Starting phenix.real_space_refine on Thu Jul 31 13:20:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c23_7334/07_2025/6c23_7334.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c23_7334/07_2025/6c23_7334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6c23_7334/07_2025/6c23_7334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c23_7334/07_2025/6c23_7334.map" model { file = "/net/cci-nas-00/data/ceres_data/6c23_7334/07_2025/6c23_7334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c23_7334/07_2025/6c23_7334.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 8471 2.51 5 N 2389 2.21 5 O 2496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13440 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 860 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 118 Chain: "E" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 181 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 25} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "K" Number of atoms: 2406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2406 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 16, 'TRANS': 308} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 7, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 125 Chain: "L" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2877 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 349} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "M" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 962 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "N" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3058 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 22, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "O" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 51 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "P" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 484 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 58} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "Q" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 496 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 63} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "Z" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 674 Classifications: {'peptide': 135} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 134} Link IDs: {'TRANS': 134} Chain breaks: 6 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 407 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "C" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1307 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 7, 'TRANS': 185} Chain breaks: 1 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 157 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 84 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 11} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 8.33, per 1000 atoms: 0.62 Number of scatterers: 13440 At special positions: 0 Unit cell: (146.16, 109.2, 111.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2496 8.00 N 2389 7.00 C 8471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 450 " - pdb=" SG CYS A 453 " distance=2.07 Simple disulfide: pdb=" SG CYS K 289 " - pdb=" SG CYS K 294 " distance=2.01 Simple disulfide: pdb=" SG CYS K 523 " - pdb=" SG CYS K 530 " distance=2.05 Simple disulfide: pdb=" SG CYS K 523 " - pdb=" SG CYS K 547 " distance=2.03 Simple disulfide: pdb=" SG CYS K 523 " - pdb=" SG CYS K 549 " distance=2.02 Simple disulfide: pdb=" SG CYS K 530 " - pdb=" SG CYS K 549 " distance=2.03 Simple disulfide: pdb=" SG CYS K 530 " - pdb=" SG CYS K 553 " distance=2.05 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 429 " distance=2.07 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 1.8 seconds 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB UNK Z 25 " Number of C-beta restraints generated: 3500 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 24 sheets defined 23.6% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 459 through 470 Processing helix chain 'A' and resid 543 through 548 removed outlier: 3.565A pdb=" N ASP A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 150 Processing helix chain 'K' and resid 273 through 278 Processing helix chain 'K' and resid 278 through 284 Processing helix chain 'K' and resid 435 through 448 removed outlier: 3.513A pdb=" N ILE K 444 " --> pdb=" O PHE K 440 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY K 445 " --> pdb=" O ARG K 441 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR K 446 " --> pdb=" O VAL K 442 " (cutoff:3.500A) Processing helix chain 'K' and resid 452 through 458 Processing helix chain 'K' and resid 462 through 477 Processing helix chain 'K' and resid 534 through 539 Processing helix chain 'K' and resid 571 through 576 Processing helix chain 'K' and resid 604 through 609 removed outlier: 3.804A pdb=" N ARG K 608 " --> pdb=" O CYS K 604 " (cutoff:3.500A) Processing helix chain 'K' and resid 647 through 662 removed outlier: 3.681A pdb=" N ALA K 651 " --> pdb=" O SER K 647 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL K 657 " --> pdb=" O ARG K 653 " (cutoff:3.500A) Processing helix chain 'K' and resid 682 through 687 Processing helix chain 'L' and resid 127 through 131 Processing helix chain 'L' and resid 267 through 279 Processing helix chain 'L' and resid 281 through 285 removed outlier: 3.729A pdb=" N THR L 285 " --> pdb=" O PRO L 282 " (cutoff:3.500A) Processing helix chain 'M' and resid 576 through 580 Processing helix chain 'M' and resid 591 through 603 removed outlier: 3.540A pdb=" N GLU M 601 " --> pdb=" O ILE M 597 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU M 602 " --> pdb=" O THR M 598 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE M 603 " --> pdb=" O GLN M 599 " (cutoff:3.500A) Processing helix chain 'M' and resid 607 through 625 Processing helix chain 'M' and resid 628 through 651 removed outlier: 3.769A pdb=" N MET M 632 " --> pdb=" O ALA M 628 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN M 633 " --> pdb=" O ASP M 629 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N MET M 637 " --> pdb=" O ASN M 633 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN M 645 " --> pdb=" O GLU M 641 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LYS M 646 " --> pdb=" O ASN M 642 " (cutoff:3.500A) Processing helix chain 'M' and resid 652 through 664 Processing helix chain 'M' and resid 670 through 682 Processing helix chain 'N' and resid 5 through 28 removed outlier: 3.556A pdb=" N ALA N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 155 through 157 No H-bonds generated for 'chain 'N' and resid 155 through 157' Processing helix chain 'N' and resid 355 through 362 removed outlier: 3.540A pdb=" N ALA N 359 " --> pdb=" O SER N 355 " (cutoff:3.500A) Processing helix chain 'P' and resid 244 through 257 Proline residue: P 250 - end of helix Processing helix chain 'P' and resid 277 through 281 Processing helix chain 'Q' and resid 82 through 105 removed outlier: 3.946A pdb=" N PHE Q 86 " --> pdb=" O ASP Q 82 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS Q 92 " --> pdb=" O GLN Q 88 " (cutoff:3.500A) Proline residue: Q 93 - end of helix Processing helix chain 'C' and resid 18 through 61 removed outlier: 3.712A pdb=" N LEU C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 167 through 180 Processing helix chain 'C' and resid 221 through 231 removed outlier: 4.213A pdb=" N ALA C 226 " --> pdb=" O LYS C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 247 removed outlier: 3.530A pdb=" N LEU C 247 " --> pdb=" O LYS C 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 112 Processing sheet with id=AA1, first strand: chain 'A' and resid 432 through 433 removed outlier: 4.320A pdb=" N ILE A 491 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG A 486 " --> pdb=" O VAL A 479 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL A 479 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 529 through 530 removed outlier: 6.329A pdb=" N GLN N 403 " --> pdb=" O ASP N 33 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL N 35 " --> pdb=" O VAL N 401 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL N 401 " --> pdb=" O VAL N 35 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR N 37 " --> pdb=" O MET N 399 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET N 399 " --> pdb=" O THR N 37 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE N 398 " --> pdb=" O SER N 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 285 through 286 removed outlier: 3.560A pdb=" N LYS K 291 " --> pdb=" O CYS K 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 614 through 618 Processing sheet with id=AA5, first strand: chain 'K' and resid 637 through 640 removed outlier: 7.003A pdb=" N ILE K 710 " --> pdb=" O ILE K 638 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU K 640 " --> pdb=" O ILE K 708 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE K 708 " --> pdb=" O GLU K 640 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 666 through 668 Processing sheet with id=AA7, first strand: chain 'L' and resid 82 through 84 removed outlier: 3.540A pdb=" N VAL L 428 " --> pdb=" O GLN L 415 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLN L 415 " --> pdb=" O VAL L 428 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 88 through 90 Processing sheet with id=AA9, first strand: chain 'L' and resid 98 through 101 removed outlier: 3.686A pdb=" N GLY L 98 " --> pdb=" O VAL L 116 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU L 111 " --> pdb=" O CYS L 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 151 through 154 removed outlier: 3.936A pdb=" N GLY L 167 " --> pdb=" O ILE L 171 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE L 171 " --> pdb=" O GLY L 167 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 195 through 196 removed outlier: 3.565A pdb=" N GLU L 195 " --> pdb=" O VAL L 209 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL L 209 " --> pdb=" O GLU L 195 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU L 215 " --> pdb=" O ILE L 228 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE L 228 " --> pdb=" O LEU L 215 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU L 217 " --> pdb=" O VAL L 226 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N GLN L 292 " --> pdb=" O THR L 224 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL L 226 " --> pdb=" O GLN L 292 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE L 294 " --> pdb=" O VAL L 226 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE L 228 " --> pdb=" O ILE L 294 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 239 through 244 removed outlier: 6.747A pdb=" N CYS L 254 " --> pdb=" O LEU L 240 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA L 242 " --> pdb=" O MET L 252 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N MET L 252 " --> pdb=" O ALA L 242 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR L 244 " --> pdb=" O LYS L 250 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LYS L 250 " --> pdb=" O TYR L 244 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 312 through 315 removed outlier: 3.938A pdb=" N GLY L 354 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LYS L 332 " --> pdb=" O ILE L 352 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ILE L 352 " --> pdb=" O LYS L 332 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 376 through 377 Processing sheet with id=AB6, first strand: chain 'M' and resid 565 through 566 removed outlier: 4.805A pdb=" N TYR M 565 " --> pdb=" O LEU M 574 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 48 through 49 Processing sheet with id=AB8, first strand: chain 'N' and resid 61 through 62 Processing sheet with id=AB9, first strand: chain 'N' and resid 139 through 142 Processing sheet with id=AC1, first strand: chain 'N' and resid 184 through 185 Processing sheet with id=AC2, first strand: chain 'N' and resid 230 through 235 removed outlier: 3.556A pdb=" N PHE N 243 " --> pdb=" O TRP N 255 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 280 through 281 removed outlier: 3.846A pdb=" N HIS N 311 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP N 302 " --> pdb=" O LYS N 309 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LYS N 309 " --> pdb=" O ASP N 302 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 320 through 323 removed outlier: 7.034A pdb=" N SER N 336 " --> pdb=" O PHE N 321 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL N 323 " --> pdb=" O ALA N 334 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA N 334 " --> pdb=" O VAL N 323 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASP N 346 " --> pdb=" O LEU N 366 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU N 366 " --> pdb=" O ASP N 346 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Z' and resid 19 through 20 Processing sheet with id=AC6, first strand: chain 'C' and resid 82 through 83 391 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.09 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2273 1.29 - 1.43: 3651 1.43 - 1.56: 7691 1.56 - 1.70: 7 1.70 - 1.84: 114 Bond restraints: 13736 Sorted by residual: bond pdb=" CA GLY L 234 " pdb=" C GLY L 234 " ideal model delta sigma weight residual 1.514 1.149 0.366 1.41e-02 5.03e+03 6.72e+02 bond pdb=" N UNK Z 24 " pdb=" CA UNK Z 24 " ideal model delta sigma weight residual 1.458 1.168 0.290 1.90e-02 2.77e+03 2.32e+02 bond pdb=" CA UNK Z 25 " pdb=" C UNK Z 25 " ideal model delta sigma weight residual 1.525 1.206 0.319 2.10e-02 2.27e+03 2.31e+02 bond pdb=" CA CYS N 391 " pdb=" C CYS N 391 " ideal model delta sigma weight residual 1.522 1.453 0.069 1.19e-02 7.06e+03 3.39e+01 bond pdb=" CA ASN L 146 " pdb=" C ASN L 146 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.10e-02 8.26e+03 3.33e+01 ... (remaining 13731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.56: 18648 6.56 - 13.12: 40 13.12 - 19.67: 5 19.67 - 26.23: 4 26.23 - 32.79: 4 Bond angle restraints: 18701 Sorted by residual: angle pdb=" N UNK Z 25 " pdb=" CA UNK Z 25 " pdb=" CB UNK Z 25 " ideal model delta sigma weight residual 110.50 78.75 31.75 1.70e+00 3.46e-01 3.49e+02 angle pdb=" C UNK Z 25 " pdb=" CA UNK Z 25 " pdb=" CB UNK Z 25 " ideal model delta sigma weight residual 110.08 142.87 -32.79 1.90e+00 2.77e-01 2.98e+02 angle pdb=" CA GLY L 234 " pdb=" C GLY L 234 " pdb=" O GLY L 234 " ideal model delta sigma weight residual 120.57 98.19 22.38 1.74e+00 3.30e-01 1.65e+02 angle pdb=" C UNK Z 24 " pdb=" CA UNK Z 24 " pdb=" CB UNK Z 24 " ideal model delta sigma weight residual 110.08 88.67 21.41 1.90e+00 2.77e-01 1.27e+02 angle pdb=" N UNK Z 24 " pdb=" CA UNK Z 24 " pdb=" CB UNK Z 24 " ideal model delta sigma weight residual 110.50 129.03 -18.53 1.70e+00 3.46e-01 1.19e+02 ... (remaining 18696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 7529 16.61 - 33.22: 568 33.22 - 49.83: 82 49.83 - 66.43: 16 66.43 - 83.04: 8 Dihedral angle restraints: 8203 sinusoidal: 2855 harmonic: 5348 Sorted by residual: dihedral pdb=" N UNK Z 24 " pdb=" C UNK Z 24 " pdb=" CA UNK Z 24 " pdb=" CB UNK Z 24 " ideal model delta harmonic sigma weight residual 122.80 171.90 -49.10 0 2.50e+00 1.60e-01 3.86e+02 dihedral pdb=" C UNK Z 24 " pdb=" N UNK Z 24 " pdb=" CA UNK Z 24 " pdb=" CB UNK Z 24 " ideal model delta harmonic sigma weight residual -122.60 -169.56 46.96 0 2.50e+00 1.60e-01 3.53e+02 dihedral pdb=" CA HIS C 129 " pdb=" C HIS C 129 " pdb=" N ASN C 130 " pdb=" CA ASN C 130 " ideal model delta harmonic sigma weight residual -180.00 -125.52 -54.48 0 5.00e+00 4.00e-02 1.19e+02 ... (remaining 8200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.508: 2110 0.508 - 1.016: 2 1.016 - 1.524: 0 1.524 - 2.032: 0 2.032 - 2.540: 2 Chirality restraints: 2114 Sorted by residual: chirality pdb=" CA UNK Z 25 " pdb=" N UNK Z 25 " pdb=" C UNK Z 25 " pdb=" CB UNK Z 25 " both_signs ideal model delta sigma weight residual False 2.52 -0.02 2.54 2.00e-01 2.50e+01 1.61e+02 chirality pdb=" CA UNK Z 24 " pdb=" N UNK Z 24 " pdb=" C UNK Z 24 " pdb=" CB UNK Z 24 " both_signs ideal model delta sigma weight residual False 2.52 0.24 2.28 2.00e-01 2.50e+01 1.30e+02 chirality pdb=" CA TYR L 148 " pdb=" N TYR L 148 " pdb=" C TYR L 148 " pdb=" CB TYR L 148 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.47e+00 ... (remaining 2111 not shown) Planarity restraints: 2439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 148 " 0.055 2.00e-02 2.50e+03 2.89e-02 1.66e+01 pdb=" CG TYR L 148 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR L 148 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR L 148 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR L 148 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR L 148 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR L 148 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR L 148 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 151 " 0.053 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO E 152 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO E 152 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 152 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 380 " -0.034 2.00e-02 2.50e+03 2.15e-02 8.07e+00 pdb=" CG PHE N 380 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE N 380 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE N 380 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE N 380 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE N 380 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE N 380 " -0.011 2.00e-02 2.50e+03 ... (remaining 2436 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.80: 7 1.80 - 2.57: 182 2.57 - 3.35: 17247 3.35 - 4.12: 31407 4.12 - 4.90: 56673 Nonbonded interactions: 105516 Sorted by model distance: nonbonded pdb=" O VAL N 151 " pdb=" OD1 ASP N 170 " model vdw 1.020 3.040 nonbonded pdb=" O LEU K 443 " pdb=" CD1 TYR K 447 " model vdw 1.548 3.340 nonbonded pdb=" CD1 TRP L 389 " pdb=" O LYS L 400 " model vdw 1.593 3.260 nonbonded pdb=" C SER K 729 " pdb=" OE1 GLN K 730 " model vdw 1.693 3.270 nonbonded pdb=" CD1 PHE N 152 " pdb=" OD2 ASP N 170 " model vdw 1.713 3.340 ... (remaining 105511 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.280 Find NCS groups from input model: 0.190 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: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 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 : 0.013 0.366 13746 Z= 0.869 Angle : 1.589 32.789 18717 Z= 0.965 Chirality : 0.114 2.540 2114 Planarity : 0.006 0.081 2439 Dihedral : 12.198 78.205 4679 Min Nonbonded Distance : 1.020 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 1.57 % Allowed : 14.68 % Favored : 83.75 % Rotamer: Outliers : 1.02 % Allowed : 5.18 % Favored : 93.80 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (0.17), residues: 1655 helix: -1.81 (0.24), residues: 336 sheet: -3.79 (0.23), residues: 317 loop : -3.60 (0.16), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.006 TRP K 624 HIS 0.014 0.003 HIS A 471 PHE 0.040 0.005 PHE N 380 TYR 0.055 0.006 TYR L 148 ARG 0.011 0.001 ARG Q 113 Details of bonding type rmsd hydrogen bonds : bond 0.17496 ( 391) hydrogen bonds : angle 7.99319 ( 1065) SS BOND : bond 0.02396 ( 8) SS BOND : angle 3.71209 ( 16) covalent geometry : bond 0.01260 (13736) covalent geometry : angle 1.58595 (18701) Misc. bond : bond 0.18300 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 464 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ILE cc_start: 0.8784 (mt) cc_final: 0.8420 (mt) REVERT: A 429 PHE cc_start: 0.8016 (m-10) cc_final: 0.7708 (t80) REVERT: A 459 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8565 (mmtp) REVERT: A 468 LYS cc_start: 0.8922 (mttt) cc_final: 0.8680 (tttp) REVERT: A 499 TYR cc_start: 0.8617 (t80) cc_final: 0.8150 (t80) REVERT: E 155 GLU cc_start: 0.8116 (tt0) cc_final: 0.7551 (tm-30) REVERT: K 536 CYS cc_start: 0.7517 (m) cc_final: 0.7181 (p) REVERT: K 581 ASP cc_start: 0.7351 (t0) cc_final: 0.5909 (m-30) REVERT: K 602 LYS cc_start: 0.8802 (mmtt) cc_final: 0.8229 (mmpt) REVERT: K 605 SER cc_start: 0.9050 (m) cc_final: 0.8751 (t) REVERT: K 607 GLN cc_start: 0.9035 (mt0) cc_final: 0.8833 (mt0) REVERT: K 644 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8039 (mt-10) REVERT: K 662 MET cc_start: 0.7687 (tpp) cc_final: 0.7086 (tpp) REVERT: K 694 ASN cc_start: 0.8709 (p0) cc_final: 0.7868 (p0) REVERT: L 89 LYS cc_start: 0.8295 (tttm) cc_final: 0.8053 (tmtt) REVERT: L 145 GLU cc_start: 0.8464 (pt0) cc_final: 0.8242 (pt0) REVERT: L 181 GLN cc_start: 0.8534 (tt0) cc_final: 0.8242 (mm-40) REVERT: L 191 ASN cc_start: 0.9143 (m110) cc_final: 0.8935 (m110) REVERT: L 238 GLU cc_start: 0.9060 (pt0) cc_final: 0.8688 (pt0) REVERT: L 250 LYS cc_start: 0.9008 (ttpt) cc_final: 0.8729 (tttp) REVERT: L 262 LEU cc_start: 0.9270 (mt) cc_final: 0.8835 (mt) REVERT: L 292 GLN cc_start: 0.9152 (tp-100) cc_final: 0.8559 (tp-100) REVERT: L 307 ASN cc_start: 0.8514 (t0) cc_final: 0.8196 (t0) REVERT: L 342 LYS cc_start: 0.9065 (mptm) cc_final: 0.8746 (tptt) REVERT: L 382 GLN cc_start: 0.8072 (pt0) cc_final: 0.7705 (pt0) REVERT: L 436 ARG cc_start: 0.8734 (tmt90) cc_final: 0.8417 (ttt-90) REVERT: M 569 ASP cc_start: 0.8928 (p0) cc_final: 0.8598 (p0) REVERT: M 620 HIS cc_start: 0.8714 (t-90) cc_final: 0.8450 (t-90) REVERT: M 642 ASN cc_start: 0.8450 (m-40) cc_final: 0.8250 (m-40) REVERT: M 653 CYS cc_start: 0.8344 (m) cc_final: 0.7379 (t) REVERT: M 676 LYS cc_start: 0.8879 (tttt) cc_final: 0.8482 (tptp) REVERT: N 37 THR cc_start: 0.9347 (m) cc_final: 0.9134 (p) REVERT: N 41 GLU cc_start: 0.8864 (pt0) cc_final: 0.8493 (tp30) REVERT: N 48 GLN cc_start: 0.8304 (tp40) cc_final: 0.8065 (tt0) REVERT: N 55 ARG cc_start: 0.8630 (pmm-80) cc_final: 0.7681 (ptp90) REVERT: N 64 HIS cc_start: 0.8514 (m-70) cc_final: 0.8161 (m90) REVERT: N 65 ARG cc_start: 0.8300 (mtt-85) cc_final: 0.7830 (mpt180) REVERT: N 66 LEU cc_start: 0.9335 (mm) cc_final: 0.9084 (mt) REVERT: N 122 ASN cc_start: 0.8616 (m110) cc_final: 0.8326 (p0) REVERT: N 172 ARG cc_start: 0.8829 (ttt180) cc_final: 0.8607 (mmm-85) REVERT: N 310 LEU cc_start: 0.9292 (mp) cc_final: 0.8965 (tt) REVERT: N 342 LEU cc_start: 0.9600 (tt) cc_final: 0.9336 (tt) REVERT: N 379 ASP cc_start: 0.8829 (t0) cc_final: 0.8404 (t0) REVERT: N 385 ASN cc_start: 0.8526 (m-40) cc_final: 0.8023 (t0) REVERT: N 396 ASP cc_start: 0.9062 (p0) cc_final: 0.8783 (p0) REVERT: O 28 PHE cc_start: 0.5537 (m-10) cc_final: 0.4950 (t80) REVERT: Q 117 TYR cc_start: 0.8738 (p90) cc_final: 0.8461 (p90) REVERT: C 36 ASP cc_start: 0.8647 (m-30) cc_final: 0.8433 (p0) REVERT: C 55 ILE cc_start: 0.9502 (mt) cc_final: 0.9035 (mt) REVERT: C 61 LYS cc_start: 0.9112 (mttt) cc_final: 0.8837 (mtmm) REVERT: C 64 ARG cc_start: 0.8327 (mtt90) cc_final: 0.7871 (mmm160) REVERT: C 65 ILE cc_start: 0.8287 (mm) cc_final: 0.7875 (tt) REVERT: C 230 MET cc_start: 0.7700 (mmp) cc_final: 0.7220 (mmm) outliers start: 13 outliers final: 4 residues processed: 474 average time/residue: 0.3157 time to fit residues: 203.8424 Evaluate side-chains 319 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 315 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 668 ASN Chi-restraints excluded: chain N residue 149 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 30.0000 chunk 134 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 555 ASN K 668 ASN L 94 GLN L 136 GLN L 213 HIS L 221 GLN ** M 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 655 ASN N 18 ASN ** N 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 ASN ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 HIS N 343 ASN P 268 HIS Q 83 HIS C 45 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.139405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.115003 restraints weight = 26110.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.114700 restraints weight = 21552.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.115650 restraints weight = 23177.994| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13746 Z= 0.173 Angle : 0.792 11.857 18717 Z= 0.411 Chirality : 0.048 0.192 2114 Planarity : 0.005 0.064 2439 Dihedral : 7.078 47.802 1927 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.16 % Favored : 91.54 % Rotamer: Outliers : 3.53 % Allowed : 13.80 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.18), residues: 1655 helix: -0.31 (0.27), residues: 358 sheet: -3.15 (0.24), residues: 301 loop : -3.06 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 345 HIS 0.007 0.001 HIS N 157 PHE 0.016 0.002 PHE M 639 TYR 0.025 0.002 TYR L 148 ARG 0.006 0.001 ARG K 679 Details of bonding type rmsd hydrogen bonds : bond 0.05461 ( 391) hydrogen bonds : angle 5.94380 ( 1065) SS BOND : bond 0.00933 ( 8) SS BOND : angle 3.25589 ( 16) covalent geometry : bond 0.00360 (13736) covalent geometry : angle 0.78708 (18701) Misc. bond : bond 0.00177 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 369 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8148 (tp) REVERT: K 276 GLN cc_start: 0.8251 (tp40) cc_final: 0.7790 (tp40) REVERT: K 581 ASP cc_start: 0.7343 (t0) cc_final: 0.5905 (m-30) REVERT: K 721 GLU cc_start: 0.7973 (tt0) cc_final: 0.7758 (tt0) REVERT: L 168 SER cc_start: 0.8829 (p) cc_final: 0.8585 (t) REVERT: L 256 MET cc_start: 0.9167 (ttm) cc_final: 0.8660 (ttm) REVERT: L 313 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8223 (mmt-90) REVERT: M 565 TYR cc_start: 0.7301 (m-80) cc_final: 0.7057 (m-80) REVERT: M 599 GLN cc_start: 0.8321 (tp40) cc_final: 0.8093 (tp40) REVERT: M 634 HIS cc_start: 0.8094 (t-90) cc_final: 0.7658 (t-170) REVERT: M 653 CYS cc_start: 0.7768 (m) cc_final: 0.7014 (t) REVERT: N 242 LEU cc_start: 0.7613 (mp) cc_final: 0.7180 (mt) REVERT: N 310 LEU cc_start: 0.8803 (mp) cc_final: 0.8602 (tt) REVERT: N 354 GLN cc_start: 0.7409 (pt0) cc_final: 0.7031 (pt0) REVERT: N 388 TRP cc_start: 0.8512 (m-10) cc_final: 0.8259 (m-10) REVERT: O 28 PHE cc_start: 0.5484 (m-10) cc_final: 0.5186 (t80) REVERT: Q 118 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7843 (mpp) REVERT: C 54 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7264 (tm-30) REVERT: C 55 ILE cc_start: 0.8959 (mt) cc_final: 0.8686 (mt) REVERT: C 65 ILE cc_start: 0.8443 (mm) cc_final: 0.7995 (tt) REVERT: C 117 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7692 (mm-40) outliers start: 45 outliers final: 24 residues processed: 393 average time/residue: 0.2556 time to fit residues: 144.8929 Evaluate side-chains 314 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 287 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain K residue 525 HIS Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 642 CYS Chi-restraints excluded: chain K residue 672 ASP Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 313 ARG Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain M residue 600 ILE Chi-restraints excluded: chain M residue 610 GLU Chi-restraints excluded: chain M residue 627 ILE Chi-restraints excluded: chain M residue 637 MET Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain Q residue 118 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 149 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 6 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 109 optimal weight: 0.4980 chunk 74 optimal weight: 0.2980 chunk 170 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 52 optimal weight: 0.0980 chunk 39 optimal weight: 9.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS K 607 GLN ** L 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 659 HIS N 38 HIS ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 385 ASN ** 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 = 0.3930 r_free = 0.3930 target = 0.136906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.112801 restraints weight = 26735.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.112444 restraints weight = 23826.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.113826 restraints weight = 24017.541| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13746 Z= 0.164 Angle : 0.738 9.604 18717 Z= 0.382 Chirality : 0.046 0.158 2114 Planarity : 0.004 0.052 2439 Dihedral : 6.442 48.953 1925 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.55 % Favored : 90.09 % Rotamer: Outliers : 4.16 % Allowed : 16.63 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.19), residues: 1655 helix: 0.17 (0.28), residues: 354 sheet: -2.74 (0.26), residues: 283 loop : -2.79 (0.17), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 345 HIS 0.005 0.001 HIS A 466 PHE 0.028 0.002 PHE M 656 TYR 0.029 0.001 TYR L 148 ARG 0.011 0.001 ARG C 63 Details of bonding type rmsd hydrogen bonds : bond 0.05071 ( 391) hydrogen bonds : angle 5.62005 ( 1065) SS BOND : bond 0.00892 ( 8) SS BOND : angle 3.09623 ( 16) covalent geometry : bond 0.00363 (13736) covalent geometry : angle 0.73301 (18701) Misc. bond : bond 0.00176 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 321 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 276 GLN cc_start: 0.8124 (tp40) cc_final: 0.7710 (tp40) REVERT: K 293 ASP cc_start: 0.7847 (t70) cc_final: 0.7504 (t70) REVERT: K 581 ASP cc_start: 0.7431 (t0) cc_final: 0.5716 (m-30) REVERT: K 608 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7801 (mtt-85) REVERT: K 701 MET cc_start: 0.8626 (tpp) cc_final: 0.8350 (tpp) REVERT: K 721 GLU cc_start: 0.8117 (tt0) cc_final: 0.7829 (tt0) REVERT: L 221 GLN cc_start: 0.8161 (pp30) cc_final: 0.7916 (pp30) REVERT: L 252 MET cc_start: 0.8485 (tpp) cc_final: 0.8276 (tpp) REVERT: L 256 MET cc_start: 0.9202 (ttm) cc_final: 0.8476 (ttm) REVERT: M 599 GLN cc_start: 0.8479 (tp40) cc_final: 0.8213 (tp40) REVERT: M 607 ASN cc_start: 0.8738 (p0) cc_final: 0.8291 (p0) REVERT: M 634 HIS cc_start: 0.8114 (t-90) cc_final: 0.7521 (t70) REVERT: M 653 CYS cc_start: 0.7785 (m) cc_final: 0.7025 (t) REVERT: N 66 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8725 (mt) REVERT: N 354 GLN cc_start: 0.7386 (pt0) cc_final: 0.6951 (pt0) REVERT: C 54 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7411 (tm-30) REVERT: C 99 LYS cc_start: 0.8591 (tppp) cc_final: 0.8308 (tptp) REVERT: C 151 LYS cc_start: 0.8658 (ttpp) cc_final: 0.8367 (ptmm) outliers start: 53 outliers final: 31 residues processed: 348 average time/residue: 0.3440 time to fit residues: 174.8736 Evaluate side-chains 314 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 281 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 525 HIS Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 586 LEU Chi-restraints excluded: chain K residue 608 ARG Chi-restraints excluded: chain K residue 642 CYS Chi-restraints excluded: chain K residue 672 ASP Chi-restraints excluded: chain K residue 691 VAL Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 371 ASP Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 600 ILE Chi-restraints excluded: chain M residue 640 VAL Chi-restraints excluded: chain M residue 655 ASN Chi-restraints excluded: chain M residue 659 HIS Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 301 TRP Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 149 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 53 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 149 optimal weight: 40.0000 chunk 140 optimal weight: 1.9990 chunk 173 optimal weight: 20.0000 chunk 93 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 706 HIS L 307 ASN M 633 ASN N 122 ASN N 188 ASN ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.136010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.111679 restraints weight = 26842.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.111993 restraints weight = 24857.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.113017 restraints weight = 24508.824| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13746 Z= 0.184 Angle : 0.739 10.353 18717 Z= 0.381 Chirality : 0.046 0.170 2114 Planarity : 0.004 0.065 2439 Dihedral : 6.266 48.865 1925 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.31 % Favored : 90.39 % Rotamer: Outliers : 4.78 % Allowed : 18.35 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.19), residues: 1655 helix: 0.21 (0.27), residues: 353 sheet: -2.54 (0.26), residues: 286 loop : -2.70 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 594 HIS 0.025 0.001 HIS K 593 PHE 0.028 0.002 PHE N 243 TYR 0.029 0.002 TYR L 148 ARG 0.004 0.001 ARG C 46 Details of bonding type rmsd hydrogen bonds : bond 0.05030 ( 391) hydrogen bonds : angle 5.56036 ( 1065) SS BOND : bond 0.00899 ( 8) SS BOND : angle 3.05410 ( 16) covalent geometry : bond 0.00409 (13736) covalent geometry : angle 0.73344 (18701) Misc. bond : bond 0.00946 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 301 time to evaluate : 1.511 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: E 155 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7596 (tm-30) REVERT: K 276 GLN cc_start: 0.8128 (tp40) cc_final: 0.7774 (tp40) REVERT: K 581 ASP cc_start: 0.7305 (t0) cc_final: 0.5754 (m-30) REVERT: K 608 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7986 (mtt-85) REVERT: K 721 GLU cc_start: 0.8266 (tt0) cc_final: 0.7997 (tt0) REVERT: L 221 GLN cc_start: 0.8404 (pp30) cc_final: 0.8068 (pp30) REVERT: L 241 SER cc_start: 0.9198 (t) cc_final: 0.8939 (t) REVERT: L 252 MET cc_start: 0.8617 (tpp) cc_final: 0.8387 (tpp) REVERT: M 568 SER cc_start: 0.8558 (p) cc_final: 0.8253 (p) REVERT: M 599 GLN cc_start: 0.8601 (tp40) cc_final: 0.8316 (tp40) REVERT: M 634 HIS cc_start: 0.8024 (t-90) cc_final: 0.7517 (t70) REVERT: M 653 CYS cc_start: 0.7533 (m) cc_final: 0.6814 (t) REVERT: N 45 LEU cc_start: 0.9257 (mp) cc_final: 0.8960 (mt) REVERT: N 66 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8837 (mt) REVERT: N 354 GLN cc_start: 0.7385 (pt0) cc_final: 0.6975 (pt0) REVERT: N 366 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8591 (tt) REVERT: C 54 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7422 (tm-30) REVERT: C 55 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8508 (tt) REVERT: C 151 LYS cc_start: 0.8639 (ttpp) cc_final: 0.8320 (ptmm) outliers start: 61 outliers final: 46 residues processed: 333 average time/residue: 0.2855 time to fit residues: 143.6173 Evaluate side-chains 324 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 274 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 525 HIS Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 586 LEU Chi-restraints excluded: chain K residue 599 VAL Chi-restraints excluded: chain K residue 608 ARG Chi-restraints excluded: chain K residue 642 CYS Chi-restraints excluded: chain K residue 672 ASP Chi-restraints excluded: chain K residue 691 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 370 MET Chi-restraints excluded: chain L residue 371 ASP Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 600 ILE Chi-restraints excluded: chain M residue 627 ILE Chi-restraints excluded: chain M residue 659 HIS Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 122 ASN Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 149 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 124 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 9 optimal weight: 0.1980 chunk 58 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 1 optimal weight: 0.0060 chunk 150 optimal weight: 30.0000 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 HIS M 633 ASN M 659 HIS N 122 ASN ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.140054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.116009 restraints weight = 26335.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.116128 restraints weight = 22909.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.117457 restraints weight = 22601.295| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13746 Z= 0.126 Angle : 0.686 9.639 18717 Z= 0.352 Chirality : 0.044 0.158 2114 Planarity : 0.004 0.060 2439 Dihedral : 5.823 46.069 1925 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.16 % Favored : 91.54 % Rotamer: Outliers : 3.22 % Allowed : 20.94 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.19), residues: 1655 helix: 0.27 (0.27), residues: 360 sheet: -2.18 (0.28), residues: 284 loop : -2.52 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 364 HIS 0.009 0.001 HIS K 593 PHE 0.027 0.001 PHE N 243 TYR 0.016 0.001 TYR L 148 ARG 0.004 0.000 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 391) hydrogen bonds : angle 5.29331 ( 1065) SS BOND : bond 0.00875 ( 8) SS BOND : angle 2.99163 ( 16) covalent geometry : bond 0.00276 (13736) covalent geometry : angle 0.68115 (18701) Misc. bond : bond 0.00576 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 327 time to evaluate : 2.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 581 ASP cc_start: 0.6956 (t0) cc_final: 0.5405 (m-30) REVERT: K 608 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7938 (mtt-85) REVERT: K 721 GLU cc_start: 0.8086 (tt0) cc_final: 0.7804 (tt0) REVERT: L 153 THR cc_start: 0.9250 (t) cc_final: 0.8984 (m) REVERT: L 221 GLN cc_start: 0.8272 (pp30) cc_final: 0.7937 (pp30) REVERT: L 241 SER cc_start: 0.9175 (t) cc_final: 0.8837 (t) REVERT: M 634 HIS cc_start: 0.7877 (t-90) cc_final: 0.7485 (t70) REVERT: M 653 CYS cc_start: 0.7418 (m) cc_final: 0.6559 (t) REVERT: N 66 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8739 (mt) REVERT: N 354 GLN cc_start: 0.7245 (pt0) cc_final: 0.6899 (pt0) REVERT: N 366 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8591 (tt) REVERT: C 54 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7124 (tm-30) REVERT: C 55 ILE cc_start: 0.8593 (tt) cc_final: 0.8140 (tt) REVERT: C 65 ILE cc_start: 0.8555 (mm) cc_final: 0.8328 (mm) outliers start: 41 outliers final: 27 residues processed: 346 average time/residue: 0.3544 time to fit residues: 183.3000 Evaluate side-chains 311 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 281 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 599 VAL Chi-restraints excluded: chain K residue 608 ARG Chi-restraints excluded: chain K residue 642 CYS Chi-restraints excluded: chain K residue 672 ASP Chi-restraints excluded: chain K residue 691 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 370 MET Chi-restraints excluded: chain L residue 371 ASP Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 659 HIS Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 149 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 64 optimal weight: 6.9990 chunk 164 optimal weight: 20.0000 chunk 153 optimal weight: 30.0000 chunk 34 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 144 optimal weight: 50.0000 chunk 117 optimal weight: 0.0770 chunk 41 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 191 ASN M 633 ASN M 659 HIS N 71 HIS N 261 ASN ** N 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 290 GLN Q 83 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.133764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.109662 restraints weight = 27107.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.109578 restraints weight = 24100.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.110707 restraints weight = 24578.795| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13746 Z= 0.243 Angle : 0.768 10.258 18717 Z= 0.398 Chirality : 0.046 0.194 2114 Planarity : 0.005 0.062 2439 Dihedral : 6.197 52.619 1925 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.18 % Favored : 90.57 % Rotamer: Outliers : 5.41 % Allowed : 21.49 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.19), residues: 1655 helix: 0.35 (0.27), residues: 354 sheet: -2.28 (0.28), residues: 282 loop : -2.59 (0.18), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 235 HIS 0.010 0.001 HIS M 659 PHE 0.019 0.002 PHE C 120 TYR 0.028 0.002 TYR L 148 ARG 0.005 0.001 ARG C 46 Details of bonding type rmsd hydrogen bonds : bond 0.05109 ( 391) hydrogen bonds : angle 5.52594 ( 1065) SS BOND : bond 0.00809 ( 8) SS BOND : angle 3.07368 ( 16) covalent geometry : bond 0.00541 (13736) covalent geometry : angle 0.76337 (18701) Misc. bond : bond 0.00409 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 292 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 581 ASP cc_start: 0.7408 (t0) cc_final: 0.5847 (m-30) REVERT: K 608 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7979 (mtt-85) REVERT: L 148 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7389 (p90) REVERT: L 153 THR cc_start: 0.9248 (t) cc_final: 0.8895 (m) REVERT: L 221 GLN cc_start: 0.8553 (pp30) cc_final: 0.8116 (pp30) REVERT: L 238 GLU cc_start: 0.8172 (pt0) cc_final: 0.7877 (pt0) REVERT: L 370 MET cc_start: 0.8919 (mtp) cc_final: 0.8500 (ptp) REVERT: L 374 GLN cc_start: 0.8466 (mt0) cc_final: 0.7765 (mm110) REVERT: M 634 HIS cc_start: 0.8045 (t-90) cc_final: 0.7595 (t70) REVERT: M 653 CYS cc_start: 0.7676 (m) cc_final: 0.6856 (t) REVERT: N 10 ASP cc_start: 0.8663 (m-30) cc_final: 0.8450 (m-30) REVERT: N 66 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8853 (mt) REVERT: N 354 GLN cc_start: 0.7324 (pt0) cc_final: 0.6926 (pt0) REVERT: N 366 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8688 (tt) outliers start: 69 outliers final: 54 residues processed: 325 average time/residue: 0.4238 time to fit residues: 215.2616 Evaluate side-chains 331 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 273 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 525 HIS Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 599 VAL Chi-restraints excluded: chain K residue 608 ARG Chi-restraints excluded: chain K residue 642 CYS Chi-restraints excluded: chain K residue 657 VAL Chi-restraints excluded: chain K residue 691 VAL Chi-restraints excluded: chain K residue 700 MET Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 371 ASP Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 407 HIS Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 627 ILE Chi-restraints excluded: chain M residue 655 ASN Chi-restraints excluded: chain M residue 659 HIS Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain N residue 318 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 389 VAL Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 257 SER Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain P residue 288 MET Chi-restraints excluded: chain P residue 290 GLN Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 149 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 66 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 176 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 170 optimal weight: 20.0000 chunk 166 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 191 ASN L 397 HIS M 633 ASN M 659 HIS M 667 ASN ** N 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.136841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.112189 restraints weight = 26609.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.111722 restraints weight = 22680.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.112570 restraints weight = 23292.299| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13746 Z= 0.151 Angle : 0.722 9.818 18717 Z= 0.369 Chirality : 0.044 0.170 2114 Planarity : 0.004 0.061 2439 Dihedral : 5.904 48.725 1925 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.70 % Favored : 91.06 % Rotamer: Outliers : 4.63 % Allowed : 22.51 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.19), residues: 1655 helix: 0.45 (0.27), residues: 355 sheet: -2.07 (0.29), residues: 282 loop : -2.46 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 185 HIS 0.007 0.001 HIS K 593 PHE 0.017 0.001 PHE A 429 TYR 0.019 0.001 TYR L 148 ARG 0.004 0.001 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 391) hydrogen bonds : angle 5.24980 ( 1065) SS BOND : bond 0.00848 ( 8) SS BOND : angle 3.01704 ( 16) covalent geometry : bond 0.00341 (13736) covalent geometry : angle 0.71715 (18701) Misc. bond : bond 0.00359 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 313 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 581 ASP cc_start: 0.7162 (t0) cc_final: 0.5610 (m-30) REVERT: K 608 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7948 (mtt-85) REVERT: K 721 GLU cc_start: 0.8372 (tt0) cc_final: 0.8171 (tt0) REVERT: L 88 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7145 (tt) REVERT: L 148 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7220 (p90) REVERT: L 153 THR cc_start: 0.9266 (t) cc_final: 0.8939 (m) REVERT: L 221 GLN cc_start: 0.8469 (pp30) cc_final: 0.8026 (pp30) REVERT: L 238 GLU cc_start: 0.7984 (pt0) cc_final: 0.7559 (pt0) REVERT: L 256 MET cc_start: 0.9208 (tpp) cc_final: 0.8785 (tpp) REVERT: M 568 SER cc_start: 0.8585 (p) cc_final: 0.7982 (m) REVERT: M 634 HIS cc_start: 0.8073 (t-90) cc_final: 0.7609 (t70) REVERT: M 653 CYS cc_start: 0.7651 (m) cc_final: 0.6846 (t) REVERT: N 66 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8843 (mt) REVERT: N 354 GLN cc_start: 0.7263 (pt0) cc_final: 0.6887 (pt0) REVERT: N 366 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8668 (tt) REVERT: Q 105 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8502 (tt) outliers start: 59 outliers final: 41 residues processed: 338 average time/residue: 0.3661 time to fit residues: 187.0371 Evaluate side-chains 335 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 288 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 586 LEU Chi-restraints excluded: chain K residue 599 VAL Chi-restraints excluded: chain K residue 608 ARG Chi-restraints excluded: chain K residue 642 CYS Chi-restraints excluded: chain K residue 657 VAL Chi-restraints excluded: chain K residue 691 VAL Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 371 ASP Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 407 HIS Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 592 LEU Chi-restraints excluded: chain M residue 627 ILE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 318 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 149 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 3 optimal weight: 10.0000 chunk 60 optimal weight: 0.0980 chunk 29 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 173 optimal weight: 8.9990 chunk 168 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 282 HIS K 555 ASN K 689 HIS ** L 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN M 633 ASN M 659 HIS ** N 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.131699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.108030 restraints weight = 27155.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.107515 restraints weight = 23804.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.108407 restraints weight = 24095.999| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13746 Z= 0.272 Angle : 0.819 11.059 18717 Z= 0.422 Chirality : 0.048 0.176 2114 Planarity : 0.005 0.069 2439 Dihedral : 6.437 57.447 1925 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.51 % Favored : 89.24 % Rotamer: Outliers : 5.65 % Allowed : 22.90 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.19), residues: 1655 helix: 0.28 (0.27), residues: 360 sheet: -2.20 (0.28), residues: 300 loop : -2.61 (0.18), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 437 HIS 0.007 0.001 HIS K 593 PHE 0.038 0.002 PHE M 626 TYR 0.030 0.002 TYR L 148 ARG 0.006 0.001 ARG K 707 Details of bonding type rmsd hydrogen bonds : bond 0.05316 ( 391) hydrogen bonds : angle 5.58249 ( 1065) SS BOND : bond 0.00855 ( 8) SS BOND : angle 3.13011 ( 16) covalent geometry : bond 0.00605 (13736) covalent geometry : angle 0.81465 (18701) Misc. bond : bond 0.00347 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 280 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 276 GLN cc_start: 0.8047 (tp40) cc_final: 0.7727 (tp40) REVERT: K 581 ASP cc_start: 0.7566 (t0) cc_final: 0.6023 (m-30) REVERT: K 608 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8003 (mtt-85) REVERT: K 701 MET cc_start: 0.8517 (tpp) cc_final: 0.8193 (tpp) REVERT: L 88 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7367 (tt) REVERT: L 148 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.7558 (p90) REVERT: L 153 THR cc_start: 0.9281 (t) cc_final: 0.8914 (m) REVERT: L 221 GLN cc_start: 0.8632 (pp30) cc_final: 0.8198 (pp30) REVERT: L 236 ARG cc_start: 0.7212 (mtp85) cc_final: 0.7005 (mtm110) REVERT: M 634 HIS cc_start: 0.8084 (t-90) cc_final: 0.7657 (t70) REVERT: M 653 CYS cc_start: 0.7943 (m) cc_final: 0.7029 (t) REVERT: N 66 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8885 (mt) REVERT: N 177 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7515 (tm-30) REVERT: N 354 GLN cc_start: 0.7379 (pt0) cc_final: 0.6937 (pt0) REVERT: N 366 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8814 (tt) REVERT: C 65 ILE cc_start: 0.8574 (mp) cc_final: 0.8083 (tt) outliers start: 72 outliers final: 58 residues processed: 319 average time/residue: 0.2676 time to fit residues: 129.2478 Evaluate side-chains 331 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 268 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 525 HIS Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 586 LEU Chi-restraints excluded: chain K residue 599 VAL Chi-restraints excluded: chain K residue 608 ARG Chi-restraints excluded: chain K residue 642 CYS Chi-restraints excluded: chain K residue 657 VAL Chi-restraints excluded: chain K residue 691 VAL Chi-restraints excluded: chain K residue 700 MET Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 371 ASP Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 407 HIS Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 592 LEU Chi-restraints excluded: chain M residue 600 ILE Chi-restraints excluded: chain M residue 614 MET Chi-restraints excluded: chain M residue 627 ILE Chi-restraints excluded: chain M residue 655 ASN Chi-restraints excluded: chain M residue 659 HIS Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 318 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 389 VAL Chi-restraints excluded: chain N residue 394 SER Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 151 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 112 optimal weight: 0.1980 chunk 163 optimal weight: 50.0000 chunk 9 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 36 optimal weight: 0.2980 chunk 10 optimal weight: 0.0000 chunk 173 optimal weight: 30.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 555 ASN L 191 ASN L 292 GLN ** L 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN ** N 385 ASN ** 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 = 0.3927 r_free = 0.3927 target = 0.136251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.111733 restraints weight = 26362.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.111193 restraints weight = 22485.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.112112 restraints weight = 22691.591| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13746 Z= 0.151 Angle : 0.759 10.995 18717 Z= 0.386 Chirality : 0.045 0.193 2114 Planarity : 0.004 0.068 2439 Dihedral : 5.952 50.363 1925 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.64 % Favored : 91.12 % Rotamer: Outliers : 3.69 % Allowed : 25.10 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.19), residues: 1655 helix: 0.47 (0.27), residues: 354 sheet: -1.96 (0.29), residues: 293 loop : -2.45 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 185 HIS 0.006 0.001 HIS K 593 PHE 0.035 0.002 PHE N 243 TYR 0.017 0.001 TYR L 148 ARG 0.004 0.001 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.04637 ( 391) hydrogen bonds : angle 5.25377 ( 1065) SS BOND : bond 0.00843 ( 8) SS BOND : angle 3.01581 ( 16) covalent geometry : bond 0.00344 (13736) covalent geometry : angle 0.75393 (18701) Misc. bond : bond 0.00332 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 299 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 276 GLN cc_start: 0.8080 (tp40) cc_final: 0.7679 (tp40) REVERT: K 581 ASP cc_start: 0.7323 (t0) cc_final: 0.5675 (m-30) REVERT: K 608 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8000 (mtt-85) REVERT: L 88 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7144 (tt) REVERT: L 148 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7314 (p90) REVERT: L 153 THR cc_start: 0.9295 (t) cc_final: 0.8919 (m) REVERT: L 221 GLN cc_start: 0.8545 (pp30) cc_final: 0.8081 (pp30) REVERT: L 376 MET cc_start: 0.6972 (mtt) cc_final: 0.6563 (mtp) REVERT: M 634 HIS cc_start: 0.8006 (t-90) cc_final: 0.7637 (t70) REVERT: M 653 CYS cc_start: 0.7949 (m) cc_final: 0.6951 (t) REVERT: N 66 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8875 (mt) REVERT: N 354 GLN cc_start: 0.7249 (pt0) cc_final: 0.6793 (pt0) REVERT: N 366 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8720 (tt) REVERT: Q 105 LEU cc_start: 0.8999 (tp) cc_final: 0.8542 (tt) REVERT: Q 115 LEU cc_start: 0.9207 (tt) cc_final: 0.8978 (tt) REVERT: C 38 VAL cc_start: 0.9061 (m) cc_final: 0.8858 (p) outliers start: 47 outliers final: 36 residues processed: 321 average time/residue: 0.2713 time to fit residues: 133.5561 Evaluate side-chains 325 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 284 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 599 VAL Chi-restraints excluded: chain K residue 608 ARG Chi-restraints excluded: chain K residue 657 VAL Chi-restraints excluded: chain K residue 691 VAL Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 407 HIS Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 592 LEU Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 318 ASP Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 394 SER Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain C residue 149 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 9.9990 chunk 3 optimal weight: 0.3980 chunk 85 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 133 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 194 ASN ** L 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 659 HIS ** N 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 385 ASN ** 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 = 0.3949 r_free = 0.3949 target = 0.138105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.114139 restraints weight = 26142.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.113698 restraints weight = 21631.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.115110 restraints weight = 21149.854| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13746 Z= 0.139 Angle : 0.745 12.780 18717 Z= 0.379 Chirality : 0.044 0.163 2114 Planarity : 0.004 0.069 2439 Dihedral : 5.671 46.592 1925 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.12 % Favored : 90.69 % Rotamer: Outliers : 3.61 % Allowed : 25.57 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.20), residues: 1655 helix: 0.59 (0.27), residues: 355 sheet: -1.72 (0.30), residues: 284 loop : -2.35 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 185 HIS 0.006 0.001 HIS K 593 PHE 0.037 0.001 PHE N 243 TYR 0.015 0.001 TYR L 358 ARG 0.007 0.000 ARG P 286 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 391) hydrogen bonds : angle 5.19757 ( 1065) SS BOND : bond 0.00989 ( 8) SS BOND : angle 3.08385 ( 16) covalent geometry : bond 0.00315 (13736) covalent geometry : angle 0.73981 (18701) Misc. bond : bond 0.00316 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 304 time to evaluate : 1.455 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: K 581 ASP cc_start: 0.7116 (t0) cc_final: 0.5421 (m-30) REVERT: K 608 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7937 (mtt-85) REVERT: L 88 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7060 (tt) REVERT: L 148 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.7268 (p90) REVERT: L 221 GLN cc_start: 0.8428 (pp30) cc_final: 0.7953 (pp30) REVERT: M 634 HIS cc_start: 0.7903 (t-90) cc_final: 0.7614 (t70) REVERT: M 653 CYS cc_start: 0.7781 (m) cc_final: 0.6851 (t) REVERT: N 66 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8884 (mt) REVERT: N 177 GLN cc_start: 0.7990 (tm-30) cc_final: 0.7554 (tm-30) REVERT: N 318 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8104 (m-30) REVERT: N 354 GLN cc_start: 0.7175 (pt0) cc_final: 0.6810 (pt0) REVERT: N 366 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8674 (tt) REVERT: N 396 ASP cc_start: 0.8202 (p0) cc_final: 0.7836 (t70) REVERT: P 286 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7785 (ttp80) REVERT: Q 105 LEU cc_start: 0.9025 (tp) cc_final: 0.8623 (tt) outliers start: 46 outliers final: 38 residues processed: 328 average time/residue: 0.2274 time to fit residues: 111.5356 Evaluate side-chains 323 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 279 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 599 VAL Chi-restraints excluded: chain K residue 608 ARG Chi-restraints excluded: chain K residue 657 VAL Chi-restraints excluded: chain K residue 691 VAL Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 592 LEU Chi-restraints excluded: chain M residue 600 ILE Chi-restraints excluded: chain M residue 624 HIS Chi-restraints excluded: chain M residue 627 ILE Chi-restraints excluded: chain M residue 659 HIS Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 318 ASP Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 394 SER Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 251 ASP Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain C residue 149 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 97 optimal weight: 10.0000 chunk 150 optimal weight: 30.0000 chunk 158 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 153 optimal weight: 30.0000 chunk 49 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 101 optimal weight: 8.9990 chunk 87 optimal weight: 0.6980 chunk 84 optimal weight: 0.0070 overall best weight: 1.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 292 GLN ** L 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 633 ASN M 659 HIS ** N 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.136624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.112928 restraints weight = 26764.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.112702 restraints weight = 22417.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.114047 restraints weight = 22584.055| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13746 Z= 0.163 Angle : 0.763 12.634 18717 Z= 0.390 Chirality : 0.045 0.202 2114 Planarity : 0.004 0.069 2439 Dihedral : 5.751 46.684 1925 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.61 % Favored : 90.21 % Rotamer: Outliers : 3.92 % Allowed : 25.65 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.20), residues: 1655 helix: 0.56 (0.28), residues: 354 sheet: -1.68 (0.30), residues: 290 loop : -2.37 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 437 HIS 0.007 0.001 HIS N 226 PHE 0.034 0.002 PHE N 243 TYR 0.038 0.002 TYR Q 117 ARG 0.007 0.001 ARG P 286 Details of bonding type rmsd hydrogen bonds : bond 0.04538 ( 391) hydrogen bonds : angle 5.23998 ( 1065) SS BOND : bond 0.00747 ( 8) SS BOND : angle 3.01312 ( 16) covalent geometry : bond 0.00371 (13736) covalent geometry : angle 0.75847 (18701) Misc. bond : bond 0.00323 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6079.99 seconds wall clock time: 115 minutes 53.00 seconds (6953.00 seconds total)