Starting phenix.real_space_refine on Mon Sep 14 12:13:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wkr_21707/09_2026/6wkr_21707.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wkr_21707/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6wkr_21707/09_2026/6wkr_21707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wkr_21707/09_2026/6wkr_21707.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wkr_21707/09_2026/6wkr_21707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wkr_21707/09_2026/6wkr_21707.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6wkr_21707/09_2026/6wkr_21707.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wkr_21707/09_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 5.84, per 1000 atoms: 0.20 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: 2.96 Conformation dependent library (CDL) restraints added in 3.2 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: 3.99 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: 7.38 Time building geometry restraints manager: 3.63 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=" C3' DA H 299 " pdb=" O3' DA H 299 " ideal model delta sigma weight residual 1.435 1.370 0.065 1.30e-02 5.92e+03 2.47e+01 bond pdb=" N1 DC H 21 " pdb=" C6 DC H 21 " ideal model delta sigma weight residual 1.367 1.340 0.027 6.00e-03 2.78e+04 2.08e+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 ... (remaining 30536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 41950 2.77 - 5.55: 747 5.55 - 8.32: 60 8.32 - 11.09: 10 11.09 - 13.87: 3 Bond angle restraints: 42770 Sorted by residual: angle pdb=" O4' DC H 296 " pdb=" C4' DC H 296 " pdb=" C3' DC H 296 " ideal model delta sigma weight residual 106.00 101.61 4.39 6.00e-01 2.78e+00 5.35e+01 angle pdb=" O4' DC H 110 " pdb=" C4' DC H 110 " pdb=" C3' DC H 110 " ideal model delta sigma weight residual 106.00 101.72 4.28 6.00e-01 2.78e+00 5.10e+01 angle pdb=" O4' DA H 120 " pdb=" C4' DA H 120 " pdb=" C3' DA H 120 " ideal model delta sigma weight residual 106.00 102.20 3.80 6.00e-01 2.78e+00 4.00e+01 angle pdb=" O4' DG H 111 " pdb=" C4' DG H 111 " pdb=" C3' DG H 111 " ideal model delta sigma weight residual 106.00 102.37 3.63 6.00e-01 2.78e+00 3.65e+01 angle pdb=" O4' DT H 95 " pdb=" C4' DT H 95 " pdb=" C3' DT H 95 " ideal model delta sigma weight residual 106.00 102.57 3.43 6.00e-01 2.78e+00 3.26e+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: 3500 0.053 - 0.106: 1079 0.106 - 0.159: 236 0.159 - 0.212: 26 0.212 - 0.265: 9 Chirality restraints: 4850 Sorted by residual: chirality pdb=" C3' DA H 20 " pdb=" C4' DA H 20 " pdb=" O3' DA H 20 " pdb=" C2' DA H 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.47 -0.27 2.00e-01 2.50e+01 1.76e+00 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=" C3' DC H 185 " pdb=" C4' DC H 185 " pdb=" O3' DC H 185 " pdb=" C2' DC H 185 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -0.24 2.00e-01 2.50e+01 1.45e+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: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 34.220 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 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= 1.020 Angle : 1.028 40.543 42796 Z= 0.721 Chirality : 0.053 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/Z covalent geometry : bond 0.01030 / 0.76 (30541) covalent geometry : angle 0.98708 / 0.71 (42770) SS BOND : bond 0.42091 / 28.35 ( 13) SS BOND : angle 11.62864 / 8.48 ( 26) hydrogen bonds : bond 0.22413 / 15.00 ( 1279) hydrogen bonds : angle 8.62521 / 5.95 ( 3270) metal coordination : bond 0.65385 / 34.41 ( 1) Misc. bond : bond 0.90126 / 47.43 ( 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 : 1.083 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: 0.9014 (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: 0.8785 (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: 0.9006 (mp0) REVERT: J 84 MET cc_start: 0.8346 (mmm) cc_final: 0.8016 (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: 0.9120 (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: 0.8796 (tpp) outliers start: 7 outliers final: 4 residues processed: 180 average time/residue: 0.2346 time to fit residues: 64.0245 Evaluate side-chains 127 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 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: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 ASN A 166 HIS A 235 ASN A 241 ASN A 243 HIS A 431 GLN L 94 GLN ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 GLN L 235 HIS L 382 GLN N 123 HIS ** N 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 ASN N 239 HIS N 329 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 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.051957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.030160 restraints weight = 221082.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.030844 restraints weight = 119093.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.031275 restraints weight = 86636.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.031374 restraints weight = 73683.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.031531 restraints weight = 69592.826| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 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 = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 30556 Z= 0.180 Angle : 0.811 29.328 42796 Z= 0.439 Chirality : 0.054 0.334 4850 Planarity : 0.005 0.056 4397 Dihedral : 28.715 179.308 6658 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.84 % Allowed : 10.41 % Favored : 88.75 % 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: -2.86 (0.14), residues: 2956 helix: -0.80 (0.15), residues: 1038 sheet: -2.05 (0.22), residues: 437 loop : -2.70 (0.14), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 134 TYR 0.015 0.001 TYR A 495 PHE 0.016 0.002 PHE A 86 TRP 0.025 0.002 TRP P 106 HIS 0.010 0.001 HIS C 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.18 (30541) covalent geometry : angle 0.78634 / 0.43 (42770) SS BOND : bond 0.02972 / 2.23 ( 13) SS BOND : angle 8.15769 / 6.47 ( 26) hydrogen bonds : bond 0.08937 / 6.15 ( 1279) hydrogen bonds : angle 5.74996 / 3.99 ( 3270) metal coordination : bond 0.07033 / 3.70 ( 1) Misc. bond : bond 0.00368 / 0.19 ( 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 187 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 1.019 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: 0.7602 (tmm) cc_final: 0.7294 (ppp) REVERT: A 612 GLU cc_start: 0.9422 (tp30) cc_final: 0.9109 (tp30) REVERT: A 657 MET cc_start: 0.9505 (mtp) cc_final: 0.9291 (mmt) REVERT: L 181 GLN cc_start: 0.8995 (mt0) cc_final: 0.8481 (mp10) REVERT: L 252 MET cc_start: 0.8518 (tpp) cc_final: 0.8253 (mmm) REVERT: L 256 MET cc_start: 0.9141 (mtm) cc_final: 0.8667 (mtm) REVERT: L 376 MET cc_start: 0.9441 (ttp) cc_final: 0.9161 (tmm) REVERT: C 121 MET cc_start: 0.8190 (mtm) cc_final: 0.7307 (mtp) REVERT: P 188 ASP cc_start: 0.9294 (p0) cc_final: 0.8966 (t70) REVERT: I 105 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8678 (tm-30) REVERT: J 53 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8826 (mp0) REVERT: J 84 MET cc_start: 0.8427 (mmm) cc_final: 0.7732 (mmm) REVERT: K 39 TYR cc_start: 0.9180 (m-80) cc_final: 0.7948 (m-80) REVERT: K 56 GLU cc_start: 0.8718 (tt0) cc_final: 0.8234 (mt-10) REVERT: K 118 LYS cc_start: 0.9249 (mtpt) cc_final: 0.8780 (tptt) REVERT: M 31 LYS cc_start: 0.8799 (mmmm) cc_final: 0.8523 (mmtt) REVERT: M 68 GLU cc_start: 0.8815 (tt0) cc_final: 0.8490 (tp30) REVERT: M 110 GLU cc_start: 0.9427 (mm-30) cc_final: 0.9221 (tm-30) REVERT: O 50 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8532 (mm-30) REVERT: O 105 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8236 (pp20) REVERT: O 120 MET cc_start: 0.8566 (mmm) cc_final: 0.8249 (mmm) REVERT: R 56 GLU cc_start: 0.8832 (tt0) cc_final: 0.8343 (tt0) REVERT: R 64 GLU cc_start: 0.9219 (pp20) cc_final: 0.8971 (pp20) outliers start: 19 outliers final: 10 residues processed: 182 average time/residue: 0.2104 time to fit residues: 61.0950 Evaluate side-chains 149 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU 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 62 ILE Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain O residue 112 ILE 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: 7.9990 chunk 96 optimal weight: 7.9990 chunk 141 optimal weight: 50.0000 chunk 165 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 256 optimal weight: 3.9990 chunk 35 optimal weight: 0.0170 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 HIS A 507 HIS ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 235 HIS ** L 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 283 ASN ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.050600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.029084 restraints weight = 228598.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.029705 restraints weight = 126183.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.029904 restraints weight = 91855.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.030199 restraints weight = 80977.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.030260 restraints weight = 75020.550| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 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 = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 30556 Z= 0.280 Angle : 0.799 27.074 42796 Z= 0.429 Chirality : 0.052 0.355 4850 Planarity : 0.004 0.041 4397 Dihedral : 28.469 179.869 6652 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.12 % Allowed : 13.06 % Favored : 84.82 % 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: -2.43 (0.14), residues: 2956 helix: -0.30 (0.15), residues: 1042 sheet: -1.79 (0.23), residues: 428 loop : -2.59 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 29 TYR 0.023 0.002 TYR R 39 PHE 0.014 0.001 PHE A 86 TRP 0.017 0.002 TRP A 361 HIS 0.006 0.001 HIS C 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.28 (30541) covalent geometry : angle 0.77650 / 0.42 (42770) SS BOND : bond 0.02159 / 1.58 ( 13) SS BOND : angle 7.62993 / 6.07 ( 26) hydrogen bonds : bond 0.09790 / 6.81 ( 1279) hydrogen bonds : angle 5.68270 / 3.94 ( 3270) metal coordination : bond 0.00460 / 0.24 ( 1) Misc. bond : bond 0.00199 / 0.10 ( 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: 48 poor density : 136 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 1 MET cc_start: 0.7491 (tmm) cc_final: 0.7181 (ppp) REVERT: A 612 GLU cc_start: 0.9451 (tp30) cc_final: 0.9159 (tp30) REVERT: L 256 MET cc_start: 0.9056 (mtm) cc_final: 0.8563 (mtm) REVERT: N 36 MET cc_start: 0.9089 (tpp) cc_final: 0.8804 (tpp) REVERT: N 399 MET cc_start: 0.8987 (tmm) cc_final: 0.8613 (ppp) REVERT: C 121 MET cc_start: 0.8082 (mtm) cc_final: 0.7649 (mtt) REVERT: C 296 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9270 (pp) REVERT: C 530 CYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8435 (t) REVERT: P 288 MET cc_start: 0.8364 (mmm) cc_final: 0.7997 (tpp) REVERT: I 105 GLU cc_start: 0.9218 (tm-30) cc_final: 0.8693 (tm-30) REVERT: J 53 GLU cc_start: 0.9403 (mm-30) cc_final: 0.9030 (mp0) REVERT: J 84 MET cc_start: 0.8504 (mmm) cc_final: 0.7859 (mmm) REVERT: K 39 TYR cc_start: 0.9314 (m-80) cc_final: 0.7992 (m-80) REVERT: K 56 GLU cc_start: 0.8742 (tt0) cc_final: 0.8267 (mt-10) REVERT: K 118 LYS cc_start: 0.9220 (mtpt) cc_final: 0.8707 (tptt) REVERT: M 31 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8727 (mmtt) REVERT: M 56 MET cc_start: 0.9291 (tpp) cc_final: 0.9088 (tpp) REVERT: M 68 GLU cc_start: 0.8843 (tt0) cc_final: 0.8559 (tp30) REVERT: O 50 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8547 (mm-30) REVERT: O 105 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8446 (tm-30) REVERT: O 120 MET cc_start: 0.8730 (mmm) cc_final: 0.8461 (mmm) REVERT: R 56 GLU cc_start: 0.8896 (tt0) cc_final: 0.8407 (tt0) REVERT: R 64 GLU cc_start: 0.9277 (pp20) cc_final: 0.9064 (pp20) outliers start: 48 outliers final: 28 residues processed: 175 average time/residue: 0.1979 time to fit residues: 55.8752 Evaluate side-chains 157 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 250 LEU Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain N residue 133 MET Chi-restraints excluded: chain C residue 110 MET 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 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 130 ILE 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 70 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 103 LEU 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 O residue 124 ILE Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain E residue 25 GLU 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: 2.9990 chunk 206 optimal weight: 7.9990 chunk 171 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 257 optimal weight: 0.8980 chunk 176 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 504 GLN ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 235 HIS ** L 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 268 HIS Q 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.051976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.030193 restraints weight = 221464.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.030831 restraints weight = 121085.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.031040 restraints weight = 88129.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.031407 restraints weight = 77574.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.031472 restraints weight = 71141.572| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 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 = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30556 Z= 0.147 Angle : 0.713 23.166 42796 Z= 0.386 Chirality : 0.050 0.341 4850 Planarity : 0.004 0.045 4397 Dihedral : 28.343 178.746 6652 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.68 % Allowed : 14.17 % Favored : 84.16 % 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: -1.79 (0.15), residues: 2956 helix: 0.46 (0.16), residues: 1039 sheet: -1.65 (0.22), residues: 465 loop : -2.33 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 181 TYR 0.011 0.001 TYR A 495 PHE 0.016 0.001 PHE L 418 TRP 0.015 0.001 TRP N 205 HIS 0.004 0.001 HIS N 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (30541) covalent geometry : angle 0.69484 / 0.38 (42770) SS BOND : bond 0.01375 / 1.00 ( 13) SS BOND : angle 6.56318 / 5.16 ( 26) hydrogen bonds : bond 0.07712 / 5.34 ( 1279) hydrogen bonds : angle 4.99397 / 3.46 ( 3270) metal coordination : bond 0.00216 / 0.11 ( 1) Misc. bond : bond 0.00046 / 0.02 ( 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 196 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 1.038 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: 0.7486 (tmm) cc_final: 0.7175 (ppp) REVERT: A 612 GLU cc_start: 0.9416 (tp30) cc_final: 0.9086 (tp30) REVERT: L 376 MET cc_start: 0.9088 (tmm) cc_final: 0.8882 (tmm) REVERT: N 36 MET cc_start: 0.9084 (tpp) cc_final: 0.8814 (tpp) REVERT: N 399 MET cc_start: 0.9107 (tmm) cc_final: 0.8625 (ppp) REVERT: C 121 MET cc_start: 0.8315 (mtm) cc_final: 0.7872 (mtt) REVERT: C 296 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9265 (pp) REVERT: C 439 MET cc_start: 0.9477 (ttp) cc_final: 0.9276 (ptt) REVERT: P 288 MET cc_start: 0.8191 (mmm) cc_final: 0.7933 (tpp) REVERT: I 105 GLU cc_start: 0.9189 (tm-30) cc_final: 0.8631 (tm-30) REVERT: I 106 ASP cc_start: 0.9210 (m-30) cc_final: 0.8764 (m-30) REVERT: I 120 MET cc_start: 0.8704 (mpp) cc_final: 0.8396 (mpp) REVERT: J 53 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8933 (mp0) REVERT: J 84 MET cc_start: 0.8358 (mmm) cc_final: 0.7725 (mmm) REVERT: K 39 TYR cc_start: 0.9168 (m-80) cc_final: 0.7938 (m-80) REVERT: K 56 GLU cc_start: 0.8715 (tt0) cc_final: 0.8206 (mt-10) REVERT: K 110 ASN cc_start: 0.9475 (t0) cc_final: 0.9273 (t0) REVERT: K 118 LYS cc_start: 0.9285 (mtpt) cc_final: 0.8816 (tptt) REVERT: M 31 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8710 (mmtt) REVERT: M 68 GLU cc_start: 0.8839 (tt0) cc_final: 0.8477 (tp30) REVERT: O 50 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8527 (mm-30) REVERT: O 105 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8425 (tm-30) REVERT: O 106 ASP cc_start: 0.8969 (m-30) cc_final: 0.8578 (m-30) REVERT: O 120 MET cc_start: 0.8761 (mmm) cc_final: 0.8519 (mmm) REVERT: R 56 GLU cc_start: 0.8819 (tt0) cc_final: 0.8367 (tt0) REVERT: S 51 ILE cc_start: 0.9450 (tp) cc_final: 0.9245 (mm) REVERT: S 77 LEU cc_start: 0.9694 (tp) cc_final: 0.9473 (tp) outliers start: 38 outliers final: 25 residues processed: 187 average time/residue: 0.1952 time to fit residues: 58.3237 Evaluate side-chains 159 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 250 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 187 VAL 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 P residue 221 VAL Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain K residue 62 ILE 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 80 THR Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 273 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 205 optimal weight: 9.9990 chunk 189 optimal weight: 50.0000 chunk 196 optimal weight: 9.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 504 GLN ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 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 = 0.3516 r_free = 0.3516 target = 0.050134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.030421 restraints weight = 229416.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.031185 restraints weight = 131155.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.030291 restraints weight = 87888.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.030381 restraints weight = 80867.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.030406 restraints weight = 80724.813| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 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 = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 30556 Z= 0.342 Angle : 0.836 21.565 42796 Z= 0.443 Chirality : 0.051 0.377 4850 Planarity : 0.005 0.040 4397 Dihedral : 28.217 179.990 6652 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.15 % Favored : 91.81 % Rotamer: Outliers : 2.82 % Allowed : 15.45 % Favored : 81.73 % 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: -1.99 (0.15), residues: 2956 helix: 0.17 (0.16), residues: 1036 sheet: -1.64 (0.23), residues: 447 loop : -2.38 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 83 TYR 0.021 0.002 TYR R 39 PHE 0.015 0.002 PHE L 418 TRP 0.010 0.002 TRP L 314 HIS 0.007 0.002 HIS Q 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.34 (30541) covalent geometry : angle 0.81152 / 0.43 (42770) SS BOND : bond 0.01200 / 0.86 ( 13) SS BOND : angle 8.14371 / 5.83 ( 26) hydrogen bonds : bond 0.10350 / 7.23 ( 1279) hydrogen bonds : angle 5.41819 / 3.76 ( 3270) metal coordination : bond 0.00420 / 0.22 ( 1) Misc. bond : bond 0.00142 / 0.07 ( 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 188 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 124 time to evaluate : 1.016 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: 0.7694 (tmm) cc_final: 0.7332 (ppp) REVERT: A 612 GLU cc_start: 0.9458 (tp30) cc_final: 0.9173 (tp30) REVERT: A 657 MET cc_start: 0.9567 (mtp) cc_final: 0.9278 (mmt) REVERT: L 252 MET cc_start: 0.8786 (mmm) cc_final: 0.8282 (mmm) REVERT: N 36 MET cc_start: 0.8998 (tpp) cc_final: 0.8726 (tpp) REVERT: N 318 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7260 (m-30) REVERT: N 399 MET cc_start: 0.9212 (tmm) cc_final: 0.8767 (ppp) REVERT: C 439 MET cc_start: 0.9526 (ttp) cc_final: 0.9324 (ptm) REVERT: C 553 CYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8401 (t) REVERT: P 288 MET cc_start: 0.8355 (mmm) cc_final: 0.7973 (tpp) REVERT: I 105 GLU cc_start: 0.9297 (tm-30) cc_final: 0.8777 (tm-30) REVERT: I 120 MET cc_start: 0.8586 (mpp) cc_final: 0.8177 (mpp) REVERT: J 53 GLU cc_start: 0.9405 (mm-30) cc_final: 0.9054 (mp0) REVERT: J 63 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8653 (mp0) REVERT: J 84 MET cc_start: 0.8571 (mmm) cc_final: 0.7974 (mmm) REVERT: K 39 TYR cc_start: 0.9319 (m-80) cc_final: 0.8042 (m-80) REVERT: K 56 GLU cc_start: 0.8767 (tt0) cc_final: 0.8246 (mt-10) REVERT: K 118 LYS cc_start: 0.9110 (mtpt) cc_final: 0.8647 (tptt) REVERT: M 68 GLU cc_start: 0.8826 (tt0) cc_final: 0.8576 (tp30) REVERT: O 50 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8596 (mm-30) REVERT: O 105 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8444 (tm-30) REVERT: O 120 MET cc_start: 0.8843 (mmm) cc_final: 0.8636 (mmm) REVERT: Q 59 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.9005 (tptm) REVERT: R 56 GLU cc_start: 0.8892 (tt0) cc_final: 0.8421 (tt0) REVERT: S 31 LYS cc_start: 0.8908 (mmmm) cc_final: 0.8427 (mmmm) outliers start: 64 outliers final: 44 residues processed: 179 average time/residue: 0.1882 time to fit residues: 55.0181 Evaluate side-chains 164 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 117 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 250 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 640 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 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 553 CYS 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 I residue 32 THR Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 130 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 74 LYS 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 O residue 124 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 62 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 83 ARG Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain E residue 25 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 47 optimal weight: 0.8980 chunk 314 optimal weight: 1.9990 chunk 232 optimal weight: 20.0000 chunk 137 optimal weight: 0.0270 chunk 181 optimal weight: 0.8980 chunk 141 optimal weight: 40.0000 chunk 264 optimal weight: 0.8980 chunk 15 optimal weight: 40.0000 chunk 309 optimal weight: 0.7980 chunk 281 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 504 GLN ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.052098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.030540 restraints weight = 218642.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.031202 restraints weight = 117751.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.031416 restraints weight = 85894.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.031822 restraints weight = 75601.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.031924 restraints weight = 68676.009| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (17 function evaluations) r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30556 Z= 0.142 Angle : 0.717 19.736 42796 Z= 0.385 Chirality : 0.050 0.345 4850 Planarity : 0.004 0.048 4397 Dihedral : 28.126 178.032 6652 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.72 % Allowed : 16.73 % Favored : 81.55 % 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: -1.47 (0.15), residues: 2956 helix: 0.77 (0.16), residues: 1042 sheet: -1.38 (0.23), residues: 454 loop : -2.21 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG I 134 TYR 0.013 0.001 TYR S 37 PHE 0.014 0.001 PHE A 86 TRP 0.015 0.001 TRP N 205 HIS 0.005 0.001 HIS C 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (30541) covalent geometry : angle 0.69482 / 0.38 (42770) SS BOND : bond 0.01275 / 0.80 ( 13) SS BOND : angle 7.18547 / 5.13 ( 26) hydrogen bonds : bond 0.07372 / 5.11 ( 1279) hydrogen bonds : angle 4.71115 / 3.27 ( 3270) metal coordination : bond 0.00595 / 0.31 ( 1) Misc. bond : bond 0.00050 / 0.03 ( 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 180 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.947 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: 0.7489 (tmm) cc_final: 0.7170 (ppp) REVERT: A 612 GLU cc_start: 0.9430 (tp30) cc_final: 0.9093 (tp30) REVERT: L 252 MET cc_start: 0.8761 (mmm) cc_final: 0.8306 (mmm) REVERT: L 370 MET cc_start: 0.8536 (mmm) cc_final: 0.8153 (mmm) REVERT: N 36 MET cc_start: 0.9081 (tpp) cc_final: 0.8809 (tpp) REVERT: N 318 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7178 (m-30) REVERT: N 399 MET cc_start: 0.9251 (tmm) cc_final: 0.8821 (ppp) REVERT: N 404 MET cc_start: 0.8542 (pmm) cc_final: 0.8270 (pmm) REVERT: C 121 MET cc_start: 0.8273 (mtm) cc_final: 0.7812 (mtt) REVERT: P 288 MET cc_start: 0.8257 (mmm) cc_final: 0.7940 (tpp) REVERT: I 105 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8588 (tm-30) REVERT: I 106 ASP cc_start: 0.9231 (m-30) cc_final: 0.8668 (m-30) REVERT: I 120 MET cc_start: 0.8571 (mpp) cc_final: 0.8190 (mpp) REVERT: J 53 GLU cc_start: 0.9298 (mm-30) cc_final: 0.8926 (mp0) REVERT: J 84 MET cc_start: 0.8343 (mmm) cc_final: 0.7762 (mmm) REVERT: K 39 TYR cc_start: 0.9082 (m-80) cc_final: 0.7775 (m-80) REVERT: K 56 GLU cc_start: 0.8687 (tt0) cc_final: 0.8171 (mt-10) REVERT: K 118 LYS cc_start: 0.9292 (mtpt) cc_final: 0.8862 (tptt) REVERT: M 68 GLU cc_start: 0.8725 (tt0) cc_final: 0.8510 (tp30) REVERT: M 110 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8466 (tm-30) REVERT: O 50 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8593 (mm-30) REVERT: O 105 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8423 (tm-30) REVERT: Q 59 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.9034 (tptm) REVERT: R 56 GLU cc_start: 0.8788 (tt0) cc_final: 0.8350 (tt0) REVERT: S 31 LYS cc_start: 0.8790 (mmmm) cc_final: 0.8301 (mmmm) REVERT: S 90 GLU cc_start: 0.8822 (mp0) cc_final: 0.8607 (pm20) outliers start: 39 outliers final: 29 residues processed: 172 average time/residue: 0.1995 time to fit residues: 55.4534 Evaluate side-chains 162 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 250 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 429 CYS 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 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 110 CYS Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain K residue 62 ILE 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 97 GLU Chi-restraints excluded: chain O residue 104 PHE Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain Q residue 59 LYS Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain E residue 25 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 299 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 15 optimal weight: 40.0000 chunk 219 optimal weight: 10.0000 chunk 313 optimal weight: 50.0000 chunk 250 optimal weight: 0.0020 chunk 287 optimal weight: 0.4980 chunk 56 optimal weight: 7.9990 chunk 215 optimal weight: 20.0000 chunk 235 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 overall best weight: 3.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3537 r_free = 0.3537 target = 0.050876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.029288 restraints weight = 224609.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.029977 restraints weight = 125006.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.030180 restraints weight = 92055.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.030549 restraints weight = 81356.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.030654 restraints weight = 74528.375| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 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 = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 30556 Z= 0.244 Angle : 0.759 18.693 42796 Z= 0.401 Chirality : 0.049 0.354 4850 Planarity : 0.004 0.049 4397 Dihedral : 28.016 178.859 6652 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.38 % Allowed : 17.08 % Favored : 80.54 % 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: -1.52 (0.15), residues: 2956 helix: 0.68 (0.16), residues: 1045 sheet: -1.33 (0.23), residues: 451 loop : -2.24 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 98 TYR 0.018 0.001 TYR R 39 PHE 0.029 0.001 PHE A 99 TRP 0.012 0.001 TRP N 185 HIS 0.005 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.24 (30541) covalent geometry : angle 0.74180 / 0.39 (42770) SS BOND : bond 0.00857 / 0.57 ( 13) SS BOND : angle 6.46965 / 4.72 ( 26) hydrogen bonds : bond 0.08483 / 5.92 ( 1279) hydrogen bonds : angle 4.93894 / 3.41 ( 3270) metal coordination : bond 0.00298 / 0.16 ( 1) Misc. bond : bond 0.00085 / 0.04 ( 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 181 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 127 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 1 MET cc_start: 0.7482 (tmm) cc_final: 0.7170 (ppp) REVERT: A 612 GLU cc_start: 0.9446 (tp30) cc_final: 0.9111 (tp30) REVERT: A 657 MET cc_start: 0.9544 (mtp) cc_final: 0.9261 (mmt) REVERT: L 252 MET cc_start: 0.8737 (mmm) cc_final: 0.8263 (mmm) REVERT: N 36 MET cc_start: 0.9052 (tpp) cc_final: 0.8802 (tpp) REVERT: N 318 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7312 (m-30) REVERT: N 399 MET cc_start: 0.9338 (tmm) cc_final: 0.9128 (tmm) REVERT: N 404 MET cc_start: 0.8568 (pmm) cc_final: 0.8208 (pmm) REVERT: C 121 MET cc_start: 0.8225 (mtm) cc_final: 0.7799 (mtp) REVERT: P 288 MET cc_start: 0.8329 (mmm) cc_final: 0.8024 (tpp) REVERT: I 105 GLU cc_start: 0.9277 (tm-30) cc_final: 0.8727 (tm-30) REVERT: I 120 MET cc_start: 0.8546 (mpp) cc_final: 0.8086 (mpp) REVERT: J 53 GLU cc_start: 0.9366 (mm-30) cc_final: 0.9020 (mp0) REVERT: J 84 MET cc_start: 0.8525 (mmm) cc_final: 0.7888 (mmm) REVERT: K 56 GLU cc_start: 0.8794 (tt0) cc_final: 0.8281 (mt-10) REVERT: K 118 LYS cc_start: 0.9272 (mtpt) cc_final: 0.8788 (tptt) REVERT: M 31 LYS cc_start: 0.9023 (mmmm) cc_final: 0.8747 (mmtt) REVERT: M 110 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8465 (tm-30) REVERT: O 50 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8593 (mm-30) REVERT: O 105 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8458 (tm-30) REVERT: O 120 MET cc_start: 0.8749 (mmm) cc_final: 0.8302 (mmm) REVERT: Q 59 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9149 (tptm) REVERT: R 56 GLU cc_start: 0.8878 (tt0) cc_final: 0.8470 (tt0) REVERT: S 31 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8423 (mmmm) outliers start: 54 outliers final: 36 residues processed: 173 average time/residue: 0.1945 time to fit residues: 54.7709 Evaluate side-chains 160 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 250 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 523 THR 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 405 THR Chi-restraints excluded: chain L residue 429 CYS 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 577 VAL 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 110 CYS Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 111 ILE 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 O residue 124 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 35 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 286 optimal weight: 20.0000 chunk 198 optimal weight: 9.9990 chunk 163 optimal weight: 0.0370 chunk 132 optimal weight: 7.9990 chunk 203 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 189 optimal weight: 50.0000 chunk 150 optimal weight: 50.0000 overall best weight: 2.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3545 r_free = 0.3545 target = 0.051195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.031335 restraints weight = 222184.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.032021 restraints weight = 126722.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.031142 restraints weight = 93766.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.031343 restraints weight = 78399.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.031335 restraints weight = 76835.227| |-----------------------------------------------------------------------------| 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30556 Z= 0.195 Angle : 0.733 18.019 42796 Z= 0.389 Chirality : 0.049 0.362 4850 Planarity : 0.004 0.040 4397 Dihedral : 27.970 179.098 6652 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.99 % Allowed : 17.70 % Favored : 80.32 % 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: -1.40 (0.15), residues: 2956 helix: 0.83 (0.16), residues: 1039 sheet: -1.32 (0.23), residues: 461 loop : -2.18 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 134 TYR 0.021 0.001 TYR K 39 PHE 0.026 0.001 PHE A 99 TRP 0.013 0.001 TRP N 205 HIS 0.004 0.001 HIS Q 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 (30541) covalent geometry : angle 0.71749 / 0.38 (42770) SS BOND : bond 0.00989 / 0.56 ( 13) SS BOND : angle 6.20077 / 4.50 ( 26) hydrogen bonds : bond 0.07790 / 5.42 ( 1279) hydrogen bonds : angle 4.80223 / 3.33 ( 3270) metal coordination : bond 0.00200 / 0.11 ( 1) Misc. bond : bond 0.00025 / 0.01 ( 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 172 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 127 time to evaluate : 0.910 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: 0.7559 (tmm) cc_final: 0.7228 (ppp) REVERT: A 612 GLU cc_start: 0.9412 (tp30) cc_final: 0.9087 (tp30) REVERT: A 657 MET cc_start: 0.9547 (mtp) cc_final: 0.9263 (mmt) REVERT: L 252 MET cc_start: 0.8700 (mmm) cc_final: 0.8251 (mmm) REVERT: N 36 MET cc_start: 0.9095 (tpp) cc_final: 0.8792 (mmm) REVERT: N 133 MET cc_start: 0.7928 (ppp) cc_final: 0.7662 (ppp) REVERT: N 318 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7279 (m-30) REVERT: N 399 MET cc_start: 0.9344 (tmm) cc_final: 0.9119 (tmm) REVERT: N 404 MET cc_start: 0.8620 (pmm) cc_final: 0.8229 (pmm) REVERT: C 121 MET cc_start: 0.8276 (mtm) cc_final: 0.7321 (mtp) REVERT: P 288 MET cc_start: 0.8303 (mmm) cc_final: 0.8007 (tpp) REVERT: I 105 GLU cc_start: 0.9231 (tm-30) cc_final: 0.8624 (tm-30) REVERT: I 120 MET cc_start: 0.8518 (mpp) cc_final: 0.8033 (mpp) REVERT: J 53 GLU cc_start: 0.9352 (mm-30) cc_final: 0.9007 (mp0) REVERT: J 84 MET cc_start: 0.8436 (mmm) cc_final: 0.7813 (mmm) REVERT: K 39 TYR cc_start: 0.9135 (m-80) cc_final: 0.7443 (m-10) REVERT: K 56 GLU cc_start: 0.8775 (tt0) cc_final: 0.8247 (mt-10) REVERT: K 118 LYS cc_start: 0.9098 (mtpt) cc_final: 0.8638 (tptt) REVERT: M 68 GLU cc_start: 0.8747 (tt0) cc_final: 0.8413 (tp30) REVERT: M 110 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8469 (tm-30) REVERT: O 50 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8598 (mm-30) REVERT: O 105 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8292 (tm-30) REVERT: O 106 ASP cc_start: 0.8985 (m-30) cc_final: 0.8463 (m-30) REVERT: R 56 GLU cc_start: 0.8837 (tt0) cc_final: 0.8411 (tt0) REVERT: S 31 LYS cc_start: 0.8910 (mmmm) cc_final: 0.8459 (mmmm) outliers start: 45 outliers final: 37 residues processed: 165 average time/residue: 0.1941 time to fit residues: 52.0876 Evaluate side-chains 161 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 1.240 ------------------------------------------------------------------------------- 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 250 LEU Chi-restraints excluded: chain A residue 252 PHE 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 405 THR Chi-restraints excluded: chain L residue 429 CYS 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 571 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 110 CYS 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 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 87 SER Chi-restraints excluded: chain O residue 104 PHE Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 124 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 108 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 0 optimal weight: 80.0000 chunk 65 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 185 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 246 optimal weight: 1.9990 chunk 254 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 360 GLN ** 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 = 0.3534 r_free = 0.3534 target = 0.050705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.029282 restraints weight = 227102.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.029988 restraints weight = 125327.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.030183 restraints weight = 91862.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.030569 restraints weight = 81211.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.030665 restraints weight = 74311.743| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 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 = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 30556 Z= 0.256 Angle : 0.768 17.432 42796 Z= 0.405 Chirality : 0.049 0.370 4850 Planarity : 0.004 0.040 4397 Dihedral : 27.927 179.664 6652 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.16 % Allowed : 17.61 % Favored : 80.23 % 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: -1.43 (0.15), residues: 2956 helix: 0.74 (0.16), residues: 1032 sheet: -1.17 (0.23), residues: 445 loop : -2.19 (0.15), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 29 TYR 0.022 0.001 TYR K 39 PHE 0.024 0.001 PHE A 99 TRP 0.015 0.002 TRP L 389 HIS 0.006 0.001 HIS Q 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.26 (30541) covalent geometry : angle 0.75437 / 0.40 (42770) SS BOND : bond 0.00732 / 0.48 ( 13) SS BOND : angle 5.87997 / 4.32 ( 26) hydrogen bonds : bond 0.08670 / 6.05 ( 1279) hydrogen bonds : angle 4.92563 / 3.42 ( 3270) metal coordination : bond 0.00347 / 0.18 ( 1) Misc. bond : bond 0.00095 / 0.05 ( 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 169 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 120 time to evaluate : 1.198 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: 0.7464 (tmm) cc_final: 0.7157 (ppp) REVERT: A 612 GLU cc_start: 0.9421 (tp30) cc_final: 0.9112 (tp30) REVERT: L 252 MET cc_start: 0.8794 (mmm) cc_final: 0.8329 (mmm) REVERT: N 36 MET cc_start: 0.9089 (tpp) cc_final: 0.8800 (mmm) REVERT: N 318 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7335 (m-30) REVERT: N 399 MET cc_start: 0.9386 (tmm) cc_final: 0.9178 (tmm) REVERT: N 404 MET cc_start: 0.8682 (pmm) cc_final: 0.8204 (pmm) REVERT: C 121 MET cc_start: 0.8267 (mtm) cc_final: 0.7335 (mtp) REVERT: C 439 MET cc_start: 0.9324 (ptt) cc_final: 0.9067 (tmm) REVERT: P 288 MET cc_start: 0.8321 (mmm) cc_final: 0.8033 (tpp) REVERT: I 105 GLU cc_start: 0.9241 (tm-30) cc_final: 0.8724 (tm-30) REVERT: I 120 MET cc_start: 0.8540 (mpp) cc_final: 0.8075 (mpp) REVERT: J 53 GLU cc_start: 0.9383 (mm-30) cc_final: 0.9030 (mp0) REVERT: J 84 MET cc_start: 0.8529 (mmm) cc_final: 0.7947 (mmm) REVERT: K 39 TYR cc_start: 0.9202 (m-80) cc_final: 0.7574 (m-10) REVERT: K 56 GLU cc_start: 0.8794 (tt0) cc_final: 0.8272 (mt-10) REVERT: M 68 GLU cc_start: 0.8777 (tt0) cc_final: 0.8528 (tp30) REVERT: M 110 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8527 (tm-30) REVERT: O 50 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8583 (mm-30) REVERT: O 105 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8413 (tm-30) REVERT: R 56 GLU cc_start: 0.8865 (tt0) cc_final: 0.8404 (tt0) REVERT: S 31 LYS cc_start: 0.8948 (mmmm) cc_final: 0.8454 (mmmm) outliers start: 49 outliers final: 46 residues processed: 163 average time/residue: 0.1732 time to fit residues: 46.9076 Evaluate side-chains 165 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 118 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 250 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 523 THR 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 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 59 GLU 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 571 CYS Chi-restraints excluded: chain C residue 577 VAL 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 110 CYS Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain J residue 85 ASP 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 65 LEU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 111 ILE 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 87 SER Chi-restraints excluded: chain O residue 104 PHE Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 124 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 29 optimal weight: 9.9990 chunk 307 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 277 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 159 optimal weight: 50.0000 chunk 319 optimal weight: 30.0000 chunk 225 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 260 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3549 r_free = 0.3549 target = 0.051250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.031364 restraints weight = 220855.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.032328 restraints weight = 125027.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.031249 restraints weight = 90366.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.031465 restraints weight = 78502.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.031468 restraints weight = 74198.942| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 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 = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30556 Z= 0.182 Angle : 0.728 17.110 42796 Z= 0.385 Chirality : 0.048 0.362 4850 Planarity : 0.004 0.040 4397 Dihedral : 27.893 179.350 6652 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.12 % Allowed : 17.87 % Favored : 80.01 % 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: -1.27 (0.15), residues: 2956 helix: 0.90 (0.16), residues: 1038 sheet: -1.11 (0.23), residues: 446 loop : -2.11 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 185 TYR 0.018 0.001 TYR K 39 PHE 0.024 0.001 PHE A 99 TRP 0.017 0.001 TRP N 185 HIS 0.005 0.001 HIS Q 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (30541) covalent geometry : angle 0.71486 / 0.38 (42770) SS BOND : bond 0.00668 / 0.43 ( 13) SS BOND : angle 5.65026 / 4.17 ( 26) hydrogen bonds : bond 0.07603 / 5.30 ( 1279) hydrogen bonds : angle 4.70563 / 3.27 ( 3270) metal coordination : bond 0.00267 / 0.14 ( 1) Misc. bond : bond 0.00018 / 0.01 ( 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: 48 poor density : 126 time to evaluate : 1.004 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: 0.7565 (tmm) cc_final: 0.7205 (ppp) REVERT: A 319 MET cc_start: 0.9078 (tmm) cc_final: 0.8590 (tpp) REVERT: A 612 GLU cc_start: 0.9414 (tp30) cc_final: 0.9098 (tp30) REVERT: L 252 MET cc_start: 0.8775 (mmm) cc_final: 0.8350 (mmm) REVERT: N 36 MET cc_start: 0.9098 (tpp) cc_final: 0.8802 (mmm) REVERT: N 318 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: N 399 MET cc_start: 0.9397 (tmm) cc_final: 0.9177 (tmm) REVERT: N 404 MET cc_start: 0.8633 (pmm) cc_final: 0.8128 (pmm) REVERT: C 121 MET cc_start: 0.8295 (mtm) cc_final: 0.7457 (mtp) REVERT: C 553 CYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8233 (t) REVERT: P 185 ARG cc_start: 0.8006 (mmt180) cc_final: 0.7795 (mmp-170) REVERT: P 288 MET cc_start: 0.8303 (mmm) cc_final: 0.8017 (tpp) REVERT: I 90 MET cc_start: 0.8954 (mmm) cc_final: 0.8752 (mpp) REVERT: I 105 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8695 (tm-30) REVERT: I 120 MET cc_start: 0.8516 (mpp) cc_final: 0.8032 (mpp) REVERT: J 53 GLU cc_start: 0.9345 (mm-30) cc_final: 0.9002 (mp0) REVERT: J 84 MET cc_start: 0.8428 (mmm) cc_final: 0.7806 (mmm) REVERT: K 39 TYR cc_start: 0.9186 (m-80) cc_final: 0.7504 (m-10) REVERT: K 56 GLU cc_start: 0.8775 (tt0) cc_final: 0.8246 (mt-10) REVERT: M 68 GLU cc_start: 0.8801 (tt0) cc_final: 0.8437 (tp30) REVERT: O 50 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8577 (mm-30) REVERT: O 105 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8439 (tm-30) REVERT: O 106 ASP cc_start: 0.9025 (m-30) cc_final: 0.8616 (m-30) REVERT: R 56 GLU cc_start: 0.8829 (tt0) cc_final: 0.8414 (tt0) REVERT: S 31 LYS cc_start: 0.8944 (mmmm) cc_final: 0.8704 (mmmm) outliers start: 48 outliers final: 44 residues processed: 168 average time/residue: 0.1879 time to fit residues: 52.3386 Evaluate side-chains 168 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 250 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain L residue 115 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 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 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 110 CYS Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain J residue 85 ASP 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 65 LEU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 111 ILE 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 87 SER Chi-restraints excluded: chain O residue 104 PHE Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 124 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 33 optimal weight: 0.0070 chunk 153 optimal weight: 20.0000 chunk 187 optimal weight: 5.9990 chunk 286 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 208 optimal weight: 30.0000 chunk 161 optimal weight: 3.9990 chunk 265 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 221 optimal weight: 20.0000 overall best weight: 4.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 272 ASN ** 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 = 0.3531 r_free = 0.3531 target = 0.050548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.030747 restraints weight = 227982.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.031620 restraints weight = 130658.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.030617 restraints weight = 90327.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.030729 restraints weight = 81058.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.030748 restraints weight = 80411.012| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 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 = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 30556 Z= 0.277 Angle : 0.782 16.830 42796 Z= 0.411 Chirality : 0.049 0.371 4850 Planarity : 0.004 0.040 4397 Dihedral : 27.868 179.615 6652 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.03 % Allowed : 18.14 % Favored : 79.83 % 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: -1.37 (0.15), residues: 2956 helix: 0.76 (0.16), residues: 1023 sheet: -1.10 (0.23), residues: 442 loop : -2.12 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 29 TYR 0.018 0.002 TYR K 39 PHE 0.023 0.001 PHE A 99 TRP 0.012 0.002 TRP N 185 HIS 0.006 0.001 HIS Q 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.28 (30541) covalent geometry : angle 0.76989 / 0.41 (42770) SS BOND : bond 0.00669 / 0.44 ( 13) SS BOND : angle 5.58268 / 4.12 ( 26) hydrogen bonds : bond 0.08754 / 6.11 ( 1279) hydrogen bonds : angle 4.95368 / 3.44 ( 3270) metal coordination : bond 0.00229 / 0.12 ( 1) Misc. bond : bond 0.00114 / 0.06 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7800.99 seconds wall clock time: 134 minutes 35.28 seconds (8075.28 seconds total)