Starting phenix.real_space_refine on Thu Sep 18 02:38:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c24_7335/09_2025/6c24_7335.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c24_7335/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6c24_7335/09_2025/6c24_7335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c24_7335/09_2025/6c24_7335.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6c24_7335/09_2025/6c24_7335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c24_7335/09_2025/6c24_7335.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASN:plan1': 5, 'ARG:plan': 5, 'GLN:plan1': 4, 'GLU:plan': 5, 'TYR:plan': 1, 'HIS:plan': 2, 'ASP:plan': 4, 'PHE:plan': 1} 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: {'ARG:plan': 1, 'M3L:plan-1': 1, 'GLN:plan1': 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: {'GLU:plan': 8, 'ARG:plan': 5, 'TYR:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 7, 'PHE:plan': 1, 'GLN:plan1': 5, 'ASP:plan': 3} 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: {'GLU:plan': 4, 'GLN:plan1': 1, '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: {'GLU:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG: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: {'ASP:plan': 1, 'GLU:plan': 2} 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: {'GLU:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1, 'TYR: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: {'GLU:plan': 3, 'GLN:plan1': 1, '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: 3.29, per 1000 atoms: 0.25 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: 1.08 Conformation dependent library (CDL) restraints added in 486.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.43 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: 2.10 Time building geometry restraints manager: 1.41 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: 1.890 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.870 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.480 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG L 169 TYR 0.043 0.004 TYR L 148 PHE 0.037 0.005 PHE L 229 TRP 0.038 0.006 TRP N 49 HIS 0.016 0.003 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.01739 (13642) covalent geometry : angle 1.56404 (18535) SS BOND : bond 0.02640 ( 7) SS BOND : angle 3.79354 ( 14) hydrogen bonds : bond 0.20206 ( 352) hydrogen bonds : angle 8.12426 ( 975) 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 : 0.555 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: 0.6314 (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: 0.7927 (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: 0.7924 (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: 0.7563 (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: 0.7552 (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: 0.8433 (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: 0.8090 (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: 0.7598 (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: 0.8327 (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: 0.1375 time to fit residues: 81.0783 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 : 0.413 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 185 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 316 HIS ** 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 = 0.4092 r_free = 0.4092 target = 0.149457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.115611 restraints weight = 21833.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.118406 restraints weight = 14319.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.119470 restraints weight = 10283.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.120051 restraints weight = 8629.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.120455 restraints weight = 8016.978| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3695 r_free = 0.3695 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13651 Z= 0.175 Angle : 0.789 12.500 18549 Z= 0.409 Chirality : 0.049 0.283 2076 Planarity : 0.004 0.053 2403 Dihedral : 7.716 50.005 1905 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.56 % Favored : 90.94 % Rotamer: Outliers : 3.34 % Allowed : 13.75 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.71 (0.19), residues: 1600 helix: -0.74 (0.27), residues: 353 sheet: -3.08 (0.26), residues: 294 loop : -3.08 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 150 TYR 0.024 0.002 TYR L 148 PHE 0.024 0.002 PHE K 469 TRP 0.021 0.002 TRP N 24 HIS 0.009 0.001 HIS K 282 Details of bonding type rmsd covalent geometry : bond 0.00389 (13642) covalent geometry : angle 0.78496 (18535) SS BOND : bond 0.00686 ( 7) SS BOND : angle 2.89992 ( 14) hydrogen bonds : bond 0.04830 ( 352) hydrogen bonds : angle 5.91098 ( 975) Misc. bond : bond 0.00177 ( 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 334 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 290 time to evaluate : 0.522 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: A 474 PHE cc_start: 0.8046 (p90) cc_final: 0.7653 (p90) REVERT: E 142 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8257 (t) REVERT: K 306 TYR cc_start: 0.2919 (t80) cc_final: 0.1775 (t80) REVERT: K 639 SER cc_start: 0.7881 (t) cc_final: 0.7445 (m) REVERT: K 640 GLU cc_start: 0.8391 (tt0) cc_final: 0.8177 (tt0) REVERT: K 720 GLU cc_start: 0.8057 (tt0) cc_final: 0.7815 (tt0) REVERT: L 88 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7565 (tt) REVERT: L 94 GLN cc_start: 0.8040 (mp10) cc_final: 0.7753 (mm110) REVERT: L 109 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8320 (t70) REVERT: L 169 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7088 (ttm-80) REVERT: L 172 ILE cc_start: 0.9178 (mt) cc_final: 0.8943 (mm) REVERT: L 237 ASP cc_start: 0.8487 (t0) cc_final: 0.8239 (t0) REVERT: L 251 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8444 (mt) REVERT: L 325 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7679 (mm-30) REVERT: M 569 ASP cc_start: 0.8104 (p0) cc_final: 0.7855 (p0) REVERT: M 599 GLN cc_start: 0.8704 (tt0) cc_final: 0.8435 (tt0) REVERT: M 620 HIS cc_start: 0.7811 (t-90) cc_final: 0.7606 (t-170) REVERT: M 643 TYR cc_start: 0.7780 (m-80) cc_final: 0.7395 (m-80) REVERT: M 662 SER cc_start: 0.9021 (t) cc_final: 0.8648 (p) REVERT: N 19 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8041 (mm-30) REVERT: N 250 GLN cc_start: 0.7593 (mt0) cc_final: 0.7373 (mp10) REVERT: C 48 LYS cc_start: 0.8584 (mttt) cc_final: 0.8302 (ptpt) REVERT: C 50 LEU cc_start: 0.8902 (tt) cc_final: 0.8694 (mm) REVERT: C 104 VAL cc_start: 0.8221 (t) cc_final: 0.7946 (m) REVERT: C 222 LYS cc_start: 0.5843 (ttpp) cc_final: 0.5184 (ptmt) outliers start: 44 outliers final: 23 residues processed: 316 average time/residue: 0.1076 time to fit residues: 50.3576 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 : 0.506 ------------------------------------------------------------------------------- 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 109 ASP 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 241 SER Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 403 THR Chi-restraints excluded: chain M residue 673 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 146 SER 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 131 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 150 optimal weight: 30.0000 chunk 15 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 272 HIS ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 343 ASN ** 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 = 0.4011 r_free = 0.4011 target = 0.142574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.107474 restraints weight = 22763.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.109467 restraints weight = 12806.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.112289 restraints weight = 10453.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.112678 restraints weight = 8626.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.112459 restraints weight = 7524.274| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 13651 Z= 0.304 Angle : 0.823 12.383 18549 Z= 0.425 Chirality : 0.051 0.279 2076 Planarity : 0.005 0.049 2403 Dihedral : 7.693 56.984 1892 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.81 % Favored : 87.75 % Rotamer: Outliers : 5.47 % Allowed : 15.88 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.45 (0.20), residues: 1600 helix: -0.40 (0.27), residues: 354 sheet: -3.05 (0.25), residues: 315 loop : -2.89 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 150 TYR 0.031 0.002 TYR L 148 PHE 0.024 0.003 PHE A 474 TRP 0.019 0.003 TRP P 253 HIS 0.018 0.002 HIS K 282 Details of bonding type rmsd covalent geometry : bond 0.00680 (13642) covalent geometry : angle 0.81898 (18535) SS BOND : bond 0.00704 ( 7) SS BOND : angle 3.04333 ( 14) hydrogen bonds : bond 0.05209 ( 352) hydrogen bonds : angle 5.68447 ( 975) Misc. bond : bond 0.00027 ( 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 329 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 257 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 142 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8303 (t) REVERT: K 650 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8267 (mm-30) REVERT: L 88 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7706 (tt) REVERT: L 94 GLN cc_start: 0.8111 (mp10) cc_final: 0.7815 (mm110) REVERT: L 136 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7895 (mt0) REVERT: L 148 TYR cc_start: 0.8296 (OUTLIER) cc_final: 0.7402 (p90) REVERT: L 307 ASN cc_start: 0.7646 (m-40) cc_final: 0.7305 (m110) REVERT: L 342 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8305 (mmtm) REVERT: L 435 TRP cc_start: 0.7208 (m100) cc_final: 0.6926 (m100) REVERT: M 675 ASP cc_start: 0.8331 (t0) cc_final: 0.8103 (t0) REVERT: N 250 GLN cc_start: 0.7778 (mt0) cc_final: 0.7349 (mp10) REVERT: N 360 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7848 (tp30) REVERT: Q 100 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9112 (mp) REVERT: C 104 VAL cc_start: 0.8137 (t) cc_final: 0.7871 (m) outliers start: 72 outliers final: 40 residues processed: 307 average time/residue: 0.1104 time to fit residues: 49.6873 Evaluate side-chains 280 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 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 628 ILE 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 148 TYR 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 241 SER Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 342 LYS Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 404 LEU Chi-restraints excluded: chain N residue 18 ASN Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 86 LEU 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 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 366 LEU 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 P residue 276 THR Chi-restraints excluded: chain Q residue 100 LEU 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 5 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 599 GLN ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.146084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.110699 restraints weight = 22353.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.113126 restraints weight = 12724.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.116220 restraints weight = 9714.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.116244 restraints weight = 8116.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.116186 restraints weight = 7120.411| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 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 = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13651 Z= 0.155 Angle : 0.701 10.921 18549 Z= 0.360 Chirality : 0.046 0.217 2076 Planarity : 0.004 0.045 2403 Dihedral : 6.859 59.238 1891 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.88 % Favored : 90.81 % Rotamer: Outliers : 4.56 % Allowed : 18.47 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.01 (0.20), residues: 1600 helix: 0.10 (0.28), residues: 348 sheet: -2.76 (0.26), residues: 315 loop : -2.65 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 81 TYR 0.022 0.001 TYR L 148 PHE 0.012 0.001 PHE K 673 TRP 0.020 0.002 TRP K 432 HIS 0.017 0.001 HIS K 282 Details of bonding type rmsd covalent geometry : bond 0.00350 (13642) covalent geometry : angle 0.69652 (18535) SS BOND : bond 0.00586 ( 7) SS BOND : angle 2.80329 ( 14) hydrogen bonds : bond 0.04281 ( 352) hydrogen bonds : angle 5.30982 ( 975) Misc. bond : bond 0.00027 ( 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 322 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 262 time to evaluate : 0.498 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: 0.8472 (OUTLIER) cc_final: 0.8017 (t) REVERT: K 473 GLU cc_start: 0.8075 (mp0) cc_final: 0.7735 (mp0) REVERT: K 639 SER cc_start: 0.7839 (t) cc_final: 0.7366 (m) REVERT: L 88 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7598 (tt) REVERT: L 136 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7594 (mt0) REVERT: L 294 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8706 (mt) REVERT: L 342 LYS cc_start: 0.8545 (mptm) cc_final: 0.8288 (mmtm) REVERT: M 599 GLN cc_start: 0.8851 (tt0) cc_final: 0.8622 (tt0) REVERT: N 119 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7695 (pt) REVERT: N 297 THR cc_start: 0.8964 (p) cc_final: 0.8757 (p) REVERT: N 360 GLU cc_start: 0.8464 (mt-10) cc_final: 0.7889 (tp30) REVERT: P 246 GLU cc_start: 0.7775 (tp30) cc_final: 0.7393 (tp30) REVERT: P 291 LYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6681 (mtmm) REVERT: C 62 GLN cc_start: 0.8615 (tp40) cc_final: 0.8392 (tm-30) REVERT: C 104 VAL cc_start: 0.8170 (t) cc_final: 0.7875 (m) REVERT: C 118 GLN cc_start: 0.8159 (pt0) cc_final: 0.7746 (tt0) REVERT: C 222 LYS cc_start: 0.5730 (ttpt) cc_final: 0.5404 (ptmt) outliers start: 60 outliers final: 34 residues processed: 300 average time/residue: 0.1155 time to fit residues: 50.2161 Evaluate side-chains 274 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 261 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 K residue 586 LEU 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 241 SER Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain N residue 18 ASN 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 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 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 268 HIS Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain P residue 291 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 19 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 ASN ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 328 HIS ** 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 = 0.4051 r_free = 0.4051 target = 0.145467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.111441 restraints weight = 22586.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.112598 restraints weight = 12121.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.114874 restraints weight = 10532.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.115189 restraints weight = 8894.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.115267 restraints weight = 7714.596| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13651 Z= 0.218 Angle : 0.733 12.110 18549 Z= 0.376 Chirality : 0.047 0.287 2076 Planarity : 0.004 0.053 2403 Dihedral : 6.803 56.114 1891 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.06 % Favored : 88.56 % Rotamer: Outliers : 5.93 % Allowed : 17.86 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.96 (0.20), residues: 1600 helix: 0.17 (0.28), residues: 343 sheet: -2.80 (0.27), residues: 304 loop : -2.61 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 81 TYR 0.027 0.002 TYR L 148 PHE 0.016 0.002 PHE M 656 TRP 0.014 0.002 TRP L 389 HIS 0.014 0.001 HIS K 282 Details of bonding type rmsd covalent geometry : bond 0.00497 (13642) covalent geometry : angle 0.72925 (18535) SS BOND : bond 0.00658 ( 7) SS BOND : angle 2.85281 ( 14) hydrogen bonds : bond 0.04523 ( 352) hydrogen bonds : angle 5.25080 ( 975) Misc. bond : bond 0.00048 ( 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 318 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 240 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 142 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8033 (t) REVERT: K 530 CYS cc_start: 0.6210 (OUTLIER) cc_final: 0.5875 (m) REVERT: K 639 SER cc_start: 0.7778 (t) cc_final: 0.7266 (m) REVERT: L 88 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7667 (tt) REVERT: L 136 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7797 (mt0) REVERT: L 148 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7441 (p90) REVERT: L 276 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8105 (mm-30) REVERT: L 294 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8660 (mt) REVERT: N 360 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7956 (tp30) REVERT: P 291 LYS cc_start: 0.7202 (OUTLIER) cc_final: 0.6859 (mtmm) REVERT: C 62 GLN cc_start: 0.8605 (tp40) cc_final: 0.8389 (tm-30) REVERT: C 104 VAL cc_start: 0.8191 (t) cc_final: 0.7946 (m) REVERT: C 118 GLN cc_start: 0.8124 (pt0) cc_final: 0.7750 (tt0) REVERT: C 222 LYS cc_start: 0.5732 (ttpt) cc_final: 0.5407 (ptmt) outliers start: 78 outliers final: 48 residues processed: 295 average time/residue: 0.1067 time to fit residues: 46.3419 Evaluate side-chains 278 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 223 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 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 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 237 ASP Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain M residue 596 THR Chi-restraints excluded: chain M residue 622 MET Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 68 LEU 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 230 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 245 SER 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 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 P residue 268 HIS Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain P residue 291 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 Chi-restraints excluded: chain C residue 101 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 17 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 166 optimal weight: 1.9990 chunk 136 optimal weight: 0.0770 overall best weight: 1.1144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.149579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.111397 restraints weight = 22062.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.115180 restraints weight = 12774.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.117627 restraints weight = 9217.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.119222 restraints weight = 7495.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.120034 restraints weight = 6550.841| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13651 Z= 0.134 Angle : 0.674 11.254 18549 Z= 0.345 Chirality : 0.045 0.167 2076 Planarity : 0.004 0.052 2403 Dihedral : 6.273 55.123 1891 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.56 % Favored : 91.25 % Rotamer: Outliers : 4.26 % Allowed : 19.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.74 (0.20), residues: 1600 helix: 0.33 (0.29), residues: 343 sheet: -2.52 (0.27), residues: 310 loop : -2.50 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 81 TYR 0.041 0.001 TYR K 728 PHE 0.015 0.001 PHE M 656 TRP 0.021 0.002 TRP K 432 HIS 0.012 0.001 HIS K 282 Details of bonding type rmsd covalent geometry : bond 0.00302 (13642) covalent geometry : angle 0.67007 (18535) SS BOND : bond 0.00579 ( 7) SS BOND : angle 2.77640 ( 14) hydrogen bonds : bond 0.03952 ( 352) hydrogen bonds : angle 5.04131 ( 975) Misc. bond : bond 0.00011 ( 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 311 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 255 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 473 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7823 (mp0) REVERT: K 530 CYS cc_start: 0.6057 (OUTLIER) cc_final: 0.5676 (m) REVERT: K 721 GLU cc_start: 0.8249 (tt0) cc_final: 0.7979 (tt0) REVERT: L 88 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7504 (tt) REVERT: L 136 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7490 (mt0) REVERT: L 276 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7978 (mm-30) REVERT: L 294 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8718 (mt) REVERT: N 297 THR cc_start: 0.8973 (p) cc_final: 0.8746 (p) REVERT: P 246 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7311 (tp30) REVERT: P 251 ASP cc_start: 0.8283 (m-30) cc_final: 0.8081 (m-30) REVERT: P 291 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6910 (mtmm) REVERT: C 102 ASN cc_start: 0.7727 (m110) cc_final: 0.7349 (t0) REVERT: C 118 GLN cc_start: 0.8132 (pt0) cc_final: 0.7732 (tt0) REVERT: C 222 LYS cc_start: 0.5784 (ttpt) cc_final: 0.5497 (ptmt) outliers start: 56 outliers final: 37 residues processed: 289 average time/residue: 0.1098 time to fit residues: 46.4344 Evaluate side-chains 280 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 238 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 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 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 149 THR Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 290 ILE Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain M residue 622 MET Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 115 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 300 LEU Chi-restraints excluded: chain N residue 308 LEU 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 P residue 239 LEU Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain P residue 291 LYS Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 101 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 155 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 703 ASN ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 ASN ** N 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 177 GLN ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 385 ASN P 242 HIS Q 122 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.139579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.105491 restraints weight = 23134.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.106340 restraints weight = 13028.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.109211 restraints weight = 11060.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.109302 restraints weight = 9250.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.109220 restraints weight = 7978.874| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.090 13651 Z= 0.429 Angle : 0.900 13.693 18549 Z= 0.463 Chirality : 0.054 0.272 2076 Planarity : 0.006 0.090 2403 Dihedral : 7.374 59.638 1888 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.56 % Favored : 87.06 % Rotamer: Outliers : 6.08 % Allowed : 18.92 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.14 (0.20), residues: 1600 helix: 0.03 (0.28), residues: 341 sheet: -2.78 (0.25), residues: 326 loop : -2.75 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 81 TYR 0.031 0.003 TYR K 728 PHE 0.031 0.003 PHE K 724 TRP 0.020 0.003 TRP N 49 HIS 0.016 0.002 HIS K 282 Details of bonding type rmsd covalent geometry : bond 0.00976 (13642) covalent geometry : angle 0.89633 (18535) SS BOND : bond 0.00714 ( 7) SS BOND : angle 3.00289 ( 14) hydrogen bonds : bond 0.05403 ( 352) hydrogen bonds : angle 5.59657 ( 975) Misc. bond : bond 0.00029 ( 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 319 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 239 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 CYS cc_start: 0.8574 (m) cc_final: 0.8286 (m) REVERT: K 721 GLU cc_start: 0.8537 (tt0) cc_final: 0.8309 (tt0) REVERT: L 136 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8054 (mt0) REVERT: L 148 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7955 (p90) REVERT: L 294 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8670 (mt) REVERT: L 307 ASN cc_start: 0.7330 (m-40) cc_final: 0.6890 (t0) REVERT: L 435 TRP cc_start: 0.7253 (m100) cc_final: 0.7052 (m100) REVERT: M 650 LYS cc_start: 0.8558 (tppt) cc_final: 0.7961 (tppt) REVERT: N 360 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8070 (tp30) REVERT: P 246 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7417 (tp30) REVERT: P 291 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7132 (mtmm) outliers start: 80 outliers final: 63 residues processed: 295 average time/residue: 0.1089 time to fit residues: 48.0267 Evaluate side-chains 290 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 223 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 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 284 LEU Chi-restraints excluded: chain K residue 294 CYS Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 586 LEU Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain K residue 703 ASN Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 116 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 169 ARG Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 237 ASP Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 290 ILE Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain L residue 366 MET Chi-restraints excluded: chain L residue 376 MET Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 424 ILE Chi-restraints excluded: chain M residue 596 THR Chi-restraints excluded: chain M residue 622 MET Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 68 LEU 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 142 THR Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 189 LEU 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 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 256 GLU Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain P residue 291 LYS Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 101 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 28 optimal weight: 0.9990 chunk 147 optimal weight: 30.0000 chunk 125 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 126 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 99 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 607 GLN L 127 HIS L 185 HIS L 292 GLN N 123 HIS ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.148507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.114500 restraints weight = 21928.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.115672 restraints weight = 11800.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.117299 restraints weight = 10173.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.117934 restraints weight = 8624.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.117973 restraints weight = 7576.441| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 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 = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13651 Z= 0.138 Angle : 0.720 11.846 18549 Z= 0.366 Chirality : 0.046 0.235 2076 Planarity : 0.004 0.076 2403 Dihedral : 6.417 53.938 1888 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.25 % Favored : 91.56 % Rotamer: Outliers : 4.18 % Allowed : 21.73 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.82 (0.20), residues: 1600 helix: 0.32 (0.29), residues: 350 sheet: -2.55 (0.27), residues: 311 loop : -2.61 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 81 TYR 0.042 0.002 TYR K 728 PHE 0.029 0.001 PHE K 724 TRP 0.016 0.002 TRP K 432 HIS 0.012 0.001 HIS K 282 Details of bonding type rmsd covalent geometry : bond 0.00308 (13642) covalent geometry : angle 0.71603 (18535) SS BOND : bond 0.00622 ( 7) SS BOND : angle 2.87541 ( 14) hydrogen bonds : bond 0.04092 ( 352) hydrogen bonds : angle 5.11524 ( 975) Misc. bond : bond 0.00006 ( 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 298 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 243 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 470 CYS cc_start: 0.8509 (m) cc_final: 0.8307 (m) REVERT: K 530 CYS cc_start: 0.6269 (OUTLIER) cc_final: 0.5860 (m) REVERT: K 721 GLU cc_start: 0.8297 (tt0) cc_final: 0.8003 (tt0) REVERT: L 136 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7540 (mt0) REVERT: L 148 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.7303 (p90) REVERT: L 294 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8645 (mt) REVERT: M 650 LYS cc_start: 0.8511 (tppt) cc_final: 0.7871 (tppt) REVERT: N 119 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7612 (pt) REVERT: N 194 LEU cc_start: 0.9180 (mt) cc_final: 0.8951 (mt) REVERT: N 235 TRP cc_start: 0.8955 (m100) cc_final: 0.8749 (m100) REVERT: N 360 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7865 (tp30) REVERT: P 246 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7367 (tp30) REVERT: P 251 ASP cc_start: 0.8264 (m-30) cc_final: 0.8044 (m-30) REVERT: Q 105 LEU cc_start: 0.9385 (mm) cc_final: 0.9166 (mt) REVERT: C 34 ARG cc_start: 0.9020 (ttm170) cc_final: 0.8624 (mmm-85) REVERT: C 65 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7862 (mm) REVERT: C 102 ASN cc_start: 0.7890 (m110) cc_final: 0.7487 (t0) outliers start: 55 outliers final: 38 residues processed: 283 average time/residue: 0.1149 time to fit residues: 48.2544 Evaluate side-chains 275 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 231 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 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 674 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 VAL 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 221 GLN Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 237 ASP Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain L residue 376 MET Chi-restraints excluded: chain M residue 596 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 68 LEU 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 189 LEU 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 308 LEU 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 115 LEU Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 101 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 60 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 170 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 N 135 GLN ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.149064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.114512 restraints weight = 22386.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.115875 restraints weight = 12016.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.117384 restraints weight = 10181.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.118060 restraints weight = 8837.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.118130 restraints weight = 7781.755| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 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 = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13651 Z= 0.140 Angle : 0.710 12.157 18549 Z= 0.359 Chirality : 0.045 0.376 2076 Planarity : 0.004 0.065 2403 Dihedral : 6.080 51.149 1888 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.69 % Favored : 90.19 % Rotamer: Outliers : 3.57 % Allowed : 22.72 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.65 (0.20), residues: 1600 helix: 0.40 (0.29), residues: 349 sheet: -2.39 (0.27), residues: 318 loop : -2.48 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 81 TYR 0.020 0.001 TYR L 148 PHE 0.028 0.001 PHE N 8 TRP 0.013 0.001 TRP N 49 HIS 0.011 0.001 HIS K 282 Details of bonding type rmsd covalent geometry : bond 0.00315 (13642) covalent geometry : angle 0.70630 (18535) SS BOND : bond 0.00578 ( 7) SS BOND : angle 2.73910 ( 14) hydrogen bonds : bond 0.04045 ( 352) hydrogen bonds : angle 4.99724 ( 975) Misc. bond : bond 0.00006 ( 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 294 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 247 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 CYS cc_start: 0.8509 (m) cc_final: 0.8307 (m) REVERT: K 530 CYS cc_start: 0.6050 (OUTLIER) cc_final: 0.5601 (m) REVERT: K 612 LYS cc_start: 0.8470 (mmmt) cc_final: 0.8222 (mmtm) REVERT: K 720 GLU cc_start: 0.8124 (tt0) cc_final: 0.7819 (tt0) REVERT: K 721 GLU cc_start: 0.8249 (tt0) cc_final: 0.7925 (tt0) REVERT: L 136 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7622 (mt0) REVERT: L 148 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7499 (p90) REVERT: L 294 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8657 (mt) REVERT: N 119 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7651 (pt) REVERT: N 360 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7950 (tp30) REVERT: P 246 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7339 (tp30) REVERT: P 251 ASP cc_start: 0.8291 (m-30) cc_final: 0.7993 (m-30) REVERT: P 291 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6973 (mtmm) REVERT: Q 105 LEU cc_start: 0.9377 (mm) cc_final: 0.9146 (mt) REVERT: C 34 ARG cc_start: 0.9035 (ttm170) cc_final: 0.8650 (mmm-85) REVERT: C 65 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7839 (mm) REVERT: C 102 ASN cc_start: 0.7695 (m110) cc_final: 0.7343 (t0) outliers start: 47 outliers final: 39 residues processed: 278 average time/residue: 0.1139 time to fit residues: 46.9406 Evaluate side-chains 282 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 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 674 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 VAL 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 221 GLN Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 237 ASP Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain L residue 370 MET Chi-restraints excluded: chain L residue 376 MET Chi-restraints excluded: chain M residue 622 MET Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 68 LEU 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 189 LEU 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 300 LEU Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain P residue 291 LYS Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 77 optimal weight: 5.9990 chunk 135 optimal weight: 0.0570 chunk 27 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 46 optimal weight: 0.0170 chunk 36 optimal weight: 0.9980 chunk 153 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 overall best weight: 1.5938 ------------------------------------------------------------------------------- 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** ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.148413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.109805 restraints weight = 22299.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.113536 restraints weight = 13011.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.115919 restraints weight = 9384.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.117519 restraints weight = 7672.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.118386 restraints weight = 6725.401| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13651 Z= 0.158 Angle : 0.722 12.217 18549 Z= 0.364 Chirality : 0.046 0.368 2076 Planarity : 0.005 0.069 2403 Dihedral : 6.040 48.116 1888 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.25 % Favored : 90.62 % Rotamer: Outliers : 3.57 % Allowed : 23.10 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.20), residues: 1600 helix: 0.39 (0.29), residues: 350 sheet: -2.25 (0.27), residues: 324 loop : -2.43 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 81 TYR 0.021 0.001 TYR L 148 PHE 0.019 0.001 PHE M 656 TRP 0.039 0.002 TRP N 235 HIS 0.011 0.001 HIS K 282 Details of bonding type rmsd covalent geometry : bond 0.00361 (13642) covalent geometry : angle 0.71795 (18535) SS BOND : bond 0.00554 ( 7) SS BOND : angle 2.72981 ( 14) hydrogen bonds : bond 0.04085 ( 352) hydrogen bonds : angle 5.02224 ( 975) Misc. bond : bond 0.00012 ( 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 291 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 CYS cc_start: 0.8496 (m) cc_final: 0.8295 (m) REVERT: K 473 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7720 (mp0) REVERT: K 530 CYS cc_start: 0.6034 (OUTLIER) cc_final: 0.5513 (m) REVERT: K 612 LYS cc_start: 0.8482 (mmmt) cc_final: 0.8231 (mmtm) REVERT: K 720 GLU cc_start: 0.8123 (tt0) cc_final: 0.7919 (tt0) REVERT: K 721 GLU cc_start: 0.8241 (tt0) cc_final: 0.7927 (tt0) REVERT: L 136 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7591 (mt0) REVERT: L 148 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.7508 (p90) REVERT: L 294 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8537 (mp) REVERT: N 119 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7658 (pt) REVERT: N 360 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7902 (tp30) REVERT: P 246 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7312 (tp30) REVERT: P 291 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6888 (mtmm) REVERT: Q 105 LEU cc_start: 0.9383 (mm) cc_final: 0.9155 (mt) REVERT: C 24 MET cc_start: 0.0244 (mmt) cc_final: -0.0078 (mmm) REVERT: C 34 ARG cc_start: 0.9083 (ttm170) cc_final: 0.8838 (mmm-85) REVERT: C 102 ASN cc_start: 0.7742 (m110) cc_final: 0.7397 (t0) outliers start: 47 outliers final: 39 residues processed: 277 average time/residue: 0.1112 time to fit residues: 45.8242 Evaluate side-chains 286 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 241 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 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 674 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 VAL 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 221 GLN Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 237 ASP Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 290 ILE Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain L residue 376 MET Chi-restraints excluded: chain M residue 596 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 68 LEU 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 142 THR Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 189 LEU 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 332 ILE Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain P residue 291 LYS Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 124 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 148 optimal weight: 30.0000 chunk 70 optimal weight: 0.9980 chunk 158 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 143 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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** N 316 HIS N 343 ASN C 118 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.150824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.117195 restraints weight = 22338.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.118580 restraints weight = 11878.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.120837 restraints weight = 10064.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.121450 restraints weight = 8416.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.121975 restraints weight = 7552.603| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3733 r_free = 0.3733 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13651 Z= 0.133 Angle : 0.704 12.068 18549 Z= 0.354 Chirality : 0.045 0.366 2076 Planarity : 0.004 0.069 2403 Dihedral : 5.800 45.333 1888 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.06 % Favored : 90.81 % Rotamer: Outliers : 3.57 % Allowed : 23.25 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.20), residues: 1600 helix: 0.45 (0.29), residues: 347 sheet: -2.14 (0.28), residues: 329 loop : -2.40 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 81 TYR 0.015 0.001 TYR L 148 PHE 0.020 0.001 PHE M 656 TRP 0.046 0.002 TRP N 235 HIS 0.009 0.001 HIS K 282 Details of bonding type rmsd covalent geometry : bond 0.00304 (13642) covalent geometry : angle 0.70047 (18535) SS BOND : bond 0.00549 ( 7) SS BOND : angle 2.70156 ( 14) hydrogen bonds : bond 0.03837 ( 352) hydrogen bonds : angle 4.90764 ( 975) Misc. bond : bond 0.00011 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2482.86 seconds wall clock time: 43 minutes 46.55 seconds (2626.55 seconds total)