Starting phenix.real_space_refine on Thu Sep 26 15:55:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c23_7334/09_2024/6c23_7334.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c23_7334/09_2024/6c23_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c23_7334/09_2024/6c23_7334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c23_7334/09_2024/6c23_7334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c23_7334/09_2024/6c23_7334.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c23_7334/09_2024/6c23_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.05, per 1000 atoms: 0.60 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.9 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: 3.75 Time building geometry restraints manager: 3.88 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: 8 1.80 - 2.57: 184 2.57 - 3.35: 17249 3.35 - 4.12: 31407 4.12 - 4.90: 56673 Nonbonded interactions: 105521 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=" ND1 HIS K 593 " pdb=" CB SER K 596 " model vdw 1.644 3.520 nonbonded pdb=" C SER K 729 " pdb=" OE1 GLN K 730 " model vdw 1.693 3.270 ... (remaining 105516 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: 1.600 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: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 31.520 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.890 ------------------------------------------------------------------------------- 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 13736 Z= 0.851 Angle : 1.586 32.789 18701 Z= 0.964 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 *********************** 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 fitting. rotamer outliers: 13 poor density : 464 time to evaluate : 1.577 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: 0.2990 time to fit residues: 193.7311 Evaluate side-chains 319 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 315 time to evaluate : 2.923 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13736 Z= 0.239 Angle : 0.788 11.628 18701 Z= 0.409 Chirality : 0.048 0.198 2114 Planarity : 0.005 0.064 2439 Dihedral : 7.104 48.017 1927 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.28 % Favored : 91.42 % Rotamer: Outliers : 3.45 % Allowed : 13.65 % Favored : 82.90 % 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: -3.59 (0.18), residues: 1655 helix: -0.33 (0.27), residues: 358 sheet: -3.16 (0.24), residues: 301 loop : -3.06 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 345 HIS 0.007 0.001 HIS N 157 PHE 0.015 0.002 PHE N 8 TYR 0.025 0.002 TYR L 148 ARG 0.007 0.001 ARG K 679 *********************** 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 413 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 369 time to evaluate : 1.579 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: A 468 LYS cc_start: 0.8897 (mttt) cc_final: 0.8631 (tttp) REVERT: A 475 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8440 (tp) REVERT: E 155 GLU cc_start: 0.7967 (tt0) cc_final: 0.7471 (tm-30) REVERT: K 276 GLN cc_start: 0.9067 (tp40) cc_final: 0.8342 (tp40) REVERT: K 581 ASP cc_start: 0.7226 (t0) cc_final: 0.5800 (m-30) REVERT: K 632 VAL cc_start: 0.8758 (m) cc_final: 0.8542 (m) REVERT: K 721 GLU cc_start: 0.9027 (tt0) cc_final: 0.8692 (tt0) REVERT: L 181 GLN cc_start: 0.8491 (tt0) cc_final: 0.8152 (mm-40) REVERT: L 250 LYS cc_start: 0.8814 (ttpt) cc_final: 0.8585 (tttp) REVERT: L 256 MET cc_start: 0.8992 (ttm) cc_final: 0.8525 (ttm) REVERT: L 313 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.9005 (mmt-90) REVERT: L 341 ASP cc_start: 0.9059 (m-30) cc_final: 0.8488 (t70) REVERT: L 342 LYS cc_start: 0.9022 (mptm) cc_final: 0.8799 (tptt) REVERT: L 357 ASP cc_start: 0.8850 (m-30) cc_final: 0.8586 (t0) REVERT: M 565 TYR cc_start: 0.7617 (m-80) cc_final: 0.7335 (m-80) REVERT: M 599 GLN cc_start: 0.8539 (tp40) cc_final: 0.8266 (tp40) REVERT: M 634 HIS cc_start: 0.8964 (t-90) cc_final: 0.8364 (t-170) REVERT: M 653 CYS cc_start: 0.8177 (m) cc_final: 0.7186 (t) REVERT: M 676 LYS cc_start: 0.8989 (tttt) cc_final: 0.8541 (tptp) REVERT: N 33 ASP cc_start: 0.8627 (m-30) cc_final: 0.7922 (t0) REVERT: N 41 GLU cc_start: 0.8889 (pt0) cc_final: 0.8415 (tp30) REVERT: N 122 ASN cc_start: 0.8650 (m110) cc_final: 0.8143 (p0) REVERT: N 242 LEU cc_start: 0.9120 (mp) cc_final: 0.8904 (mt) REVERT: N 270 ASP cc_start: 0.8848 (m-30) cc_final: 0.8488 (t0) REVERT: N 302 ASP cc_start: 0.8569 (t0) cc_final: 0.8102 (p0) REVERT: N 354 GLN cc_start: 0.7678 (pt0) cc_final: 0.7072 (pt0) REVERT: N 379 ASP cc_start: 0.8895 (t0) cc_final: 0.8599 (t0) REVERT: N 385 ASN cc_start: 0.8468 (m-40) cc_final: 0.8030 (t0) REVERT: O 28 PHE cc_start: 0.5448 (m-10) cc_final: 0.4849 (t80) REVERT: P 244 MET cc_start: 0.8317 (mtp) cc_final: 0.8070 (mmm) REVERT: Q 118 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8691 (mpp) REVERT: C 54 GLU cc_start: 0.9332 (tm-30) cc_final: 0.8980 (tm-30) REVERT: C 61 LYS cc_start: 0.9113 (mttt) cc_final: 0.8868 (mtmm) REVERT: C 64 ARG cc_start: 0.8332 (mtt90) cc_final: 0.7959 (mmm160) REVERT: C 65 ILE cc_start: 0.8346 (mm) cc_final: 0.7840 (tt) REVERT: C 66 GLN cc_start: 0.8286 (mt0) cc_final: 0.7610 (tm-30) REVERT: C 117 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8371 (mm-40) outliers start: 44 outliers final: 24 residues processed: 394 average time/residue: 0.2557 time to fit residues: 144.3903 Evaluate side-chains 325 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 298 time to evaluate : 1.591 ------------------------------------------------------------------------------- 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 89 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 109 optimal weight: 0.0170 chunk 44 optimal weight: 0.5980 chunk 161 optimal weight: 9.9990 chunk 173 optimal weight: 20.0000 chunk 143 optimal weight: 0.0770 chunk 159 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 N 38 HIS ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13736 Z= 0.183 Angle : 0.715 9.569 18701 Z= 0.368 Chirality : 0.045 0.155 2114 Planarity : 0.004 0.052 2439 Dihedral : 6.207 44.412 1925 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.28 % Favored : 91.36 % Rotamer: Outliers : 3.22 % Allowed : 16.39 % Favored : 80.39 % 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: -3.00 (0.19), residues: 1655 helix: 0.18 (0.27), residues: 355 sheet: -2.65 (0.26), residues: 287 loop : -2.74 (0.17), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 60 HIS 0.005 0.001 HIS N 176 PHE 0.028 0.002 PHE N 243 TYR 0.024 0.001 TYR L 148 ARG 0.008 0.001 ARG L 367 *********************** 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 389 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 348 time to evaluate : 1.495 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: A 475 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8548 (tp) REVERT: E 155 GLU cc_start: 0.8007 (tt0) cc_final: 0.7692 (tm-30) REVERT: K 276 GLN cc_start: 0.9085 (tp40) cc_final: 0.8292 (tp40) REVERT: K 293 ASP cc_start: 0.8296 (t70) cc_final: 0.7760 (t70) REVERT: K 581 ASP cc_start: 0.7004 (t0) cc_final: 0.5555 (m-30) REVERT: K 701 MET cc_start: 0.8881 (tpp) cc_final: 0.8414 (tpp) REVERT: L 153 THR cc_start: 0.9562 (t) cc_final: 0.9165 (m) REVERT: L 181 GLN cc_start: 0.8474 (tt0) cc_final: 0.8124 (mm-40) REVERT: L 250 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8416 (tttp) REVERT: L 256 MET cc_start: 0.9040 (ttm) cc_final: 0.8264 (ttm) REVERT: L 341 ASP cc_start: 0.8995 (m-30) cc_final: 0.8498 (t70) REVERT: L 342 LYS cc_start: 0.9028 (mptm) cc_final: 0.8795 (tptt) REVERT: L 357 ASP cc_start: 0.8854 (m-30) cc_final: 0.8498 (t0) REVERT: L 376 MET cc_start: 0.8784 (mmt) cc_final: 0.8373 (ttm) REVERT: M 607 ASN cc_start: 0.8580 (p0) cc_final: 0.8196 (p0) REVERT: M 653 CYS cc_start: 0.8215 (m) cc_final: 0.7299 (t) REVERT: M 676 LYS cc_start: 0.8902 (tttt) cc_final: 0.8525 (tptp) REVERT: N 22 LYS cc_start: 0.9181 (tppt) cc_final: 0.8826 (tppp) REVERT: N 33 ASP cc_start: 0.8596 (m-30) cc_final: 0.7896 (t0) REVERT: N 41 GLU cc_start: 0.8807 (pt0) cc_final: 0.8355 (tp30) REVERT: N 66 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8757 (mt) REVERT: N 270 ASP cc_start: 0.8803 (m-30) cc_final: 0.8496 (t0) REVERT: N 302 ASP cc_start: 0.8486 (t0) cc_final: 0.8118 (p0) REVERT: N 354 GLN cc_start: 0.7530 (pt0) cc_final: 0.7085 (pt0) REVERT: N 379 ASP cc_start: 0.8987 (t0) cc_final: 0.8489 (m-30) REVERT: N 385 ASN cc_start: 0.8441 (m-40) cc_final: 0.8003 (t0) REVERT: P 257 SER cc_start: 0.9222 (m) cc_final: 0.8868 (p) REVERT: Q 95 GLN cc_start: 0.8509 (mt0) cc_final: 0.8244 (mt0) REVERT: C 54 GLU cc_start: 0.9295 (tm-30) cc_final: 0.8797 (tm-30) REVERT: C 61 LYS cc_start: 0.9148 (mttt) cc_final: 0.8902 (mtmm) REVERT: C 65 ILE cc_start: 0.8483 (mm) cc_final: 0.8114 (tt) REVERT: C 99 LYS cc_start: 0.8787 (tppp) cc_final: 0.8253 (tptp) outliers start: 41 outliers final: 25 residues processed: 367 average time/residue: 0.2549 time to fit residues: 135.1166 Evaluate side-chains 316 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 289 time to evaluate : 1.453 ------------------------------------------------------------------------------- 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 475 ILE Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 536 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 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 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 N residue 66 LEU Chi-restraints excluded: chain N residue 73 SER 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 Q residue 85 LEU Chi-restraints excluded: chain C residue 51 GLU 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 159 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 171 optimal weight: 20.0000 chunk 84 optimal weight: 0.8980 chunk 153 optimal weight: 30.0000 chunk 46 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS K 706 HIS L 191 ASN M 620 HIS M 633 ASN M 659 HIS N 71 HIS N 188 ASN ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 HIS ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13736 Z= 0.310 Angle : 0.743 9.732 18701 Z= 0.385 Chirality : 0.046 0.183 2114 Planarity : 0.004 0.067 2439 Dihedral : 6.296 49.382 1925 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.88 % Favored : 90.82 % Rotamer: Outliers : 4.86 % Allowed : 18.75 % Favored : 76.39 % 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: -2.94 (0.19), residues: 1655 helix: 0.21 (0.27), residues: 354 sheet: -2.59 (0.25), residues: 299 loop : -2.70 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP N 235 HIS 0.007 0.001 HIS A 466 PHE 0.028 0.002 PHE N 243 TYR 0.033 0.002 TYR L 148 ARG 0.003 0.001 ARG K 707 *********************** 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 375 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 313 time to evaluate : 1.654 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: 0.7922 (tt0) cc_final: 0.7325 (tm-30) REVERT: K 276 GLN cc_start: 0.9084 (tp40) cc_final: 0.8340 (tp40) REVERT: K 581 ASP cc_start: 0.7246 (t0) cc_final: 0.5723 (m-30) REVERT: K 701 MET cc_start: 0.9019 (tpp) cc_final: 0.8736 (tpp) REVERT: K 721 GLU cc_start: 0.9267 (tt0) cc_final: 0.9046 (tt0) REVERT: L 80 TYR cc_start: 0.6873 (m-10) cc_final: 0.6629 (m-10) REVERT: L 181 GLN cc_start: 0.8477 (tt0) cc_final: 0.8149 (mm-40) REVERT: L 221 GLN cc_start: 0.8958 (pp30) cc_final: 0.8736 (pp30) REVERT: L 341 ASP cc_start: 0.8963 (m-30) cc_final: 0.8441 (t70) REVERT: L 342 LYS cc_start: 0.9068 (mptm) cc_final: 0.8844 (tptt) REVERT: L 357 ASP cc_start: 0.8860 (m-30) cc_final: 0.8519 (t0) REVERT: M 568 SER cc_start: 0.9011 (p) cc_final: 0.8664 (p) REVERT: M 599 GLN cc_start: 0.8614 (tp40) cc_final: 0.8288 (tp40) REVERT: M 634 HIS cc_start: 0.8813 (t-90) cc_final: 0.8167 (t70) REVERT: M 637 MET cc_start: 0.9104 (ppp) cc_final: 0.8897 (ppp) REVERT: M 653 CYS cc_start: 0.7930 (m) cc_final: 0.7042 (t) REVERT: M 676 LYS cc_start: 0.9004 (tttt) cc_final: 0.8581 (tptp) REVERT: N 22 LYS cc_start: 0.9161 (tppt) cc_final: 0.8789 (tppp) REVERT: N 85 GLN cc_start: 0.7410 (tt0) cc_final: 0.7139 (mt0) REVERT: N 177 GLN cc_start: 0.8674 (mp10) cc_final: 0.8288 (tm-30) REVERT: N 270 ASP cc_start: 0.8854 (m-30) cc_final: 0.8519 (t0) REVERT: N 302 ASP cc_start: 0.8338 (t0) cc_final: 0.8051 (p0) REVERT: N 324 GLN cc_start: 0.9343 (mm-40) cc_final: 0.9127 (mm-40) REVERT: N 342 LEU cc_start: 0.9492 (tp) cc_final: 0.9193 (tt) REVERT: N 354 GLN cc_start: 0.7598 (pt0) cc_final: 0.7087 (pt0) REVERT: N 366 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8398 (tt) REVERT: N 385 ASN cc_start: 0.8597 (m-40) cc_final: 0.8144 (t0) REVERT: C 61 LYS cc_start: 0.9162 (mttt) cc_final: 0.8941 (mtmm) REVERT: C 65 ILE cc_start: 0.8858 (mm) cc_final: 0.8585 (mm) REVERT: C 99 LYS cc_start: 0.8819 (tppp) cc_final: 0.8311 (tptp) outliers start: 62 outliers final: 46 residues processed: 343 average time/residue: 0.2354 time to fit residues: 119.0644 Evaluate side-chains 330 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 283 time to evaluate : 1.595 ------------------------------------------------------------------------------- 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 527 HIS Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain E residue 147 LEU 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 642 CYS Chi-restraints excluded: chain K residue 657 VAL Chi-restraints excluded: chain K residue 672 ASP Chi-restraints excluded: chain L residue 112 VAL 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 377 LEU 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 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 73 SER 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 344 VAL 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 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 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 142 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 145 optimal weight: 50.0000 chunk 118 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 153 optimal weight: 30.0000 chunk 43 optimal weight: 5.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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 M 633 ASN M 659 HIS ** N 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 13736 Z= 0.447 Angle : 0.811 11.202 18701 Z= 0.425 Chirality : 0.048 0.205 2114 Planarity : 0.005 0.072 2439 Dihedral : 6.690 56.699 1925 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.33 % Favored : 89.31 % Rotamer: Outliers : 5.73 % Allowed : 20.24 % Favored : 74.04 % 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: -3.08 (0.19), residues: 1655 helix: 0.11 (0.27), residues: 352 sheet: -2.67 (0.26), residues: 288 loop : -2.79 (0.17), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP N 235 HIS 0.017 0.002 HIS M 659 PHE 0.029 0.003 PHE N 243 TYR 0.033 0.002 TYR L 148 ARG 0.005 0.001 ARG K 707 *********************** 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 363 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 290 time to evaluate : 1.464 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: A 487 ILE cc_start: 0.9121 (mt) cc_final: 0.8917 (mp) REVERT: K 276 GLN cc_start: 0.9071 (tp40) cc_final: 0.8259 (tp40) REVERT: K 432 TRP cc_start: 0.6918 (m100) cc_final: 0.6572 (m100) REVERT: K 581 ASP cc_start: 0.7391 (t0) cc_final: 0.5850 (m-30) REVERT: K 701 MET cc_start: 0.9001 (tpp) cc_final: 0.8710 (tpp) REVERT: L 148 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.7849 (p90) REVERT: L 181 GLN cc_start: 0.8539 (tt0) cc_final: 0.8178 (mm-40) REVERT: L 221 GLN cc_start: 0.9099 (pp30) cc_final: 0.8860 (pp30) REVERT: L 236 ARG cc_start: 0.8581 (mtp85) cc_final: 0.7993 (mtm110) REVERT: L 252 MET cc_start: 0.8951 (tpp) cc_final: 0.8554 (tpt) REVERT: L 341 ASP cc_start: 0.8972 (m-30) cc_final: 0.8424 (t70) REVERT: L 342 LYS cc_start: 0.9085 (mptm) cc_final: 0.8884 (tptt) REVERT: L 357 ASP cc_start: 0.8808 (m-30) cc_final: 0.8524 (t0) REVERT: L 360 GLN cc_start: 0.8536 (mt0) cc_final: 0.8065 (mp10) REVERT: L 376 MET cc_start: 0.9114 (ttm) cc_final: 0.8658 (mtt) REVERT: M 568 SER cc_start: 0.8948 (p) cc_final: 0.8693 (p) REVERT: M 586 GLU cc_start: 0.7580 (tt0) cc_final: 0.6744 (mm-30) REVERT: M 599 GLN cc_start: 0.8870 (tp40) cc_final: 0.8482 (tp-100) REVERT: M 634 HIS cc_start: 0.8824 (t-90) cc_final: 0.8226 (t70) REVERT: M 637 MET cc_start: 0.9031 (ppp) cc_final: 0.8720 (ppp) REVERT: M 641 GLU cc_start: 0.9390 (tm-30) cc_final: 0.9050 (pp20) REVERT: M 653 CYS cc_start: 0.8214 (m) cc_final: 0.7185 (t) REVERT: M 676 LYS cc_start: 0.9072 (tttt) cc_final: 0.8596 (tptp) REVERT: N 41 GLU cc_start: 0.8855 (pt0) cc_final: 0.8301 (tm-30) REVERT: N 270 ASP cc_start: 0.8848 (m-30) cc_final: 0.8510 (t0) REVERT: N 354 GLN cc_start: 0.7663 (pt0) cc_final: 0.7041 (pt0) REVERT: N 379 ASP cc_start: 0.8963 (t0) cc_final: 0.8724 (t0) REVERT: N 385 ASN cc_start: 0.8722 (m-40) cc_final: 0.8232 (t0) REVERT: C 61 LYS cc_start: 0.9172 (mttt) cc_final: 0.8933 (mtmm) REVERT: C 99 LYS cc_start: 0.8867 (tppp) cc_final: 0.8343 (tptp) REVERT: C 116 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8234 (tp) outliers start: 73 outliers final: 57 residues processed: 327 average time/residue: 0.2435 time to fit residues: 116.9936 Evaluate side-chains 331 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 272 time to evaluate : 1.524 ------------------------------------------------------------------------------- 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 E residue 147 LEU Chi-restraints excluded: chain E residue 154 THR 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 628 ILE 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 112 VAL Chi-restraints excluded: chain L residue 122 THR 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 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 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 627 ILE Chi-restraints excluded: chain M residue 638 LEU Chi-restraints excluded: chain M residue 655 ASN Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 140 ILE 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 344 VAL 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 251 ASP Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 102 THR 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 116 LEU 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 57 optimal weight: 0.9990 chunk 154 optimal weight: 30.0000 chunk 33 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 171 optimal weight: 40.0000 chunk 142 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 194 ASN N 261 ASN P 290 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13736 Z= 0.254 Angle : 0.719 10.055 18701 Z= 0.368 Chirality : 0.045 0.164 2114 Planarity : 0.004 0.060 2439 Dihedral : 6.196 51.956 1925 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.31 % Favored : 90.45 % Rotamer: Outliers : 5.49 % Allowed : 21.65 % Favored : 72.86 % 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: -2.82 (0.19), residues: 1655 helix: 0.24 (0.27), residues: 361 sheet: -2.33 (0.28), residues: 278 loop : -2.68 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP N 235 HIS 0.005 0.001 HIS A 466 PHE 0.029 0.002 PHE N 243 TYR 0.029 0.002 TYR Q 117 ARG 0.004 0.001 ARG C 63 *********************** 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 377 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 307 time to evaluate : 1.638 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: 0.9047 (tp40) cc_final: 0.8228 (tp40) REVERT: K 432 TRP cc_start: 0.6913 (m100) cc_final: 0.6583 (m100) REVERT: K 581 ASP cc_start: 0.7222 (t0) cc_final: 0.5647 (m-30) REVERT: K 701 MET cc_start: 0.8872 (tpp) cc_final: 0.8622 (tpp) REVERT: L 148 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7743 (p90) REVERT: L 153 THR cc_start: 0.9521 (t) cc_final: 0.9157 (m) REVERT: L 181 GLN cc_start: 0.8519 (tt0) cc_final: 0.8154 (mm-40) REVERT: L 221 GLN cc_start: 0.9071 (pp30) cc_final: 0.8803 (pp30) REVERT: L 238 GLU cc_start: 0.8842 (pt0) cc_final: 0.8319 (pt0) REVERT: L 251 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8341 (mt) REVERT: L 256 MET cc_start: 0.8879 (ttm) cc_final: 0.8519 (ttm) REVERT: L 341 ASP cc_start: 0.8928 (m-30) cc_final: 0.8402 (t70) REVERT: L 342 LYS cc_start: 0.9084 (mptm) cc_final: 0.8877 (tptt) REVERT: L 357 ASP cc_start: 0.8777 (m-30) cc_final: 0.8510 (t0) REVERT: M 586 GLU cc_start: 0.7484 (tt0) cc_final: 0.6758 (mm-30) REVERT: M 599 GLN cc_start: 0.8730 (tp40) cc_final: 0.8415 (tp40) REVERT: M 634 HIS cc_start: 0.8731 (t-90) cc_final: 0.8239 (t70) REVERT: M 637 MET cc_start: 0.9008 (ppp) cc_final: 0.8795 (ppp) REVERT: M 653 CYS cc_start: 0.8204 (m) cc_final: 0.7092 (t) REVERT: M 676 LYS cc_start: 0.9076 (tttt) cc_final: 0.8608 (tptp) REVERT: N 22 LYS cc_start: 0.9183 (tptt) cc_final: 0.8798 (tppp) REVERT: N 33 ASP cc_start: 0.8547 (m-30) cc_final: 0.7740 (t0) REVERT: N 270 ASP cc_start: 0.8840 (m-30) cc_final: 0.8493 (t0) REVERT: N 324 GLN cc_start: 0.9345 (mm-40) cc_final: 0.9139 (mm-40) REVERT: N 354 GLN cc_start: 0.7570 (pt0) cc_final: 0.6936 (pt0) REVERT: N 379 ASP cc_start: 0.8939 (t0) cc_final: 0.8682 (t0) REVERT: N 385 ASN cc_start: 0.8585 (m-40) cc_final: 0.8236 (t0) REVERT: N 396 ASP cc_start: 0.9101 (p0) cc_final: 0.8597 (t70) REVERT: P 275 ASP cc_start: 0.8577 (t70) cc_final: 0.8333 (m-30) REVERT: C 65 ILE cc_start: 0.8511 (mp) cc_final: 0.7678 (tt) REVERT: C 99 LYS cc_start: 0.8872 (tppp) cc_final: 0.8348 (tptp) outliers start: 70 outliers final: 52 residues processed: 341 average time/residue: 0.2321 time to fit residues: 117.0581 Evaluate side-chains 334 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 280 time to evaluate : 1.561 ------------------------------------------------------------------------------- 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 E residue 147 LEU 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 599 VAL 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 122 THR Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 150 CYS 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 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 600 ILE Chi-restraints excluded: chain M residue 638 LEU Chi-restraints excluded: chain N residue 34 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 190 SER Chi-restraints excluded: chain N residue 261 ASN Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 378 SER 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 P residue 274 LYS 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 165 optimal weight: 7.9990 chunk 19 optimal weight: 40.0000 chunk 97 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 50.0000 chunk 95 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 555 ASN L 397 HIS ** N 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13736 Z= 0.298 Angle : 0.743 12.290 18701 Z= 0.381 Chirality : 0.046 0.179 2114 Planarity : 0.004 0.057 2439 Dihedral : 6.203 55.822 1925 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.57 % Favored : 89.12 % Rotamer: Outliers : 5.25 % Allowed : 22.75 % Favored : 72.00 % 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: -2.68 (0.19), residues: 1655 helix: 0.34 (0.27), residues: 361 sheet: -2.17 (0.29), residues: 278 loop : -2.61 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP N 235 HIS 0.007 0.001 HIS L 160 PHE 0.026 0.002 PHE M 656 TYR 0.025 0.002 TYR L 148 ARG 0.004 0.001 ARG K 707 *********************** 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 366 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 299 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 276 GLN cc_start: 0.9055 (tp40) cc_final: 0.8248 (tp40) REVERT: K 432 TRP cc_start: 0.6903 (m100) cc_final: 0.6568 (m100) REVERT: K 581 ASP cc_start: 0.7290 (t0) cc_final: 0.5720 (m-30) REVERT: K 701 MET cc_start: 0.8848 (tpp) cc_final: 0.8603 (tpp) REVERT: L 88 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7080 (tt) REVERT: L 148 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.7770 (p90) REVERT: L 153 THR cc_start: 0.9517 (t) cc_final: 0.9136 (m) REVERT: L 181 GLN cc_start: 0.8571 (tt0) cc_final: 0.8190 (mm-40) REVERT: L 221 GLN cc_start: 0.9143 (pp30) cc_final: 0.8873 (pp30) REVERT: L 236 ARG cc_start: 0.8469 (mtp85) cc_final: 0.7903 (mtm110) REVERT: L 238 GLU cc_start: 0.8777 (pt0) cc_final: 0.8163 (pt0) REVERT: L 256 MET cc_start: 0.8828 (ttm) cc_final: 0.8387 (ttm) REVERT: L 341 ASP cc_start: 0.8917 (m-30) cc_final: 0.8382 (t70) REVERT: L 342 LYS cc_start: 0.9099 (mptm) cc_final: 0.8879 (tptt) REVERT: L 357 ASP cc_start: 0.8714 (m-30) cc_final: 0.8506 (t0) REVERT: L 360 GLN cc_start: 0.8620 (mt0) cc_final: 0.8069 (mp10) REVERT: L 376 MET cc_start: 0.9193 (ttm) cc_final: 0.8947 (mtt) REVERT: M 586 GLU cc_start: 0.7393 (tt0) cc_final: 0.6820 (mm-30) REVERT: M 599 GLN cc_start: 0.8760 (tp40) cc_final: 0.8450 (tp40) REVERT: M 634 HIS cc_start: 0.8732 (t-90) cc_final: 0.8253 (t70) REVERT: M 637 MET cc_start: 0.9006 (ppp) cc_final: 0.8752 (ppp) REVERT: M 641 GLU cc_start: 0.9409 (tm-30) cc_final: 0.9104 (pp20) REVERT: M 653 CYS cc_start: 0.8359 (m) cc_final: 0.7223 (t) REVERT: M 676 LYS cc_start: 0.9101 (tttt) cc_final: 0.8654 (tptp) REVERT: N 41 GLU cc_start: 0.8843 (pt0) cc_final: 0.8323 (tm-30) REVERT: N 270 ASP cc_start: 0.8894 (m-30) cc_final: 0.8500 (t0) REVERT: N 324 GLN cc_start: 0.9321 (mm-40) cc_final: 0.9106 (mm-40) REVERT: N 354 GLN cc_start: 0.7590 (pt0) cc_final: 0.6954 (pt0) REVERT: N 379 ASP cc_start: 0.8943 (t0) cc_final: 0.8675 (t0) REVERT: N 385 ASN cc_start: 0.8598 (m-40) cc_final: 0.8269 (t0) REVERT: P 246 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7924 (mm-30) REVERT: Q 105 LEU cc_start: 0.9516 (tp) cc_final: 0.9266 (tt) REVERT: C 65 ILE cc_start: 0.8346 (mp) cc_final: 0.7981 (tt) REVERT: C 99 LYS cc_start: 0.8938 (tppp) cc_final: 0.8370 (tptp) REVERT: C 116 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8204 (tp) outliers start: 67 outliers final: 57 residues processed: 333 average time/residue: 0.2290 time to fit residues: 113.1156 Evaluate side-chains 342 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 281 time to evaluate : 1.554 ------------------------------------------------------------------------------- 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 147 LEU 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 599 VAL 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 122 THR Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 150 CYS 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 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 600 ILE Chi-restraints excluded: chain M residue 627 ILE Chi-restraints excluded: chain M residue 638 LEU Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 378 SER Chi-restraints excluded: chain N residue 394 SER Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 246 GLU Chi-restraints excluded: chain P residue 251 ASP Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 274 LYS 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 107 VAL Chi-restraints excluded: chain C residue 116 LEU 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 105 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 15 optimal weight: 30.0000 chunk 134 optimal weight: 8.9990 chunk 155 optimal weight: 30.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 689 HIS L 191 ASN L 194 ASN L 292 GLN M 620 HIS ** N 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 261 ASN ** N 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13736 Z= 0.393 Angle : 0.799 11.860 18701 Z= 0.413 Chirality : 0.048 0.215 2114 Planarity : 0.005 0.059 2439 Dihedral : 6.489 59.161 1925 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.36 % Favored : 88.34 % Rotamer: Outliers : 6.12 % Allowed : 22.67 % Favored : 71.22 % 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: -2.75 (0.19), residues: 1655 helix: 0.25 (0.27), residues: 361 sheet: -2.24 (0.29), residues: 283 loop : -2.62 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP N 235 HIS 0.007 0.001 HIS A 466 PHE 0.025 0.002 PHE M 656 TYR 0.029 0.002 TYR L 148 ARG 0.005 0.001 ARG K 707 *********************** 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 357 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 279 time to evaluate : 1.723 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: 0.9058 (tp40) cc_final: 0.8266 (tp40) REVERT: K 581 ASP cc_start: 0.7130 (t0) cc_final: 0.5854 (m-30) REVERT: K 701 MET cc_start: 0.8948 (tpp) cc_final: 0.8496 (tpp) REVERT: L 88 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7243 (tt) REVERT: L 148 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.7877 (p90) REVERT: L 153 THR cc_start: 0.9506 (t) cc_final: 0.9089 (m) REVERT: L 181 GLN cc_start: 0.8521 (tt0) cc_final: 0.8156 (mm-40) REVERT: L 221 GLN cc_start: 0.9227 (pp30) cc_final: 0.8952 (pp30) REVERT: L 236 ARG cc_start: 0.8554 (mtp85) cc_final: 0.7979 (mtm110) REVERT: L 341 ASP cc_start: 0.8883 (m-30) cc_final: 0.8384 (t70) REVERT: L 357 ASP cc_start: 0.8764 (m-30) cc_final: 0.8560 (t0) REVERT: L 376 MET cc_start: 0.9194 (ttm) cc_final: 0.8949 (mtt) REVERT: M 586 GLU cc_start: 0.7348 (tt0) cc_final: 0.6888 (mp0) REVERT: M 599 GLN cc_start: 0.8906 (tp40) cc_final: 0.8527 (tp-100) REVERT: M 634 HIS cc_start: 0.8767 (t-90) cc_final: 0.8287 (t70) REVERT: M 637 MET cc_start: 0.9025 (ppp) cc_final: 0.8713 (ppp) REVERT: M 641 GLU cc_start: 0.9432 (tm-30) cc_final: 0.9112 (pp20) REVERT: M 653 CYS cc_start: 0.8489 (m) cc_final: 0.7362 (t) REVERT: M 676 LYS cc_start: 0.9135 (tttt) cc_final: 0.8651 (tptp) REVERT: N 33 ASP cc_start: 0.8524 (m-30) cc_final: 0.7729 (t0) REVERT: N 41 GLU cc_start: 0.8847 (pt0) cc_final: 0.8292 (tm-30) REVERT: N 270 ASP cc_start: 0.8864 (m-30) cc_final: 0.8501 (t0) REVERT: N 354 GLN cc_start: 0.7662 (pt0) cc_final: 0.7008 (pt0) REVERT: N 379 ASP cc_start: 0.8959 (t0) cc_final: 0.8725 (t0) REVERT: N 385 ASN cc_start: 0.8668 (m-40) cc_final: 0.8302 (t0) REVERT: C 65 ILE cc_start: 0.8451 (mp) cc_final: 0.7932 (tt) REVERT: C 99 LYS cc_start: 0.8851 (tppp) cc_final: 0.8335 (tptp) outliers start: 78 outliers final: 65 residues processed: 325 average time/residue: 0.2353 time to fit residues: 114.1611 Evaluate side-chains 336 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 269 time to evaluate : 1.848 ------------------------------------------------------------------------------- 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 E residue 147 LEU 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 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 122 THR Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 150 CYS Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 246 LEU 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 600 ILE Chi-restraints excluded: chain M residue 622 MET Chi-restraints excluded: chain M residue 627 ILE Chi-restraints excluded: chain M residue 638 LEU Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 83 SER Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 378 SER Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 251 ASP Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 274 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 30.0000 chunk 149 optimal weight: 40.0000 chunk 158 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 150 optimal weight: 30.0000 chunk 104 optimal weight: 2.9990 chunk 168 optimal weight: 0.3980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 292 GLN ** L 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 633 ASN ** N 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 261 ASN ** N 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13736 Z= 0.236 Angle : 0.734 10.479 18701 Z= 0.374 Chirality : 0.045 0.179 2114 Planarity : 0.004 0.054 2439 Dihedral : 6.080 52.660 1925 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.09 % Favored : 89.67 % Rotamer: Outliers : 4.94 % Allowed : 23.84 % Favored : 71.22 % 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: -2.53 (0.20), residues: 1655 helix: 0.44 (0.27), residues: 361 sheet: -2.09 (0.29), residues: 283 loop : -2.49 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP N 235 HIS 0.005 0.001 HIS N 226 PHE 0.025 0.002 PHE M 656 TYR 0.022 0.002 TYR L 358 ARG 0.004 0.000 ARG A 458 *********************** 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 365 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 302 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 527 HIS cc_start: 0.8170 (m170) cc_final: 0.7728 (m170) REVERT: A 535 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.6450 (ppt170) REVERT: K 432 TRP cc_start: 0.6923 (m100) cc_final: 0.6451 (m100) REVERT: K 581 ASP cc_start: 0.6871 (t0) cc_final: 0.5551 (m-30) REVERT: K 701 MET cc_start: 0.8772 (tpp) cc_final: 0.8568 (tpp) REVERT: L 88 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.6984 (tt) REVERT: L 148 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7788 (p90) REVERT: L 153 THR cc_start: 0.9510 (t) cc_final: 0.9103 (m) REVERT: L 181 GLN cc_start: 0.8524 (tt0) cc_final: 0.8173 (mm-40) REVERT: L 221 GLN cc_start: 0.9165 (pp30) cc_final: 0.8890 (pp30) REVERT: L 251 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8120 (mt) REVERT: L 341 ASP cc_start: 0.8821 (m-30) cc_final: 0.8363 (t70) REVERT: M 586 GLU cc_start: 0.7211 (tt0) cc_final: 0.6871 (mp0) REVERT: M 599 GLN cc_start: 0.8739 (tp40) cc_final: 0.8311 (tp-100) REVERT: M 634 HIS cc_start: 0.8685 (t-90) cc_final: 0.8244 (t70) REVERT: M 637 MET cc_start: 0.8994 (ppp) cc_final: 0.8772 (ppp) REVERT: M 641 GLU cc_start: 0.9428 (tm-30) cc_final: 0.9152 (pp20) REVERT: M 653 CYS cc_start: 0.8416 (m) cc_final: 0.7287 (t) REVERT: M 676 LYS cc_start: 0.9113 (tttt) cc_final: 0.8677 (tptp) REVERT: N 22 LYS cc_start: 0.9188 (tptt) cc_final: 0.8799 (tppp) REVERT: N 33 ASP cc_start: 0.8512 (m-30) cc_final: 0.7679 (t0) REVERT: N 251 LYS cc_start: 0.8725 (mttp) cc_final: 0.8475 (tttp) REVERT: N 270 ASP cc_start: 0.8898 (m-30) cc_final: 0.8621 (t0) REVERT: N 354 GLN cc_start: 0.7545 (pt0) cc_final: 0.6908 (pt0) REVERT: N 379 ASP cc_start: 0.8952 (t0) cc_final: 0.8668 (t0) REVERT: N 385 ASN cc_start: 0.8505 (m-40) cc_final: 0.8211 (t0) REVERT: P 275 ASP cc_start: 0.8581 (t70) cc_final: 0.8295 (m-30) REVERT: C 61 LYS cc_start: 0.9206 (mttt) cc_final: 0.8928 (mtmm) REVERT: C 65 ILE cc_start: 0.8535 (mp) cc_final: 0.8044 (tt) REVERT: C 99 LYS cc_start: 0.8909 (tppp) cc_final: 0.8384 (tptp) REVERT: C 230 MET cc_start: 0.7499 (mmt) cc_final: 0.7213 (mmm) outliers start: 63 outliers final: 51 residues processed: 332 average time/residue: 0.2420 time to fit residues: 120.2258 Evaluate side-chains 333 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 278 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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 530 VAL Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain E residue 147 LEU 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 599 VAL 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 122 THR Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 150 CYS 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 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 627 ILE Chi-restraints excluded: chain M residue 638 LEU Chi-restraints excluded: chain N residue 34 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 190 SER Chi-restraints excluded: chain N residue 328 HIS Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 378 SER 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 131 THR Chi-restraints excluded: chain C residue 42 PHE 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 102 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 176 optimal weight: 0.0770 chunk 162 optimal weight: 7.9990 chunk 140 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 149 optimal weight: 40.0000 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS L 292 GLN ** L 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN ** N 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13736 Z= 0.204 Angle : 0.727 10.358 18701 Z= 0.370 Chirality : 0.045 0.172 2114 Planarity : 0.004 0.054 2439 Dihedral : 5.821 47.335 1925 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.55 % Favored : 90.27 % Rotamer: Outliers : 3.53 % Allowed : 25.57 % Favored : 70.90 % 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: -2.43 (0.19), residues: 1655 helix: 0.51 (0.27), residues: 358 sheet: -1.91 (0.29), residues: 294 loop : -2.45 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP N 235 HIS 0.005 0.001 HIS A 527 PHE 0.025 0.001 PHE M 656 TYR 0.015 0.001 TYR L 148 ARG 0.004 0.000 ARG A 458 ********************** 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 342 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 297 time to evaluate : 1.711 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: K 432 TRP cc_start: 0.6875 (m100) cc_final: 0.6381 (m100) REVERT: K 581 ASP cc_start: 0.6873 (t0) cc_final: 0.5423 (m-30) REVERT: K 701 MET cc_start: 0.8730 (tpp) cc_final: 0.8521 (tpp) REVERT: L 88 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.6894 (tt) REVERT: L 148 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7811 (p90) REVERT: L 153 THR cc_start: 0.9507 (t) cc_final: 0.9129 (m) REVERT: L 181 GLN cc_start: 0.8534 (tt0) cc_final: 0.8185 (mm-40) REVERT: L 221 GLN cc_start: 0.9146 (pp30) cc_final: 0.8876 (pp30) REVERT: L 251 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8020 (mt) REVERT: L 308 TYR cc_start: 0.7330 (m-80) cc_final: 0.7101 (m-80) REVERT: L 341 ASP cc_start: 0.8807 (m-30) cc_final: 0.8314 (t70) REVERT: L 389 TRP cc_start: 0.7981 (m-90) cc_final: 0.7643 (m100) REVERT: M 586 GLU cc_start: 0.7115 (tt0) cc_final: 0.6895 (mp0) REVERT: M 599 GLN cc_start: 0.8657 (tp40) cc_final: 0.8250 (tp40) REVERT: M 634 HIS cc_start: 0.8722 (t-90) cc_final: 0.8195 (t70) REVERT: M 637 MET cc_start: 0.8952 (ppp) cc_final: 0.8688 (ppp) REVERT: M 641 GLU cc_start: 0.9431 (tm-30) cc_final: 0.9104 (pp20) REVERT: M 653 CYS cc_start: 0.8392 (m) cc_final: 0.7287 (t) REVERT: M 676 LYS cc_start: 0.9095 (tttt) cc_final: 0.8666 (tptp) REVERT: N 22 LYS cc_start: 0.9189 (tptt) cc_final: 0.8765 (tppp) REVERT: N 270 ASP cc_start: 0.8930 (m-30) cc_final: 0.8544 (t0) REVERT: N 354 GLN cc_start: 0.7487 (pt0) cc_final: 0.6938 (pt0) REVERT: N 385 ASN cc_start: 0.8428 (m-40) cc_final: 0.8160 (t0) REVERT: Q 105 LEU cc_start: 0.9532 (tp) cc_final: 0.9286 (tt) REVERT: C 61 LYS cc_start: 0.9214 (mttt) cc_final: 0.8942 (mtmm) REVERT: C 65 ILE cc_start: 0.8361 (mp) cc_final: 0.7920 (tt) REVERT: C 99 LYS cc_start: 0.8957 (tppp) cc_final: 0.8454 (tptp) REVERT: C 230 MET cc_start: 0.7404 (mmt) cc_final: 0.7021 (mmt) outliers start: 45 outliers final: 37 residues processed: 315 average time/residue: 0.2575 time to fit residues: 123.7041 Evaluate side-chains 317 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 277 time to evaluate : 1.639 ------------------------------------------------------------------------------- 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 530 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain E residue 147 LEU 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 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 122 THR Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 150 CYS 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 371 ASP Chi-restraints excluded: chain L residue 377 LEU 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 M residue 600 ILE Chi-restraints excluded: chain M residue 627 ILE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 378 SER 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 149 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 144 optimal weight: 50.0000 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 8 optimal weight: 0.0570 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 292 GLN ** L 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 620 HIS ** N 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 400 GLN ** C 58 GLN ** 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 = 0.3900 r_free = 0.3900 target = 0.134483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.111009 restraints weight = 26472.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.110701 restraints weight = 23279.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.112066 restraints weight = 23368.199| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13736 Z= 0.282 Angle : 0.767 11.999 18701 Z= 0.392 Chirality : 0.046 0.178 2114 Planarity : 0.004 0.050 2439 Dihedral : 5.961 49.543 1925 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.88 % Favored : 88.94 % Rotamer: Outliers : 3.76 % Allowed : 25.88 % Favored : 70.35 % 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: -2.43 (0.20), residues: 1655 helix: 0.47 (0.27), residues: 358 sheet: -1.92 (0.29), residues: 286 loop : -2.42 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP N 235 HIS 0.006 0.001 HIS A 466 PHE 0.049 0.002 PHE M 626 TYR 0.033 0.002 TYR Q 117 ARG 0.004 0.001 ARG K 707 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3044.85 seconds wall clock time: 55 minutes 12.98 seconds (3312.98 seconds total)