Starting phenix.real_space_refine on Thu Jul 31 09:58:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c24_7335/07_2025/6c24_7335.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c24_7335/07_2025/6c24_7335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6c24_7335/07_2025/6c24_7335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c24_7335/07_2025/6c24_7335.map" model { file = "/net/cci-nas-00/data/ceres_data/6c24_7335/07_2025/6c24_7335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c24_7335/07_2025/6c24_7335.cif" } resolution = 3.5 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= 0.011 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 87 5.16 5 C 8422 2.51 5 N 2372 2.21 5 O 2465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13346 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 867 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 111 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 184 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 25} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 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: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2881 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 349} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 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: 3062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3062 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 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: 5 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: 1227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1227 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 6, 'TRANS': 141} Chain breaks: 3 Time building chain proxies: 8.08, per 1000 atoms: 0.61 Number of scatterers: 13346 At special positions: 0 Unit cell: (153.72, 109.2, 109.2, 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 87 16.00 O 2465 8.00 N 2372 7.00 C 8422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 450 " - pdb=" SG CYS A 453 " distance=2.09 Simple disulfide: pdb=" SG CYS K 289 " - pdb=" SG CYS K 294 " distance=2.02 Simple disulfide: pdb=" SG CYS K 523 " - pdb=" SG CYS K 547 " distance=2.04 Simple disulfide: pdb=" SG CYS K 523 " - pdb=" SG CYS K 549 " distance=2.05 Simple disulfide: pdb=" SG CYS K 530 " - pdb=" SG CYS K 549 " distance=2.04 Simple disulfide: pdb=" SG CYS K 530 " - pdb=" SG CYS K 553 " distance=2.03 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 429 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 1.6 seconds 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 25 sheets defined 23.3% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 459 through 470 removed outlier: 3.503A pdb=" N LEU A 463 " --> pdb=" O LYS A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 146 through 151 Processing helix chain 'K' and resid 274 through 277 Processing helix chain 'K' and resid 278 through 284 Processing helix chain 'K' and resid 435 through 448 removed outlier: 3.946A pdb=" N GLY K 445 " --> pdb=" O ARG K 441 " (cutoff:3.500A) removed outlier: 3.729A 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 476 Processing helix chain 'K' and resid 534 through 539 Processing helix chain 'K' and resid 571 through 575 removed outlier: 3.506A pdb=" N LEU K 575 " --> pdb=" O PRO K 572 " (cutoff:3.500A) Processing helix chain 'K' and resid 604 through 609 removed outlier: 3.664A pdb=" N ARG K 608 " --> pdb=" O CYS K 604 " (cutoff:3.500A) Processing helix chain 'K' and resid 647 through 662 removed outlier: 3.620A pdb=" N VAL K 657 " --> pdb=" O ARG K 653 " (cutoff:3.500A) Processing helix chain 'K' and resid 682 through 687 removed outlier: 3.576A pdb=" N ALA K 687 " --> pdb=" O ILE K 684 " (cutoff:3.500A) Processing helix chain 'L' and resid 267 through 279 Processing helix chain 'M' and resid 575 through 579 Processing helix chain 'M' and resid 591 through 601 Processing helix chain 'M' and resid 607 through 625 Processing helix chain 'M' and resid 629 through 651 removed outlier: 3.663A pdb=" N ASN M 633 " --> pdb=" O ASP M 629 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N MET M 637 " --> pdb=" O ASN M 633 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLN M 645 " --> pdb=" O GLU M 641 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LYS M 646 " --> pdb=" O ASN M 642 " (cutoff:3.500A) Processing helix chain 'M' and resid 652 through 665 Processing helix chain 'M' and resid 670 through 682 removed outlier: 3.561A pdb=" N ILE M 674 " --> pdb=" O SER M 670 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 27 removed outlier: 4.061A pdb=" N ALA N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL N 12 " --> pdb=" O PHE N 8 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU N 14 " --> pdb=" O ASP N 10 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE N 23 " --> pdb=" O GLU N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 31 Processing helix chain 'N' and resid 355 through 362 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 removed outlier: 3.758A pdb=" N ASP P 281 " --> pdb=" O LEU P 278 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 105 removed outlier: 4.163A pdb=" N PHE Q 86 " --> pdb=" O ASP Q 82 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS Q 92 " --> pdb=" O GLN Q 88 " (cutoff:3.500A) Proline residue: Q 93 - end of helix removed outlier: 3.708A pdb=" N ILE Q 96 " --> pdb=" O LYS Q 92 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR Q 97 " --> pdb=" O PRO Q 93 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 151 removed outlier: 3.693A pdb=" N UNK Z 151 " --> pdb=" O UNK Z 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 63 removed outlier: 3.951A pdb=" N GLN C 28 " --> pdb=" O MET C 24 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG C 31 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASP C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 180 removed outlier: 3.676A pdb=" N PHE C 171 " --> pdb=" O ASN C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 223 removed outlier: 3.572A pdb=" N LYS C 222 " --> pdb=" O PRO C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 229 removed outlier: 3.957A pdb=" N SER C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 247 removed outlier: 3.621A pdb=" N LEU C 240 " --> pdb=" O THR C 236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 432 through 433 removed outlier: 4.349A pdb=" N ILE A 491 " --> pdb=" O LEU A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 528 through 530 removed outlier: 6.160A pdb=" N GLN N 403 " --> pdb=" O ASP N 33 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL N 35 " --> pdb=" O VAL N 401 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL N 401 " --> pdb=" O VAL N 35 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR N 37 " --> pdb=" O MET N 399 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N MET N 399 " --> pdb=" O THR N 37 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE N 398 " --> pdb=" O SER N 394 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP N 379 " --> pdb=" O VAL N 393 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 614 through 618 Processing sheet with id=AA4, first strand: chain 'K' and resid 637 through 640 removed outlier: 6.629A pdb=" N PHE K 637 " --> pdb=" O ALA K 712 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA K 712 " --> pdb=" O PHE K 637 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER K 639 " --> pdb=" O ILE K 710 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 645 through 646 Processing sheet with id=AA6, first strand: chain 'K' and resid 680 through 681 Processing sheet with id=AA7, first strand: chain 'K' and resid 688 through 689 removed outlier: 6.519A pdb=" N ASN K 688 " --> pdb=" O PHE K 724 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 99 through 101 Processing sheet with id=AA9, first strand: chain 'L' and resid 125 through 127 removed outlier: 4.503A pdb=" N GLU L 131 " --> pdb=" O HIS L 127 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 147 through 154 removed outlier: 3.796A pdb=" N THR L 153 " --> pdb=" O LEU L 162 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY L 167 " --> pdb=" O ILE L 171 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE L 171 " --> pdb=" O GLY L 167 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS L 184 " --> pdb=" O ILE L 174 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN L 176 " --> pdb=" O CYS L 182 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N CYS L 182 " --> pdb=" O ASN L 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 195 through 197 removed outlier: 3.580A pdb=" N GLU L 195 " --> pdb=" O VAL L 209 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL L 209 " --> pdb=" O GLU L 195 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS L 197 " --> pdb=" O LEU L 207 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN L 219 " --> pdb=" O LEU L 225 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU L 225 " --> pdb=" O ASN L 219 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 239 through 244 removed outlier: 3.708A pdb=" N SER L 241 " --> pdb=" O CYS L 254 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE L 251 " --> pdb=" O TRP L 263 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU L 260 " --> pdb=" O THR L 301 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 309 through 315 removed outlier: 4.820A pdb=" N CYS L 311 " --> pdb=" O LYS L 322 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS L 322 " --> pdb=" O CYS L 311 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER L 323 " --> pdb=" O ALA L 327 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA L 327 " --> pdb=" O SER L 323 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY L 354 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS L 332 " --> pdb=" O ILE L 352 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ILE L 352 " --> pdb=" O LYS L 332 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 368 through 370 Processing sheet with id=AB6, first strand: chain 'L' and resid 413 through 417 removed outlier: 4.082A pdb=" N GLN L 415 " --> pdb=" O VAL L 428 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER L 417 " --> pdb=" O ILE L 426 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE L 426 " --> pdb=" O SER L 417 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU L 425 " --> pdb=" O TRP L 437 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 565 through 566 removed outlier: 4.787A pdb=" N TYR M 565 " --> pdb=" O LEU M 574 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 50 through 54 removed outlier: 6.442A pdb=" N ASP N 52 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG N 65 " --> pdb=" O ASP N 52 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU N 86 " --> pdb=" O SER N 62 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS N 64 " --> pdb=" O VAL N 84 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN N 77 " --> pdb=" O HIS N 123 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE N 119 " --> pdb=" O ILE N 81 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N SER N 83 " --> pdb=" O ILE N 117 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE N 117 " --> pdb=" O SER N 83 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 141 through 142 Processing sheet with id=AC1, first strand: chain 'N' and resid 183 through 185 removed outlier: 3.714A pdb=" N CYS N 203 " --> pdb=" O SER N 195 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 230 through 235 removed outlier: 3.907A pdb=" N SER N 234 " --> pdb=" O GLY N 244 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA N 247 " --> pdb=" O LYS N 251 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS N 251 " --> pdb=" O ALA N 247 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 288 through 289 Processing sheet with id=AC4, first strand: chain 'N' and resid 298 through 299 removed outlier: 3.500A pdb=" N VAL N 298 " --> pdb=" O PHE N 313 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 320 through 325 removed outlier: 4.200A pdb=" N GLN N 322 " --> pdb=" O SER N 336 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Z' and resid 35 through 36 Processing sheet with id=AC7, first strand: chain 'Z' and resid 59 through 60 removed outlier: 7.159A pdb=" N UNK Z 59 " --> pdb=" O UNK Z 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 352 hydrogen bonds defined for protein. 975 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: 3.52 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.53: 10897 1.53 - 1.86: 2744 1.86 - 2.20: 0 2.20 - 2.54: 0 2.54 - 2.87: 1 Bond restraints: 13642 Sorted by residual: bond pdb=" C UNK Z 25 " pdb=" N UNK Z 30 " ideal model delta sigma weight residual 1.329 2.875 -1.546 1.40e-02 5.10e+03 1.22e+04 bond pdb=" C GLY Q 146 " pdb=" O GLY Q 146 " ideal model delta sigma weight residual 1.231 1.570 -0.339 2.00e-02 2.50e+03 2.87e+02 bond pdb=" N GLY Q 146 " pdb=" CA GLY Q 146 " ideal model delta sigma weight residual 1.451 1.561 -0.110 1.60e-02 3.91e+03 4.69e+01 bond pdb=" CA GLY Q 146 " pdb=" C GLY Q 146 " ideal model delta sigma weight residual 1.516 1.637 -0.121 1.80e-02 3.09e+03 4.52e+01 bond pdb=" CA ALA N 334 " pdb=" C ALA N 334 " ideal model delta sigma weight residual 1.521 1.452 0.069 1.24e-02 6.50e+03 3.14e+01 ... (remaining 13637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.92: 18520 10.92 - 21.85: 13 21.85 - 32.77: 0 32.77 - 43.69: 1 43.69 - 54.61: 1 Bond angle restraints: 18535 Sorted by residual: angle pdb=" O UNK Z 25 " pdb=" C UNK Z 25 " pdb=" N UNK Z 30 " ideal model delta sigma weight residual 123.00 68.39 54.61 1.60e+00 3.91e-01 1.17e+03 angle pdb=" CA UNK Z 25 " pdb=" C UNK Z 25 " pdb=" N UNK Z 30 " ideal model delta sigma weight residual 116.20 150.37 -34.17 2.00e+00 2.50e-01 2.92e+02 angle pdb=" N THR L 405 " pdb=" CA THR L 405 " pdb=" C THR L 405 " ideal model delta sigma weight residual 108.45 126.25 -17.80 1.26e+00 6.30e-01 2.00e+02 angle pdb=" C UNK Z 25 " pdb=" N UNK Z 30 " pdb=" CA UNK Z 30 " ideal model delta sigma weight residual 121.70 105.49 16.21 1.80e+00 3.09e-01 8.11e+01 angle pdb=" N SER C 73 " pdb=" CA SER C 73 " pdb=" C SER C 73 " ideal model delta sigma weight residual 107.99 92.82 15.17 1.76e+00 3.23e-01 7.43e+01 ... (remaining 18530 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.79: 7945 25.79 - 51.57: 212 51.57 - 77.36: 14 77.36 - 103.15: 2 103.15 - 128.93: 1 Dihedral angle restraints: 8174 sinusoidal: 2970 harmonic: 5204 Sorted by residual: dihedral pdb=" CA UNK Z 25 " pdb=" C UNK Z 25 " pdb=" N UNK Z 30 " pdb=" CA UNK Z 30 " ideal model delta harmonic sigma weight residual -180.00 -51.07 -128.93 0 5.00e+00 4.00e-02 6.65e+02 dihedral pdb=" CA MET M 579 " pdb=" C MET M 579 " pdb=" N GLU M 580 " pdb=" CA GLU M 580 " ideal model delta harmonic sigma weight residual 180.00 137.74 42.26 0 5.00e+00 4.00e-02 7.14e+01 dihedral pdb=" CB CYS K 530 " pdb=" SG CYS K 530 " pdb=" SG CYS K 549 " pdb=" CB CYS K 549 " ideal model delta sinusoidal sigma weight residual 93.00 166.44 -73.44 1 1.00e+01 1.00e-02 6.86e+01 ... (remaining 8171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1707 0.111 - 0.221: 317 0.221 - 0.332: 44 0.332 - 0.443: 4 0.443 - 0.554: 4 Chirality restraints: 2076 Sorted by residual: 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 1.96 0.55 2.00e-01 2.50e+01 7.66e+00 chirality pdb=" CA THR L 405 " pdb=" N THR L 405 " pdb=" C THR L 405 " pdb=" CB THR L 405 " both_signs ideal model delta sigma weight residual False 2.53 1.98 0.55 2.00e-01 2.50e+01 7.44e+00 chirality pdb=" CA ASP E 156 " pdb=" N ASP E 156 " pdb=" C ASP E 156 " pdb=" CB ASP E 156 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.83e+00 ... (remaining 2073 not shown) Planarity restraints: 2403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA UNK Z 25 " -0.150 2.00e-02 2.50e+03 1.64e-01 2.70e+02 pdb=" C UNK Z 25 " 0.278 2.00e-02 2.50e+03 pdb=" O UNK Z 25 " -0.064 2.00e-02 2.50e+03 pdb=" N UNK Z 30 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 151 " 0.054 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO E 152 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO E 152 " 0.043 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 TYR L 148 " 0.043 2.00e-02 2.50e+03 2.28e-02 1.04e+01 pdb=" CG TYR L 148 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR L 148 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR L 148 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR L 148 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR L 148 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR L 148 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR L 148 " 0.020 2.00e-02 2.50e+03 ... (remaining 2400 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 10 1.98 - 2.71: 758 2.71 - 3.44: 18998 3.44 - 4.17: 30327 4.17 - 4.90: 53744 Nonbonded interactions: 103837 Sorted by model distance: nonbonded pdb=" CE1 TYR A 461 " pdb=" O GLU A 542 " model vdw 1.246 3.340 nonbonded pdb=" CE2 TYR A 461 " pdb=" CB GLU A 542 " model vdw 1.381 3.740 nonbonded pdb=" NE2 HIS N 157 " pdb=" OD2 ASP N 170 " model vdw 1.553 3.120 nonbonded pdb=" CD1 TYR A 461 " pdb=" O GLU A 542 " model vdw 1.598 3.340 nonbonded pdb=" OD2 ASP L 395 " pdb=" CA LYS L 398 " model vdw 1.626 3.470 ... (remaining 103832 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: 1.500 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: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.470 Find NCS groups from input model: 0.170 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 : 0.018 1.546 13651 Z= 1.248 Angle : 1.567 54.613 18549 Z= 0.961 Chirality : 0.089 0.554 2076 Planarity : 0.007 0.164 2403 Dihedral : 12.276 128.934 4745 Min Nonbonded Distance : 1.246 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 1.50 % Allowed : 15.56 % Favored : 82.94 % Rotamer: Outliers : 1.75 % Allowed : 5.32 % Favored : 92.93 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.74 (0.18), residues: 1600 helix: -1.89 (0.25), residues: 338 sheet: -3.49 (0.25), residues: 313 loop : -3.67 (0.17), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.006 TRP N 49 HIS 0.016 0.003 HIS A 466 PHE 0.037 0.005 PHE L 229 TYR 0.043 0.004 TYR L 148 ARG 0.008 0.001 ARG L 169 Details of bonding type rmsd hydrogen bonds : bond 0.20206 ( 352) hydrogen bonds : angle 8.12426 ( 975) SS BOND : bond 0.02640 ( 7) SS BOND : angle 3.79354 ( 14) covalent geometry : bond 0.01739 (13642) covalent geometry : angle 1.56404 (18535) Misc. bond : bond 0.26164 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 412 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.9243 (mtmt) cc_final: 0.8847 (mmtp) REVERT: K 452 CYS cc_start: 0.6545 (m) cc_final: 0.6313 (p) REVERT: K 548 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7592 (tm-30) REVERT: K 610 SER cc_start: 0.8293 (m) cc_final: 0.7851 (p) REVERT: K 680 LYS cc_start: 0.9222 (ptpt) cc_final: 0.8808 (ptpp) REVERT: K 721 GLU cc_start: 0.8818 (tt0) cc_final: 0.8548 (tt0) REVERT: K 726 TYR cc_start: 0.8591 (m-10) cc_final: 0.7925 (m-80) REVERT: K 727 ARG cc_start: 0.8115 (ttt180) cc_final: 0.7901 (mtp85) REVERT: L 94 GLN cc_start: 0.8515 (mp10) cc_final: 0.8276 (mm110) REVERT: L 195 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8492 (mm-30) REVERT: L 251 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8542 (mt) REVERT: L 292 GLN cc_start: 0.8448 (tp-100) cc_final: 0.8056 (tp40) REVERT: L 294 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8767 (mt) REVERT: L 307 ASN cc_start: 0.8023 (t0) cc_final: 0.7564 (m-40) REVERT: L 325 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8252 (mm-30) REVERT: L 435 TRP cc_start: 0.8434 (m100) cc_final: 0.8051 (m100) REVERT: M 620 HIS cc_start: 0.8213 (t-90) cc_final: 0.7908 (t-170) REVERT: M 622 MET cc_start: 0.8697 (mtt) cc_final: 0.8463 (mmt) REVERT: M 631 GLN cc_start: 0.7782 (mt0) cc_final: 0.7553 (mt0) REVERT: M 642 ASN cc_start: 0.8476 (m110) cc_final: 0.7967 (m-40) REVERT: M 665 ASP cc_start: 0.8702 (m-30) cc_final: 0.8434 (m-30) REVERT: M 675 ASP cc_start: 0.8837 (t0) cc_final: 0.8609 (p0) REVERT: N 55 ARG cc_start: 0.8247 (pmm-80) cc_final: 0.7575 (ttt180) REVERT: N 85 GLN cc_start: 0.8386 (tt0) cc_final: 0.8134 (mt0) REVERT: N 119 ILE cc_start: 0.8356 (tt) cc_final: 0.8091 (pt) REVERT: N 132 TYR cc_start: 0.9052 (p90) cc_final: 0.8739 (p90) REVERT: N 159 SER cc_start: 0.8280 (m) cc_final: 0.7599 (t) REVERT: N 238 LEU cc_start: 0.9086 (mt) cc_final: 0.8790 (mt) REVERT: N 250 GLN cc_start: 0.8311 (mt0) cc_final: 0.7870 (mp10) REVERT: N 251 LYS cc_start: 0.8430 (mttp) cc_final: 0.8228 (mtpp) REVERT: N 305 ASN cc_start: 0.8488 (t0) cc_final: 0.8242 (t0) REVERT: N 308 LEU cc_start: 0.8998 (tp) cc_final: 0.8780 (tp) REVERT: Q 120 HIS cc_start: 0.8561 (m-70) cc_final: 0.8326 (m170) REVERT: C 50 LEU cc_start: 0.9262 (tt) cc_final: 0.8868 (mm) REVERT: C 104 VAL cc_start: 0.7933 (t) cc_final: 0.7644 (m) outliers start: 23 outliers final: 13 residues processed: 430 average time/residue: 0.3147 time to fit residues: 184.9866 Evaluate side-chains 269 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 254 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 732 ASP Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 279 LEU Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 393 VAL Chi-restraints excluded: chain N residue 401 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 20.0000 chunk 129 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 127 HIS ** L 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 599 GLN N 18 ASN N 64 HIS N 88 ASN N 157 HIS N 192 HIS N 200 HIS N 226 HIS N 311 HIS ** N 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 HIS P 290 GLN ** Q 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.150348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.115049 restraints weight = 21878.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.117146 restraints weight = 12797.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.119570 restraints weight = 10340.726| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13651 Z= 0.163 Angle : 0.785 11.672 18549 Z= 0.407 Chirality : 0.048 0.290 2076 Planarity : 0.004 0.054 2403 Dihedral : 7.633 49.481 1905 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.50 % Favored : 91.06 % Rotamer: Outliers : 2.96 % Allowed : 13.37 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.39 % 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: -3.70 (0.19), residues: 1600 helix: -0.71 (0.27), residues: 348 sheet: -3.05 (0.26), residues: 293 loop : -3.08 (0.18), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 24 HIS 0.009 0.001 HIS K 282 PHE 0.024 0.002 PHE K 469 TYR 0.022 0.002 TYR K 520 ARG 0.005 0.001 ARG E 150 Details of bonding type rmsd hydrogen bonds : bond 0.04888 ( 352) hydrogen bonds : angle 5.93001 ( 975) SS BOND : bond 0.00711 ( 7) SS BOND : angle 2.89863 ( 14) covalent geometry : bond 0.00345 (13642) covalent geometry : angle 0.78117 (18535) Misc. bond : bond 0.00054 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 299 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 PHE cc_start: 0.7326 (t80) cc_final: 0.6996 (t80) REVERT: E 142 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8217 (t) REVERT: K 293 ASP cc_start: 0.7802 (t0) cc_final: 0.7086 (t0) REVERT: K 306 TYR cc_start: 0.2973 (t80) cc_final: 0.1690 (t80) REVERT: K 610 SER cc_start: 0.8127 (m) cc_final: 0.7828 (p) REVERT: K 639 SER cc_start: 0.7814 (t) cc_final: 0.7425 (m) REVERT: K 640 GLU cc_start: 0.8438 (tt0) cc_final: 0.8230 (tt0) REVERT: L 88 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7615 (tt) REVERT: L 94 GLN cc_start: 0.8078 (mp10) cc_final: 0.7798 (mm110) REVERT: L 169 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.6977 (ttm-80) REVERT: L 385 LYS cc_start: 0.7715 (mtpp) cc_final: 0.7403 (ptpt) REVERT: M 569 ASP cc_start: 0.8130 (p0) cc_final: 0.7880 (p0) REVERT: M 599 GLN cc_start: 0.8745 (tt0) cc_final: 0.8178 (tt0) REVERT: M 622 MET cc_start: 0.8679 (mtt) cc_final: 0.8434 (mmm) REVERT: M 623 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8571 (ttmt) REVERT: M 643 TYR cc_start: 0.7881 (m-80) cc_final: 0.7536 (m-80) REVERT: M 662 SER cc_start: 0.9091 (t) cc_final: 0.8684 (p) REVERT: N 19 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8048 (mm-30) REVERT: N 55 ARG cc_start: 0.7902 (pmm-80) cc_final: 0.7668 (ttt180) REVERT: N 119 ILE cc_start: 0.7860 (tt) cc_final: 0.7534 (mt) REVERT: N 250 GLN cc_start: 0.7525 (mt0) cc_final: 0.7317 (mp10) REVERT: N 318 ASP cc_start: 0.8514 (t0) cc_final: 0.8277 (t0) REVERT: C 48 LYS cc_start: 0.8647 (mttt) cc_final: 0.8356 (ptpt) REVERT: C 50 LEU cc_start: 0.8922 (tt) cc_final: 0.8696 (mm) REVERT: C 104 VAL cc_start: 0.8255 (t) cc_final: 0.7940 (m) REVERT: C 222 LYS cc_start: 0.5929 (ttpp) cc_final: 0.5381 (ptmt) outliers start: 39 outliers final: 19 residues processed: 321 average time/residue: 0.2840 time to fit residues: 133.0636 Evaluate side-chains 271 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 249 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain M residue 673 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain C residue 102 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 143 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 136 optimal weight: 0.0870 chunk 102 optimal weight: 10.0000 chunk 124 optimal weight: 0.1980 chunk 84 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 164 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS ** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 635 ASN L 326 ASN ** L 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 176 HIS N 239 HIS ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN C 57 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.148477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.112685 restraints weight = 22311.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.115236 restraints weight = 12863.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.118524 restraints weight = 9724.335| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13651 Z= 0.165 Angle : 0.714 11.360 18549 Z= 0.368 Chirality : 0.046 0.216 2076 Planarity : 0.004 0.043 2403 Dihedral : 6.858 49.962 1888 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.50 % Favored : 90.12 % Rotamer: Outliers : 4.26 % Allowed : 15.35 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.32 % 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: -3.17 (0.20), residues: 1600 helix: -0.19 (0.28), residues: 353 sheet: -2.82 (0.26), residues: 295 loop : -2.74 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 432 HIS 0.014 0.001 HIS K 282 PHE 0.021 0.002 PHE K 469 TYR 0.025 0.002 TYR L 148 ARG 0.007 0.000 ARG E 150 Details of bonding type rmsd hydrogen bonds : bond 0.04464 ( 352) hydrogen bonds : angle 5.37397 ( 975) SS BOND : bond 0.00663 ( 7) SS BOND : angle 2.84242 ( 14) covalent geometry : bond 0.00369 (13642) covalent geometry : angle 0.70954 (18535) Misc. bond : bond 0.00029 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 268 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7796 (p90) REVERT: E 142 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8121 (t) REVERT: K 530 CYS cc_start: 0.5973 (OUTLIER) cc_final: 0.5688 (m) REVERT: K 639 SER cc_start: 0.7803 (t) cc_final: 0.7405 (m) REVERT: K 662 MET cc_start: 0.7514 (mmt) cc_final: 0.7300 (mmm) REVERT: L 88 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7662 (tt) REVERT: L 94 GLN cc_start: 0.8039 (mp10) cc_final: 0.7807 (mm110) REVERT: L 125 GLU cc_start: 0.6209 (tt0) cc_final: 0.5975 (tt0) REVERT: L 136 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7748 (mt0) REVERT: L 237 ASP cc_start: 0.8681 (t0) cc_final: 0.8459 (t0) REVERT: L 385 LYS cc_start: 0.7738 (mtpp) cc_final: 0.7397 (ptpt) REVERT: M 579 MET cc_start: 0.7574 (ttm) cc_final: 0.7324 (mtp) REVERT: M 599 GLN cc_start: 0.8800 (tt0) cc_final: 0.8570 (tt0) REVERT: M 675 ASP cc_start: 0.8373 (t0) cc_final: 0.8149 (t0) REVERT: N 20 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7714 (pt0) REVERT: N 253 MET cc_start: 0.7674 (mpp) cc_final: 0.7437 (mpp) REVERT: N 360 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7820 (tp30) REVERT: Q 122 ASN cc_start: 0.7524 (t0) cc_final: 0.7300 (t0) REVERT: C 34 ARG cc_start: 0.8757 (ttm-80) cc_final: 0.8387 (ttt-90) REVERT: C 104 VAL cc_start: 0.8228 (t) cc_final: 0.7973 (m) REVERT: C 222 LYS cc_start: 0.5877 (ttpp) cc_final: 0.5291 (ptmt) outliers start: 56 outliers final: 33 residues processed: 305 average time/residue: 0.2512 time to fit residues: 111.0646 Evaluate side-chains 274 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 633 GLN Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 136 GLN Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 403 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain N residue 300 LEU Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain Q residue 115 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 29 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 30.0000 chunk 77 optimal weight: 2.9990 chunk 150 optimal weight: 30.0000 chunk 5 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 154 optimal weight: 20.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 548 GLN L 307 ASN N 177 GLN ** N 316 HIS ** 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 = 0.4108 r_free = 0.4108 target = 0.150718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.116670 restraints weight = 21668.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.117504 restraints weight = 12294.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.118761 restraints weight = 10626.999| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13651 Z= 0.131 Angle : 0.671 11.499 18549 Z= 0.344 Chirality : 0.045 0.253 2076 Planarity : 0.004 0.051 2403 Dihedral : 6.433 49.677 1888 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.38 % Favored : 91.38 % Rotamer: Outliers : 3.57 % Allowed : 16.72 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.26 % 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: -2.85 (0.20), residues: 1600 helix: 0.13 (0.28), residues: 347 sheet: -2.57 (0.27), residues: 301 loop : -2.55 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 432 HIS 0.014 0.001 HIS K 282 PHE 0.015 0.001 PHE M 656 TYR 0.020 0.001 TYR L 358 ARG 0.007 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 352) hydrogen bonds : angle 5.09676 ( 975) SS BOND : bond 0.00574 ( 7) SS BOND : angle 2.67716 ( 14) covalent geometry : bond 0.00293 (13642) covalent geometry : angle 0.66698 (18535) Misc. bond : bond 0.00019 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 142 THR cc_start: 0.8280 (p) cc_final: 0.7837 (t) REVERT: K 473 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7690 (mp0) REVERT: K 530 CYS cc_start: 0.6032 (OUTLIER) cc_final: 0.5737 (m) REVERT: K 639 SER cc_start: 0.7727 (t) cc_final: 0.7336 (m) REVERT: L 88 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7682 (tt) REVERT: L 119 ASN cc_start: 0.8309 (p0) cc_final: 0.7807 (p0) REVERT: L 125 GLU cc_start: 0.6371 (tt0) cc_final: 0.6107 (tt0) REVERT: L 136 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7630 (mt0) REVERT: L 169 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7171 (ttm-80) REVERT: L 238 GLU cc_start: 0.8087 (pt0) cc_final: 0.7401 (pt0) REVERT: L 276 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8077 (mm-30) REVERT: L 342 LYS cc_start: 0.8443 (mptm) cc_final: 0.8218 (mmtm) REVERT: M 622 MET cc_start: 0.8166 (mmm) cc_final: 0.7922 (mtm) REVERT: N 8 PHE cc_start: 0.7979 (t80) cc_final: 0.6720 (t80) REVERT: N 20 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7710 (pt0) REVERT: N 253 MET cc_start: 0.7464 (mpp) cc_final: 0.7184 (mtt) REVERT: N 297 THR cc_start: 0.8798 (p) cc_final: 0.8559 (p) REVERT: N 360 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7846 (tp30) REVERT: P 246 GLU cc_start: 0.7723 (tp30) cc_final: 0.7419 (tp30) REVERT: C 57 ASN cc_start: 0.8884 (t0) cc_final: 0.8666 (t0) REVERT: C 102 ASN cc_start: 0.7559 (OUTLIER) cc_final: 0.7237 (t0) outliers start: 47 outliers final: 27 residues processed: 295 average time/residue: 0.3157 time to fit residues: 138.4101 Evaluate side-chains 271 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 586 LEU Chi-restraints excluded: chain K residue 633 GLN Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 136 GLN Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 370 MET Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 102 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 0.1980 chunk 162 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 HIS L 307 ASN M 599 GLN N 88 ASN ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.147555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.112466 restraints weight = 22219.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.113669 restraints weight = 13369.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.117429 restraints weight = 10537.210| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13651 Z= 0.178 Angle : 0.684 10.843 18549 Z= 0.351 Chirality : 0.045 0.168 2076 Planarity : 0.004 0.050 2403 Dihedral : 6.477 57.545 1886 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.50 % Favored : 90.12 % Rotamer: Outliers : 4.26 % Allowed : 17.48 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.26 % 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 (0.20), residues: 1600 helix: 0.35 (0.29), residues: 342 sheet: -2.53 (0.27), residues: 304 loop : -2.43 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 389 HIS 0.015 0.001 HIS K 282 PHE 0.018 0.002 PHE C 32 TYR 0.022 0.002 TYR L 148 ARG 0.011 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 352) hydrogen bonds : angle 5.06337 ( 975) SS BOND : bond 0.00583 ( 7) SS BOND : angle 2.62442 ( 14) covalent geometry : bond 0.00406 (13642) covalent geometry : angle 0.68004 (18535) Misc. bond : bond 0.00036 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 244 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 530 CYS cc_start: 0.6060 (OUTLIER) cc_final: 0.5738 (m) REVERT: K 639 SER cc_start: 0.7753 (t) cc_final: 0.7353 (m) REVERT: K 721 GLU cc_start: 0.8342 (tt0) cc_final: 0.8032 (tt0) REVERT: L 88 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7628 (tt) REVERT: L 125 GLU cc_start: 0.6681 (tt0) cc_final: 0.6432 (tt0) REVERT: L 136 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7756 (mt0) REVERT: L 148 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7388 (p90) REVERT: L 276 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8016 (mm-30) REVERT: M 603 PHE cc_start: 0.7627 (m-80) cc_final: 0.7406 (m-80) REVERT: M 650 LYS cc_start: 0.8631 (tppt) cc_final: 0.8036 (tppt) REVERT: N 20 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7795 (pt0) REVERT: N 297 THR cc_start: 0.8814 (p) cc_final: 0.8568 (p) REVERT: N 360 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7939 (tp30) REVERT: P 246 GLU cc_start: 0.7742 (tp30) cc_final: 0.7393 (tp30) REVERT: C 102 ASN cc_start: 0.7691 (m110) cc_final: 0.7376 (t0) REVERT: C 222 LYS cc_start: 0.5631 (ttpt) cc_final: 0.5413 (ptmt) outliers start: 56 outliers final: 36 residues processed: 283 average time/residue: 0.2595 time to fit residues: 107.3780 Evaluate side-chains 267 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 227 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 145 SER 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 628 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 136 GLN Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain M residue 669 ILE Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 69 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 36 optimal weight: 1.9990 chunk 153 optimal weight: 20.0000 chunk 79 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 146 optimal weight: 30.0000 chunk 87 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 307 ASN N 135 GLN ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.146723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.111409 restraints weight = 22418.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.113801 restraints weight = 12702.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.116766 restraints weight = 9669.705| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13651 Z= 0.174 Angle : 0.681 11.272 18549 Z= 0.349 Chirality : 0.045 0.274 2076 Planarity : 0.004 0.053 2403 Dihedral : 6.197 55.838 1885 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.44 % Favored : 90.25 % Rotamer: Outliers : 4.26 % Allowed : 18.16 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.26 % 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: -2.59 (0.20), residues: 1600 helix: 0.44 (0.29), residues: 349 sheet: -2.41 (0.27), residues: 317 loop : -2.41 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 432 HIS 0.013 0.001 HIS K 282 PHE 0.019 0.002 PHE C 32 TYR 0.021 0.002 TYR L 148 ARG 0.013 0.001 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 352) hydrogen bonds : angle 5.05418 ( 975) SS BOND : bond 0.00593 ( 7) SS BOND : angle 2.61527 ( 14) covalent geometry : bond 0.00396 (13642) covalent geometry : angle 0.67765 (18535) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 530 CYS cc_start: 0.6014 (OUTLIER) cc_final: 0.5672 (m) REVERT: K 579 GLU cc_start: 0.7942 (tp30) cc_final: 0.7687 (tp30) REVERT: K 639 SER cc_start: 0.7743 (t) cc_final: 0.7307 (m) REVERT: K 701 MET cc_start: 0.8399 (ttm) cc_final: 0.8159 (ttt) REVERT: K 721 GLU cc_start: 0.8319 (tt0) cc_final: 0.8027 (tt0) REVERT: L 125 GLU cc_start: 0.6775 (tt0) cc_final: 0.6513 (tt0) REVERT: L 136 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7720 (mt0) REVERT: L 148 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7500 (p90) REVERT: L 276 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8111 (mm-30) REVERT: M 603 PHE cc_start: 0.7586 (m-80) cc_final: 0.7320 (m-80) REVERT: M 650 LYS cc_start: 0.8580 (tppt) cc_final: 0.8049 (tppt) REVERT: N 20 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7864 (pt0) REVERT: N 297 THR cc_start: 0.8851 (p) cc_final: 0.8604 (p) REVERT: N 360 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7909 (tp30) REVERT: C 48 LYS cc_start: 0.8555 (pttt) cc_final: 0.8302 (mtmm) REVERT: C 102 ASN cc_start: 0.7685 (m110) cc_final: 0.7377 (t0) outliers start: 56 outliers final: 39 residues processed: 279 average time/residue: 0.2822 time to fit residues: 114.5713 Evaluate side-chains 268 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 226 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain K residue 294 CYS 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 L residue 85 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 136 GLN Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 237 ASP Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain N residue 300 LEU Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 69 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 1 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 129 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 ASN ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.145129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.110025 restraints weight = 22501.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.111953 restraints weight = 13217.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.114969 restraints weight = 10323.509| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13651 Z= 0.208 Angle : 0.728 12.023 18549 Z= 0.369 Chirality : 0.047 0.309 2076 Planarity : 0.004 0.059 2403 Dihedral : 6.269 54.379 1885 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.44 % Favored : 89.31 % Rotamer: Outliers : 4.41 % Allowed : 18.84 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.26 % 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: -2.62 (0.20), residues: 1600 helix: 0.37 (0.29), residues: 352 sheet: -2.32 (0.28), residues: 313 loop : -2.48 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 432 HIS 0.015 0.001 HIS K 282 PHE 0.019 0.002 PHE C 32 TYR 0.023 0.002 TYR L 148 ARG 0.015 0.001 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 352) hydrogen bonds : angle 5.13465 ( 975) SS BOND : bond 0.00599 ( 7) SS BOND : angle 2.68560 ( 14) covalent geometry : bond 0.00475 (13642) covalent geometry : angle 0.72435 (18535) Misc. bond : bond 0.00019 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 236 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 530 CYS cc_start: 0.6030 (OUTLIER) cc_final: 0.5699 (m) REVERT: K 639 SER cc_start: 0.7785 (t) cc_final: 0.7321 (m) REVERT: K 650 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7985 (mm-30) REVERT: K 721 GLU cc_start: 0.8339 (tt0) cc_final: 0.8024 (tt0) REVERT: L 125 GLU cc_start: 0.7073 (tt0) cc_final: 0.6848 (tt0) REVERT: L 136 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7762 (mt0) REVERT: L 148 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.7494 (p90) REVERT: L 276 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8170 (mm-30) REVERT: M 603 PHE cc_start: 0.7524 (m-80) cc_final: 0.7255 (m-80) REVERT: M 650 LYS cc_start: 0.8584 (tppt) cc_final: 0.8052 (tppt) REVERT: N 8 PHE cc_start: 0.8029 (t80) cc_final: 0.7812 (t80) REVERT: N 20 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7862 (pt0) REVERT: N 297 THR cc_start: 0.8863 (p) cc_final: 0.8599 (p) REVERT: N 360 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8153 (mt-10) REVERT: P 246 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7211 (mm-30) REVERT: C 62 GLN cc_start: 0.8570 (tp40) cc_final: 0.8351 (tm-30) REVERT: C 102 ASN cc_start: 0.7757 (m110) cc_final: 0.7449 (t0) REVERT: C 222 LYS cc_start: 0.5711 (ttpt) cc_final: 0.5313 (ptmt) outliers start: 58 outliers final: 44 residues processed: 276 average time/residue: 0.2794 time to fit residues: 114.5106 Evaluate side-chains 273 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 226 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain K residue 294 CYS Chi-restraints excluded: chain K residue 521 GLN 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 L residue 85 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 136 GLN Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 237 ASP Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain M residue 669 ILE Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain N residue 300 LEU Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 69 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 154 optimal weight: 20.0000 chunk 78 optimal weight: 0.0970 chunk 72 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 307 ASN N 123 HIS ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.149305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.115473 restraints weight = 22259.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.116228 restraints weight = 11917.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.118943 restraints weight = 9844.777| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13651 Z= 0.126 Angle : 0.675 10.973 18549 Z= 0.342 Chirality : 0.044 0.283 2076 Planarity : 0.004 0.062 2403 Dihedral : 5.851 53.951 1885 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.62 % Favored : 91.25 % Rotamer: Outliers : 3.50 % Allowed : 19.68 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.26 % 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 (0.21), residues: 1600 helix: 0.50 (0.29), residues: 349 sheet: -2.04 (0.29), residues: 307 loop : -2.39 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP K 432 HIS 0.011 0.001 HIS K 282 PHE 0.025 0.001 PHE C 32 TYR 0.017 0.001 TYR N 284 ARG 0.015 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 352) hydrogen bonds : angle 4.99005 ( 975) SS BOND : bond 0.00653 ( 7) SS BOND : angle 2.70835 ( 14) covalent geometry : bond 0.00281 (13642) covalent geometry : angle 0.67074 (18535) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 250 time to evaluate : 1.620 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 473 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7907 (mp0) REVERT: K 530 CYS cc_start: 0.6130 (OUTLIER) cc_final: 0.5768 (m) REVERT: K 721 GLU cc_start: 0.8174 (tt0) cc_final: 0.7880 (tt0) REVERT: L 125 GLU cc_start: 0.6914 (tt0) cc_final: 0.6708 (tt0) REVERT: L 136 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7529 (mt0) REVERT: L 148 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.7457 (p90) REVERT: L 294 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8530 (mp) REVERT: M 603 PHE cc_start: 0.7504 (m-80) cc_final: 0.7270 (m-80) REVERT: N 253 MET cc_start: 0.7432 (mpp) cc_final: 0.7147 (mtt) REVERT: N 297 THR cc_start: 0.8798 (p) cc_final: 0.8540 (p) REVERT: N 360 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7893 (tp30) REVERT: P 246 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7075 (mm-30) REVERT: C 37 GLU cc_start: 0.7772 (pp20) cc_final: 0.7555 (pp20) REVERT: C 62 GLN cc_start: 0.8714 (tp40) cc_final: 0.8484 (tm-30) REVERT: C 102 ASN cc_start: 0.7624 (m110) cc_final: 0.7366 (t0) REVERT: C 222 LYS cc_start: 0.5528 (ttpt) cc_final: 0.5266 (ptmt) outliers start: 46 outliers final: 33 residues processed: 275 average time/residue: 0.2497 time to fit residues: 100.3058 Evaluate side-chains 274 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain K residue 294 CYS Chi-restraints excluded: chain K residue 521 GLN Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 136 GLN Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 237 ASP Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 669 ILE Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain N residue 300 LEU Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 69 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 19 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 47 optimal weight: 0.0870 chunk 73 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 ASN M 599 GLN ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.149436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.113860 restraints weight = 21874.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.115975 restraints weight = 11864.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.118375 restraints weight = 9583.670| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13651 Z= 0.167 Angle : 0.717 11.831 18549 Z= 0.363 Chirality : 0.045 0.275 2076 Planarity : 0.005 0.088 2403 Dihedral : 5.888 51.266 1884 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.56 % Favored : 90.25 % Rotamer: Outliers : 3.12 % Allowed : 20.14 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.26 % 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: -2.42 (0.21), residues: 1600 helix: 0.52 (0.29), residues: 349 sheet: -2.07 (0.28), residues: 317 loop : -2.38 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP N 235 HIS 0.012 0.001 HIS K 282 PHE 0.026 0.002 PHE C 32 TYR 0.020 0.001 TYR L 148 ARG 0.016 0.001 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 352) hydrogen bonds : angle 4.99024 ( 975) SS BOND : bond 0.00703 ( 7) SS BOND : angle 2.70021 ( 14) covalent geometry : bond 0.00383 (13642) covalent geometry : angle 0.71378 (18535) Misc. bond : bond 0.00014 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 237 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 473 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7926 (mp0) REVERT: K 530 CYS cc_start: 0.6168 (OUTLIER) cc_final: 0.5786 (m) REVERT: K 721 GLU cc_start: 0.8225 (tt0) cc_final: 0.7917 (tt0) REVERT: L 136 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7650 (mt0) REVERT: L 148 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.7514 (p90) REVERT: L 294 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8584 (mp) REVERT: L 376 MET cc_start: 0.8359 (mtp) cc_final: 0.7827 (ttt) REVERT: M 603 PHE cc_start: 0.7383 (m-80) cc_final: 0.7171 (m-80) REVERT: N 297 THR cc_start: 0.8870 (p) cc_final: 0.8659 (p) REVERT: N 360 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7913 (tp30) REVERT: P 246 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7281 (tp30) REVERT: Q 99 PHE cc_start: 0.8790 (t80) cc_final: 0.8562 (t80) REVERT: C 62 GLN cc_start: 0.8593 (tp40) cc_final: 0.8366 (tm-30) REVERT: C 102 ASN cc_start: 0.7609 (m110) cc_final: 0.7382 (t0) REVERT: C 222 LYS cc_start: 0.5551 (ttpt) cc_final: 0.5294 (ptmt) outliers start: 41 outliers final: 32 residues processed: 259 average time/residue: 0.2551 time to fit residues: 97.0895 Evaluate side-chains 265 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 229 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain K residue 294 CYS Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 136 GLN Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 237 ASP Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain M residue 663 MET Chi-restraints excluded: chain M residue 669 ILE Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain N residue 300 LEU Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 69 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 63 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 0.0770 chunk 29 optimal weight: 0.0970 chunk 100 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 7 optimal weight: 0.0000 chunk 2 optimal weight: 0.8980 chunk 133 optimal weight: 0.0030 chunk 82 optimal weight: 5.9990 overall best weight: 0.2150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 607 GLN L 307 ASN ** L 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.155264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.119415 restraints weight = 21681.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.122801 restraints weight = 11749.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.123707 restraints weight = 9036.973| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3749 r_free = 0.3749 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3749 r_free = 0.3749 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13651 Z= 0.120 Angle : 0.690 12.548 18549 Z= 0.349 Chirality : 0.044 0.253 2076 Planarity : 0.004 0.071 2403 Dihedral : 5.561 49.364 1884 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.38 % Favored : 92.44 % Rotamer: Outliers : 2.13 % Allowed : 21.50 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -2.26 (0.21), residues: 1600 helix: 0.53 (0.29), residues: 348 sheet: -1.70 (0.29), residues: 321 loop : -2.33 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP N 235 HIS 0.010 0.001 HIS K 282 PHE 0.028 0.001 PHE C 32 TYR 0.020 0.001 TYR N 284 ARG 0.017 0.001 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 352) hydrogen bonds : angle 4.89758 ( 975) SS BOND : bond 0.00618 ( 7) SS BOND : angle 2.60356 ( 14) covalent geometry : bond 0.00261 (13642) covalent geometry : angle 0.68639 (18535) Misc. bond : bond 0.00130 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 249 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 473 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7909 (mp0) REVERT: K 530 CYS cc_start: 0.6025 (OUTLIER) cc_final: 0.5632 (m) REVERT: K 721 GLU cc_start: 0.7916 (tt0) cc_final: 0.7599 (tt0) REVERT: L 136 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7419 (mt0) REVERT: L 148 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.7418 (p90) REVERT: L 294 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8562 (mp) REVERT: M 603 PHE cc_start: 0.7465 (m-80) cc_final: 0.7230 (m-80) REVERT: N 297 THR cc_start: 0.8850 (p) cc_final: 0.8641 (p) REVERT: N 360 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7979 (tp30) REVERT: C 62 GLN cc_start: 0.8678 (tp40) cc_final: 0.8323 (tm-30) REVERT: C 65 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7683 (mm) REVERT: C 118 GLN cc_start: 0.8111 (pt0) cc_final: 0.7856 (tt0) REVERT: C 222 LYS cc_start: 0.5573 (ttpt) cc_final: 0.5338 (ptmt) outliers start: 28 outliers final: 18 residues processed: 266 average time/residue: 0.2385 time to fit residues: 93.7784 Evaluate side-chains 252 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain L residue 136 GLN Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 237 ASP Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain M residue 663 MET Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain N residue 300 LEU Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 167 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 105 optimal weight: 0.0770 chunk 122 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 94 optimal weight: 5.9990 chunk 147 optimal weight: 30.0000 overall best weight: 2.8944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 ASN ** L 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.147888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.113324 restraints weight = 22244.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.114372 restraints weight = 12163.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.115948 restraints weight = 10365.255| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13651 Z= 0.231 Angle : 0.781 12.248 18549 Z= 0.396 Chirality : 0.048 0.253 2076 Planarity : 0.005 0.072 2403 Dihedral : 5.766 44.045 1880 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.88 % Favored : 89.88 % Rotamer: Outliers : 2.51 % Allowed : 21.50 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.26 % 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: -2.34 (0.21), residues: 1600 helix: 0.58 (0.29), residues: 349 sheet: -1.95 (0.28), residues: 344 loop : -2.35 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP N 235 HIS 0.011 0.001 HIS K 282 PHE 0.038 0.002 PHE K 290 TYR 0.022 0.002 TYR L 148 ARG 0.017 0.001 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.04333 ( 352) hydrogen bonds : angle 5.00551 ( 975) SS BOND : bond 0.00922 ( 7) SS BOND : angle 3.07843 ( 14) covalent geometry : bond 0.00532 (13642) covalent geometry : angle 0.77676 (18535) Misc. bond : bond 0.00011 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5182.13 seconds wall clock time: 92 minutes 53.36 seconds (5573.36 seconds total)