Starting phenix.real_space_refine (version: dev) on Tue Feb 21 00:13:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c23_7334/02_2023/6c23_7334_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c23_7334/02_2023/6c23_7334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c23_7334/02_2023/6c23_7334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c23_7334/02_2023/6c23_7334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c23_7334/02_2023/6c23_7334_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c23_7334/02_2023/6c23_7334_updated.pdb" } resolution = 3.9 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 685": "NH1" <-> "NH2" Residue "L PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 414": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13440 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 860 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 118 Chain: "E" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 181 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 25} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "K" Number of atoms: 2406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2406 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 16, 'TRANS': 308} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 7, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 125 Chain: "L" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2877 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 349} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "M" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 962 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "N" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3058 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 22, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "O" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 51 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "P" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 484 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 58} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "Q" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 496 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 63} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "Z" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 674 Classifications: {'peptide': 135} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 134} Link IDs: {'TRANS': 134} Chain breaks: 6 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 407 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "C" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1307 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 7, 'TRANS': 185} Chain breaks: 1 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 157 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 84 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 11} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 7.86, per 1000 atoms: 0.58 Number of scatterers: 13440 At special positions: 0 Unit cell: (146.16, 109.2, 111.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2496 8.00 N 2389 7.00 C 8471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 450 " - pdb=" SG CYS A 453 " distance=2.07 Simple disulfide: pdb=" SG CYS K 289 " - pdb=" SG CYS K 294 " distance=2.01 Simple disulfide: pdb=" SG CYS K 523 " - pdb=" SG CYS K 530 " distance=2.05 Simple disulfide: pdb=" SG CYS K 523 " - pdb=" SG CYS K 547 " distance=2.03 Simple disulfide: pdb=" SG CYS K 523 " - pdb=" SG CYS K 549 " distance=2.02 Simple disulfide: pdb=" SG CYS K 530 " - pdb=" SG CYS K 549 " distance=2.03 Simple disulfide: pdb=" SG CYS K 530 " - pdb=" SG CYS K 553 " distance=2.05 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 429 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.17 Conformation dependent library (CDL) restraints added in 1.9 seconds 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB UNK Z 25 " Number of C-beta restraints generated: 3500 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 20 sheets defined 20.7% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 460 through 469 Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'K' and resid 274 through 283 removed outlier: 5.206A pdb=" N SER K 280 " --> pdb=" O GLN K 276 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N PHE K 281 " --> pdb=" O SER K 277 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 447 removed outlier: 3.513A pdb=" N ILE K 444 " --> pdb=" O PHE K 440 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY K 445 " --> pdb=" O ARG K 441 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR K 446 " --> pdb=" O VAL K 442 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 457 Processing helix chain 'K' and resid 463 through 476 Processing helix chain 'K' and resid 535 through 538 No H-bonds generated for 'chain 'K' and resid 535 through 538' Processing helix chain 'K' and resid 572 through 575 No H-bonds generated for 'chain 'K' and resid 572 through 575' Processing helix chain 'K' and resid 605 through 608 No H-bonds generated for 'chain 'K' and resid 605 through 608' Processing helix chain 'K' and resid 648 through 661 removed outlier: 3.932A pdb=" N VAL K 657 " --> pdb=" O ARG K 653 " (cutoff:3.500A) Processing helix chain 'K' and resid 683 through 686 Processing helix chain 'L' and resid 128 through 130 No H-bonds generated for 'chain 'L' and resid 128 through 130' Processing helix chain 'L' and resid 268 through 278 Processing helix chain 'L' and resid 282 through 284 No H-bonds generated for 'chain 'L' and resid 282 through 284' Processing helix chain 'M' and resid 577 through 579 No H-bonds generated for 'chain 'M' and resid 577 through 579' Processing helix chain 'M' and resid 592 through 602 removed outlier: 3.540A pdb=" N GLU M 601 " --> pdb=" O ILE M 597 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU M 602 " --> pdb=" O THR M 598 " (cutoff:3.500A) Processing helix chain 'M' and resid 608 through 624 Processing helix chain 'M' and resid 629 through 650 removed outlier: 3.708A pdb=" N ASN M 633 " --> pdb=" O ASP M 629 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N MET M 637 " --> pdb=" O ASN M 633 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN M 645 " --> pdb=" O GLU M 641 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LYS M 646 " --> pdb=" O ASN M 642 " (cutoff:3.500A) Processing helix chain 'M' and resid 653 through 664 Processing helix chain 'M' and resid 671 through 681 Processing helix chain 'N' and resid 5 through 30 removed outlier: 3.556A pdb=" N ALA N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) Proline residue: N 29 - end of helix Processing helix chain 'N' and resid 154 through 156 No H-bonds generated for 'chain 'N' and resid 154 through 156' Processing helix chain 'N' and resid 356 through 361 Processing helix chain 'P' and resid 244 through 256 removed outlier: 4.807A pdb=" N LEU P 249 " --> pdb=" O GLU P 246 " (cutoff:3.500A) Proline residue: P 250 - end of helix removed outlier: 3.544A pdb=" N GLU P 256 " --> pdb=" O TRP P 253 " (cutoff:3.500A) Processing helix chain 'P' and resid 278 through 280 No H-bonds generated for 'chain 'P' and resid 278 through 280' Processing helix chain 'Q' and resid 83 through 104 removed outlier: 4.354A pdb=" N LYS Q 92 " --> pdb=" O GLN Q 88 " (cutoff:3.500A) Proline residue: Q 93 - end of helix Processing helix chain 'C' and resid 18 through 62 removed outlier: 3.712A pdb=" N LEU C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 152 removed outlier: 3.557A pdb=" N LEU C 149 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE C 150 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 179 Processing helix chain 'C' and resid 221 through 230 removed outlier: 4.213A pdb=" N ALA C 226 " --> pdb=" O LYS C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 246 Processing helix chain 'B' and resid 108 through 111 No H-bonds generated for 'chain 'B' and resid 108 through 111' Processing sheet with id= A, first strand: chain 'A' and resid 474 through 477 Processing sheet with id= B, first strand: chain 'K' and resid 614 through 618 Processing sheet with id= C, first strand: chain 'K' and resid 644 through 646 Processing sheet with id= D, first strand: chain 'K' and resid 696 through 702 Processing sheet with id= E, first strand: chain 'L' and resid 82 through 84 Processing sheet with id= F, first strand: chain 'L' and resid 98 through 101 removed outlier: 3.686A pdb=" N GLY L 98 " --> pdb=" O VAL L 116 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU L 111 " --> pdb=" O CYS L 126 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 124 through 126 Processing sheet with id= H, first strand: chain 'L' and resid 150 through 154 removed outlier: 3.936A pdb=" N GLY L 167 " --> pdb=" O ILE L 171 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE L 171 " --> pdb=" O GLY L 167 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 205 through 210 removed outlier: 4.469A pdb=" N ALA L 214 " --> pdb=" O SER L 210 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASN L 219 " --> pdb=" O LEU L 225 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU L 225 " --> pdb=" O ASN L 219 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLN L 292 " --> pdb=" O ILE L 228 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 260 through 264 Processing sheet with id= K, first strand: chain 'L' and resid 312 through 315 Processing sheet with id= L, first strand: chain 'L' and resid 331 through 333 Processing sheet with id= M, first strand: chain 'N' and resid 65 through 67 Processing sheet with id= N, first strand: chain 'N' and resid 78 through 80 Processing sheet with id= O, first strand: chain 'N' and resid 139 through 142 Processing sheet with id= P, first strand: chain 'N' and resid 267 through 270 removed outlier: 4.442A pdb=" N LYS N 251 " --> pdb=" O ALA N 247 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA N 247 " --> pdb=" O LYS N 251 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE N 243 " --> pdb=" O TRP N 255 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'N' and resid 288 through 292 removed outlier: 3.846A pdb=" N HIS N 311 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP N 302 " --> pdb=" O LYS N 309 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LYS N 309 " --> pdb=" O ASP N 302 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'N' and resid 320 through 323 removed outlier: 7.034A pdb=" N SER N 336 " --> pdb=" O PHE N 321 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL N 323 " --> pdb=" O ALA N 334 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA N 334 " --> pdb=" O VAL N 323 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASP N 346 " --> pdb=" O LEU N 366 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU N 366 " --> pdb=" O ASP N 346 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'N' and resid 32 through 39 removed outlier: 6.329A pdb=" N GLN N 403 " --> pdb=" O ASP N 33 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL N 35 " --> pdb=" O VAL N 401 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL N 401 " --> pdb=" O VAL N 35 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR N 37 " --> pdb=" O MET N 399 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET N 399 " --> pdb=" O THR N 37 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE N 398 " --> pdb=" O SER N 394 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'Z' and resid 31 through 36 removed outlier: 7.166A pdb=" N UNK Z 58 " --> pdb=" O UNK Z 32 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N UNK Z 34 " --> pdb=" O UNK Z 58 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N UNK Z 60 " --> pdb=" O UNK Z 34 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N UNK Z 36 " --> pdb=" O UNK Z 60 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N UNK Z 62 " --> pdb=" O UNK Z 36 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N UNK Z 86 " --> pdb=" O UNK Z 61 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N UNK Z 63 " --> pdb=" O UNK Z 86 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N UNK Z 88 " --> pdb=" O UNK Z 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= T 320 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.41 Time building geometry restraints manager: 5.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2273 1.29 - 1.43: 3651 1.43 - 1.56: 7691 1.56 - 1.70: 7 1.70 - 1.84: 114 Bond restraints: 13736 Sorted by residual: bond pdb=" CA GLY L 234 " pdb=" C GLY L 234 " ideal model delta sigma weight residual 1.514 1.149 0.366 1.41e-02 5.03e+03 6.72e+02 bond pdb=" N UNK Z 24 " pdb=" CA UNK Z 24 " ideal model delta sigma weight residual 1.458 1.168 0.290 1.90e-02 2.77e+03 2.32e+02 bond pdb=" CA UNK Z 25 " pdb=" C UNK Z 25 " ideal model delta sigma weight residual 1.525 1.206 0.319 2.10e-02 2.27e+03 2.31e+02 bond pdb=" CA CYS N 391 " pdb=" C CYS N 391 " ideal model delta sigma weight residual 1.522 1.453 0.069 1.19e-02 7.06e+03 3.39e+01 bond pdb=" CA ASN L 146 " pdb=" C ASN L 146 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.10e-02 8.26e+03 3.33e+01 ... (remaining 13731 not shown) Histogram of bond angle deviations from ideal: 78.75 - 91.57: 2 91.57 - 104.39: 257 104.39 - 117.22: 9982 117.22 - 130.04: 8318 130.04 - 142.87: 142 Bond angle restraints: 18701 Sorted by residual: angle pdb=" N UNK Z 25 " pdb=" CA UNK Z 25 " pdb=" CB UNK Z 25 " ideal model delta sigma weight residual 110.50 78.75 31.75 1.70e+00 3.46e-01 3.49e+02 angle pdb=" C UNK Z 25 " pdb=" CA UNK Z 25 " pdb=" CB UNK Z 25 " ideal model delta sigma weight residual 110.08 142.87 -32.79 1.90e+00 2.77e-01 2.98e+02 angle pdb=" CA GLY L 234 " pdb=" C GLY L 234 " pdb=" O GLY L 234 " ideal model delta sigma weight residual 120.57 98.19 22.38 1.74e+00 3.30e-01 1.65e+02 angle pdb=" C UNK Z 24 " pdb=" CA UNK Z 24 " pdb=" CB UNK Z 24 " ideal model delta sigma weight residual 110.08 88.67 21.41 1.90e+00 2.77e-01 1.27e+02 angle pdb=" N UNK Z 24 " pdb=" CA UNK Z 24 " pdb=" CB UNK Z 24 " ideal model delta sigma weight residual 110.50 129.03 -18.53 1.70e+00 3.46e-01 1.19e+02 ... (remaining 18696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 7529 16.61 - 33.22: 568 33.22 - 49.83: 82 49.83 - 66.43: 16 66.43 - 83.04: 8 Dihedral angle restraints: 8203 sinusoidal: 2855 harmonic: 5348 Sorted by residual: dihedral pdb=" N UNK Z 24 " pdb=" C UNK Z 24 " pdb=" CA UNK Z 24 " pdb=" CB UNK Z 24 " ideal model delta harmonic sigma weight residual 122.80 171.90 -49.10 0 2.50e+00 1.60e-01 3.86e+02 dihedral pdb=" C UNK Z 24 " pdb=" N UNK Z 24 " pdb=" CA UNK Z 24 " pdb=" CB UNK Z 24 " ideal model delta harmonic sigma weight residual -122.60 -169.56 46.96 0 2.50e+00 1.60e-01 3.53e+02 dihedral pdb=" CA HIS C 129 " pdb=" C HIS C 129 " pdb=" N ASN C 130 " pdb=" CA ASN C 130 " ideal model delta harmonic sigma weight residual -180.00 -125.52 -54.48 0 5.00e+00 4.00e-02 1.19e+02 ... (remaining 8200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.508: 2110 0.508 - 1.016: 2 1.016 - 1.524: 0 1.524 - 2.032: 0 2.032 - 2.540: 2 Chirality restraints: 2114 Sorted by residual: chirality pdb=" CA UNK Z 25 " pdb=" N UNK Z 25 " pdb=" C UNK Z 25 " pdb=" CB UNK Z 25 " both_signs ideal model delta sigma weight residual False 2.52 -0.02 2.54 2.00e-01 2.50e+01 1.61e+02 chirality pdb=" CA UNK Z 24 " pdb=" N UNK Z 24 " pdb=" C UNK Z 24 " pdb=" CB UNK Z 24 " both_signs ideal model delta sigma weight residual False 2.52 0.24 2.28 2.00e-01 2.50e+01 1.30e+02 chirality pdb=" CA TYR L 148 " pdb=" N TYR L 148 " pdb=" C TYR L 148 " pdb=" CB TYR L 148 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.47e+00 ... (remaining 2111 not shown) Planarity restraints: 2439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 148 " 0.055 2.00e-02 2.50e+03 2.89e-02 1.66e+01 pdb=" CG TYR L 148 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR L 148 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR L 148 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR L 148 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR L 148 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR L 148 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR L 148 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 151 " 0.053 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO E 152 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO E 152 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 152 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 380 " -0.034 2.00e-02 2.50e+03 2.15e-02 8.07e+00 pdb=" CG PHE N 380 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE N 380 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE N 380 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE N 380 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE N 380 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE N 380 " -0.011 2.00e-02 2.50e+03 ... (remaining 2436 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.80: 8 1.80 - 2.57: 188 2.57 - 3.35: 17309 3.35 - 4.12: 31584 4.12 - 4.90: 56716 Nonbonded interactions: 105805 Sorted by model distance: nonbonded pdb=" O VAL N 151 " pdb=" OD1 ASP N 170 " model vdw 1.020 3.040 nonbonded pdb=" O LEU K 443 " pdb=" CD1 TYR K 447 " model vdw 1.548 3.340 nonbonded pdb=" CD1 TRP L 389 " pdb=" O LYS L 400 " model vdw 1.593 3.260 nonbonded pdb=" ND1 HIS K 593 " pdb=" CB SER K 596 " model vdw 1.644 3.520 nonbonded pdb=" C SER K 729 " pdb=" OE1 GLN K 730 " model vdw 1.693 3.270 ... (remaining 105800 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 8471 2.51 5 N 2389 2.21 5 O 2496 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.300 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: 6.670 Check model and map are aligned: 0.190 Process input model: 34.140 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.110 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.366 13736 Z= 0.838 Angle : 1.586 32.789 18701 Z= 0.964 Chirality : 0.114 2.540 2114 Planarity : 0.006 0.081 2439 Dihedral : 12.198 78.205 4679 Min Nonbonded Distance : 1.020 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 1.57 % Allowed : 14.68 % Favored : 83.75 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (0.17), residues: 1655 helix: -1.81 (0.24), residues: 336 sheet: -3.79 (0.23), residues: 317 loop : -3.60 (0.16), residues: 1002 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 464 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 474 average time/residue: 0.3069 time to fit residues: 198.5506 Evaluate side-chains 299 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 295 time to evaluate : 1.308 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1217 time to fit residues: 3.1048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 30.0000 chunk 134 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 84 optimal weight: 0.0370 chunk 103 optimal weight: 8.9990 chunk 160 optimal weight: 0.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- 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 94 GLN L 136 GLN L 213 HIS ** L 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 397 HIS M 655 ASN N 18 ASN ** N 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 ASN N 188 ASN ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 HIS N 343 ASN ** N 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 268 HIS Q 83 HIS C 45 ASN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 13736 Z= 0.326 Angle : 0.806 11.430 18701 Z= 0.421 Chirality : 0.049 0.219 2114 Planarity : 0.005 0.066 2439 Dihedral : 7.110 54.252 1922 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.37 % Favored : 90.27 % Rotamer Outliers : 5.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.18), residues: 1655 helix: -0.59 (0.26), residues: 354 sheet: -3.28 (0.24), residues: 313 loop : -3.08 (0.17), residues: 988 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 347 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 41 residues processed: 379 average time/residue: 0.2560 time to fit residues: 140.9607 Evaluate side-chains 311 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 270 time to evaluate : 1.573 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.1393 time to fit residues: 12.0307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 173 optimal weight: 20.0000 chunk 143 optimal weight: 0.0770 chunk 159 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 HIS L 176 ASN M 607 ASN M 633 ASN M 634 HIS M 659 HIS ** N 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 ASN ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 ASN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 13736 Z= 0.189 Angle : 0.708 9.725 18701 Z= 0.361 Chirality : 0.045 0.168 2114 Planarity : 0.004 0.053 2439 Dihedral : 6.100 43.938 1922 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.46 % Favored : 91.12 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.19), residues: 1655 helix: 0.13 (0.28), residues: 353 sheet: -2.67 (0.26), residues: 302 loop : -2.76 (0.18), residues: 1000 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 331 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 12 residues processed: 347 average time/residue: 0.2769 time to fit residues: 141.2510 Evaluate side-chains 284 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 272 time to evaluate : 1.572 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1475 time to fit residues: 5.2457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 171 optimal weight: 50.0000 chunk 84 optimal weight: 0.9980 chunk 153 optimal weight: 30.0000 chunk 46 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS ** L 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 HIS ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 ASN ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 HIS ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 13736 Z= 0.318 Angle : 0.743 11.303 18701 Z= 0.382 Chirality : 0.046 0.192 2114 Planarity : 0.004 0.059 2439 Dihedral : 6.116 48.765 1922 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.27 % Favored : 89.37 % Rotamer Outliers : 4.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.19), residues: 1655 helix: 0.21 (0.28), residues: 352 sheet: -2.52 (0.26), residues: 316 loop : -2.66 (0.18), residues: 987 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 288 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 36 residues processed: 314 average time/residue: 0.2355 time to fit residues: 110.1120 Evaluate side-chains 302 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 266 time to evaluate : 1.439 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.1254 time to fit residues: 10.1335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 145 optimal weight: 50.0000 chunk 118 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 153 optimal weight: 30.0000 chunk 43 optimal weight: 5.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN K 276 GLN K 689 HIS K 706 HIS L 191 ASN M 620 HIS M 634 HIS M 655 ASN ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 290 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.059 13736 Z= 0.502 Angle : 0.838 11.328 18701 Z= 0.438 Chirality : 0.050 0.258 2114 Planarity : 0.005 0.061 2439 Dihedral : 6.664 55.879 1922 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.90 % Favored : 87.73 % Rotamer Outliers : 3.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.19), residues: 1655 helix: -0.15 (0.26), residues: 352 sheet: -2.62 (0.26), residues: 312 loop : -2.86 (0.17), residues: 991 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 266 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 32 residues processed: 290 average time/residue: 0.2290 time to fit residues: 100.0021 Evaluate side-chains 281 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 249 time to evaluate : 1.601 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1266 time to fit residues: 9.6220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.9990 chunk 154 optimal weight: 30.0000 chunk 33 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 171 optimal weight: 40.0000 chunk 142 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 555 ASN M 633 ASN ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 13736 Z= 0.361 Angle : 0.765 10.975 18701 Z= 0.397 Chirality : 0.047 0.190 2114 Planarity : 0.005 0.053 2439 Dihedral : 6.357 52.002 1922 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.76 % Favored : 88.88 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.19), residues: 1655 helix: -0.07 (0.27), residues: 351 sheet: -2.62 (0.26), residues: 326 loop : -2.69 (0.18), residues: 978 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 279 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 24 residues processed: 296 average time/residue: 0.2355 time to fit residues: 104.9578 Evaluate side-chains 279 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 255 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1307 time to fit residues: 7.8988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 144 optimal weight: 50.0000 chunk 95 optimal weight: 0.9980 chunk 170 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 689 HIS ** M 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 GLN B 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 13736 Z= 0.314 Angle : 0.755 10.997 18701 Z= 0.387 Chirality : 0.047 0.257 2114 Planarity : 0.004 0.048 2439 Dihedral : 6.214 51.066 1922 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.06 % Favored : 88.64 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.19), residues: 1655 helix: -0.01 (0.27), residues: 349 sheet: -2.51 (0.27), residues: 314 loop : -2.62 (0.18), residues: 992 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 277 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 20 residues processed: 288 average time/residue: 0.2415 time to fit residues: 104.1025 Evaluate side-chains 273 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 253 time to evaluate : 1.691 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1314 time to fit residues: 6.8969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 116 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 155 optimal weight: 20.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 689 HIS ** L 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 634 HIS ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 13736 Z= 0.281 Angle : 0.757 13.963 18701 Z= 0.383 Chirality : 0.046 0.175 2114 Planarity : 0.004 0.049 2439 Dihedral : 6.042 53.242 1922 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.21 % Favored : 89.49 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.19), residues: 1655 helix: 0.04 (0.27), residues: 355 sheet: -2.39 (0.27), residues: 316 loop : -2.60 (0.18), residues: 984 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 276 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 281 average time/residue: 0.2297 time to fit residues: 97.8251 Evaluate side-chains 266 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 256 time to evaluate : 1.800 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1306 time to fit residues: 4.6852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 0.4980 chunk 149 optimal weight: 40.0000 chunk 158 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 150 optimal weight: 30.0000 chunk 104 optimal weight: 8.9990 chunk 168 optimal weight: 20.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 689 HIS ** L 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 633 ASN M 655 ASN ** N 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 13736 Z= 0.332 Angle : 0.778 12.282 18701 Z= 0.398 Chirality : 0.047 0.229 2114 Planarity : 0.005 0.044 2439 Dihedral : 6.114 52.491 1922 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.18 % Favored : 88.52 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.19), residues: 1655 helix: -0.04 (0.27), residues: 356 sheet: -2.31 (0.28), residues: 320 loop : -2.64 (0.18), residues: 979 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 262 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 273 average time/residue: 0.2412 time to fit residues: 98.7503 Evaluate side-chains 266 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 255 time to evaluate : 1.469 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1254 time to fit residues: 4.5195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 0.0970 chunk 162 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 149 optimal weight: 40.0000 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 633 ASN ** N 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 13736 Z= 0.227 Angle : 0.741 13.320 18701 Z= 0.376 Chirality : 0.045 0.205 2114 Planarity : 0.004 0.045 2439 Dihedral : 5.805 53.269 1922 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.24 % Favored : 90.57 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.20), residues: 1655 helix: 0.14 (0.28), residues: 351 sheet: -2.10 (0.28), residues: 312 loop : -2.48 (0.18), residues: 992 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 288 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 292 average time/residue: 0.2342 time to fit residues: 103.6375 Evaluate side-chains 264 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 260 time to evaluate : 1.701 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1175 time to fit residues: 2.9411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 8.9990 chunk 129 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 144 optimal weight: 50.0000 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 689 HIS ** L 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 620 HIS M 633 ASN M 655 ASN ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.133323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.110010 restraints weight = 26814.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.109954 restraints weight = 23468.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.111207 restraints weight = 23174.806| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3887 r_free = 0.3887 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3884 r_free = 0.3884 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 13736 Z= 0.310 Angle : 0.780 12.986 18701 Z= 0.398 Chirality : 0.047 0.218 2114 Planarity : 0.005 0.045 2439 Dihedral : 5.935 51.790 1922 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.18 % Favored : 88.58 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.19), residues: 1655 helix: 0.02 (0.27), residues: 354 sheet: -2.07 (0.29), residues: 302 loop : -2.48 (0.18), residues: 999 =============================================================================== Job complete usr+sys time: 2811.13 seconds wall clock time: 51 minutes 53.81 seconds (3113.81 seconds total)