031 (mp0) REVERT: J 84 MET cc_start: 0.8554 (mmm) cc_final: 0.7940 (mmm) REVERT: K 56 GLU cc_start: 0.8819 (tt0) cc_final: 0.8298 (mt-10) REVERT: M 30 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.8949 (ptm160) REVERT: M 68 GLU cc_start: 0.8823 (tt0) cc_final: 0.8499 (tp30) REVERT: O 50 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8533 (mm-30) REVERT: O 90 MET cc_start: 0.9063 (mmm) cc_final: 0.8697 (mmm) REVERT: O 105 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8208 (tm-30) REVERT: O 106 ASP cc_start: 0.9116 (m-30) cc_final: 0.8462 (m-30) REVERT: O 120 MET cc_start: 0.8709 (mmm) cc_final: 0.8487 (mmm) REVERT: Q 59 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9086 (tptm) REVERT: R 56 GLU cc_start: 0.8822 (tt0) cc_final: 0.8433 (tt0) REVERT: R 61 GLU cc_start: 0.8994 (tp30) cc_final: 0.8760 (mm-30) REVERT: S 31 LYS cc_start: 0.9011 (mmmm) cc_final: 0.8587 (mmmm) outliers start: 54 outliers final: 44 residues processed: 166 average time/residue: 0.1972 time to fit residues: 53.0340 Evaluate side-chains 168 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 118 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 318 ASP Chi-restraints excluded: chain N residue 385 ASN Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain C residue 553 CYS Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 606 ILE Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 259 ARG Chi-restraints excluded: chain P residue 288 MET Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 104 PHE Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain Q residue 59 LYS Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain S residue 68 GLU Chi-restraints excluded: chain S residue 99 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 29 optimal weight: 6.9990 chunk 307 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 277 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 247 optimal weight: 2.9990 chunk 159 optimal weight: 50.0000 chunk 319 optimal weight: 30.0000 chunk 225 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 260 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** 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 = 0.3554 r_free = 0.3554 target = 0.051582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.031692 restraints weight = 222093.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.032481 restraints weight = 126319.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.031544 restraints weight = 92685.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.031647 restraints weight = 77352.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.031754 restraints weight = 76654.490| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30556 Z= 0.182 Angle : 0.674 15.542 42796 Z= 0.358 Chirality : 0.041 0.171 4850 Planarity : 0.004 0.044 4397 Dihedral : 27.843 179.407 6650 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.16 % Allowed : 18.53 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.15), residues: 2956 helix: 1.24 (0.17), residues: 1029 sheet: -0.97 (0.24), residues: 445 loop : -1.97 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 134 TYR 0.018 0.001 TYR K 39 PHE 0.011 0.001 PHE A 86 TRP 0.016 0.001 TRP N 205 HIS 0.004 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00403 (30541) covalent geometry : angle 0.66198 (42770) SS BOND : bond 0.00571 ( 13) SS BOND : angle 5.19174 ( 26) hydrogen bonds : bond 0.06782 ( 1279) hydrogen bonds : angle 4.41783 ( 3270) metal coordination : bond 0.00041 ( 1) Misc. bond : bond 0.00031 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 1 MET cc_start: 0.7453 (tmm) cc_final: 0.7178 (ppp) REVERT: A 118 MET cc_start: 0.9290 (mmm) cc_final: 0.8916 (mmm) REVERT: A 319 MET cc_start: 0.8998 (tmm) cc_final: 0.8719 (tpp) REVERT: A 612 GLU cc_start: 0.9412 (tp30) cc_final: 0.9095 (tp30) REVERT: L 179 THR cc_start: 0.9433 (OUTLIER) cc_final: 0.8776 (p) REVERT: L 181 GLN cc_start: 0.8998 (mt0) cc_final: 0.8597 (mt0) REVERT: L 252 MET cc_start: 0.8776 (mmm) cc_final: 0.8410 (mmm) REVERT: N 318 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7305 (m-30) REVERT: N 404 MET cc_start: 0.8635 (pmm) cc_final: 0.7983 (pmm) REVERT: C 121 MET cc_start: 0.8433 (mtm) cc_final: 0.7957 (mtt) REVERT: C 296 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9148 (pp) REVERT: P 288 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8064 (tpp) REVERT: I 105 GLU cc_start: 0.9251 (tm-30) cc_final: 0.8733 (tm-30) REVERT: J 53 GLU cc_start: 0.9321 (mm-30) cc_final: 0.9038 (mp0) REVERT: J 84 MET cc_start: 0.8488 (mmm) cc_final: 0.7856 (mmm) REVERT: K 56 GLU cc_start: 0.8753 (tt0) cc_final: 0.8217 (mt-10) REVERT: M 30 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.8969 (ptm160) REVERT: M 68 GLU cc_start: 0.8780 (tt0) cc_final: 0.8457 (tp30) REVERT: O 50 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8552 (mm-30) REVERT: O 90 MET cc_start: 0.9071 (mmm) cc_final: 0.8638 (mmm) REVERT: O 105 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8227 (tm-30) REVERT: O 106 ASP cc_start: 0.9122 (m-30) cc_final: 0.8434 (m-30) REVERT: Q 59 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.9129 (tptm) REVERT: R 56 GLU cc_start: 0.8793 (tt0) cc_final: 0.8370 (tt0) REVERT: R 61 GLU cc_start: 0.8938 (tp30) cc_final: 0.8686 (mm-30) REVERT: S 31 LYS cc_start: 0.9016 (mmmm) cc_final: 0.8548 (mmmm) outliers start: 49 outliers final: 40 residues processed: 167 average time/residue: 0.1936 time to fit residues: 52.6382 Evaluate side-chains 164 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 118 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 318 ASP Chi-restraints excluded: chain N residue 385 ASN Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 606 ILE Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 259 ARG Chi-restraints excluded: chain P residue 288 MET Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 104 PHE Chi-restraints excluded: chain Q residue 59 LYS Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain S residue 68 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 33 optimal weight: 10.0000 chunk 153 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 286 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 208 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 265 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** 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 = 0.3541 r_free = 0.3541 target = 0.051018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.031224 restraints weight = 226984.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.032148 restraints weight = 128936.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.031065 restraints weight = 94189.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.031286 restraints weight = 80963.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.031277 restraints weight = 75180.883| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 30556 Z= 0.234 Angle : 0.707 20.429 42796 Z= 0.372 Chirality : 0.041 0.169 4850 Planarity : 0.004 0.056 4397 Dihedral : 27.812 179.608 6650 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.38 % Allowed : 18.45 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.15), residues: 2956 helix: 1.11 (0.17), residues: 1028 sheet: -0.91 (0.24), residues: 442 loop : -1.93 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG P 230 TYR 0.018 0.001 TYR K 39 PHE 0.012 0.001 PHE A 86 TRP 0.019 0.001 TRP P 253 HIS 0.004 0.001 HIS Q 75 Details of bonding type rmsd covalent geometry : bond 0.00517 (30541) covalent geometry : angle 0.69622 (42770) SS BOND : bond 0.00533 ( 13) SS BOND : angle 5.07061 ( 26) hydrogen bonds : bond 0.07498 ( 1279) hydrogen bonds : angle 4.54517 ( 3270) metal coordination : bond 0.00045 ( 1) Misc. bond : bond 0.00077 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7903.69 seconds wall clock time: 136 minutes 15.26 seconds (8175.26 seconds total)