Starting phenix.real_space_refine on Sun Sep 29 19:00:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4t_30987/09_2024/7e4t_30987.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4t_30987/09_2024/7e4t_30987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4t_30987/09_2024/7e4t_30987.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4t_30987/09_2024/7e4t_30987.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4t_30987/09_2024/7e4t_30987.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4t_30987/09_2024/7e4t_30987.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.176 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 8 5.49 5 S 116 5.16 5 C 14632 2.51 5 N 3564 2.21 5 O 3948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22276 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5412 Classifications: {'peptide': 664} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 639} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1148 SG CYS A 176 14.234 43.015 61.526 1.00172.12 S ATOM 1162 SG CYS A 178 13.069 40.045 59.271 1.00194.88 S ATOM 1184 SG CYS A 181 16.749 40.871 59.364 1.00197.66 S Restraints were copied for chains: C, B, D Time building chain proxies: 13.85, per 1000 atoms: 0.62 Number of scatterers: 22276 At special positions: 0 Unit cell: (113.905, 113.905, 136.895, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 116 16.00 P 8 15.00 O 3948 8.00 N 3564 7.00 C 14632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 5.85 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 176 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 181 " pdb=" ZN B 804 " pdb="ZN ZN B 804 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 176 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 178 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 181 " pdb=" ZN C 804 " pdb="ZN ZN C 804 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 176 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 181 " pdb=" ZN D 804 " pdb="ZN ZN D 804 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 176 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 181 " Number of angles added : 12 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5120 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 4 sheets defined 77.3% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 44 through 59 removed outlier: 3.693A pdb=" N ILE A 57 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.810A pdb=" N LYS A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 188 through 204 removed outlier: 3.504A pdb=" N SER A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 237 through 258 removed outlier: 3.889A pdb=" N TYR A 241 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 362 through 385 removed outlier: 3.913A pdb=" N SER A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 426 Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 427 through 432 Processing helix chain 'A' and resid 435 through 460 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 493 through 500 removed outlier: 3.782A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 540 removed outlier: 4.102A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 567 through 580 removed outlier: 3.695A pdb=" N VAL A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 588 removed outlier: 3.636A pdb=" N VAL A 587 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 613 Processing helix chain 'A' and resid 614 through 633 removed outlier: 3.812A pdb=" N ASN A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN A 629 " --> pdb=" O ASN A 625 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 650 removed outlier: 3.700A pdb=" N TYR A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 731 Processing helix chain 'A' and resid 740 through 761 Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.693A pdb=" N ILE B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 98 through 106 Processing helix chain 'B' and resid 108 through 118 Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.810A pdb=" N LYS B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 204 removed outlier: 3.503A pdb=" N SER B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 215 through 234 Processing helix chain 'B' and resid 237 through 258 removed outlier: 3.889A pdb=" N TYR B 241 " --> pdb=" O PHE B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 362 through 385 removed outlier: 3.913A pdb=" N SER B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 426 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 427 through 432 Processing helix chain 'B' and resid 435 through 460 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 473 through 492 Processing helix chain 'B' and resid 493 through 500 removed outlier: 3.782A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 540 removed outlier: 4.101A pdb=" N LEU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 567 through 580 removed outlier: 3.695A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE B 580 " --> pdb=" O PHE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 588 removed outlier: 3.636A pdb=" N VAL B 587 " --> pdb=" O ASN B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 613 Processing helix chain 'B' and resid 614 through 633 removed outlier: 3.813A pdb=" N ASN B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN B 629 " --> pdb=" O ASN B 625 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 630 " --> pdb=" O ASN B 626 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 650 removed outlier: 3.700A pdb=" N TYR B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 731 Processing helix chain 'B' and resid 740 through 761 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 44 through 59 removed outlier: 3.693A pdb=" N ILE C 57 " --> pdb=" O GLN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 98 through 106 Processing helix chain 'C' and resid 108 through 118 Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 164 removed outlier: 3.810A pdb=" N LYS C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 204 removed outlier: 3.504A pdb=" N SER C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'C' and resid 237 through 258 removed outlier: 3.889A pdb=" N TYR C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 326 through 340 Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'C' and resid 362 through 385 removed outlier: 3.912A pdb=" N SER C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 426 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 435 through 460 Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 492 Processing helix chain 'C' and resid 493 through 500 removed outlier: 3.782A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 540 removed outlier: 4.101A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 567 through 580 removed outlier: 3.695A pdb=" N VAL C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE C 580 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 588 removed outlier: 3.636A pdb=" N VAL C 587 " --> pdb=" O ASN C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 613 Processing helix chain 'C' and resid 614 through 633 removed outlier: 3.812A pdb=" N ASN C 618 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN C 629 " --> pdb=" O ASN C 625 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 630 " --> pdb=" O ASN C 626 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 631 " --> pdb=" O SER C 627 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP C 633 " --> pdb=" O GLN C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 650 removed outlier: 3.701A pdb=" N TYR C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 731 Processing helix chain 'C' and resid 740 through 761 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 44 through 59 removed outlier: 3.693A pdb=" N ILE D 57 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 108 through 118 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 164 removed outlier: 3.810A pdb=" N LYS D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 188 through 204 removed outlier: 3.504A pdb=" N SER D 193 " --> pdb=" O SER D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 211 Processing helix chain 'D' and resid 215 through 234 Processing helix chain 'D' and resid 237 through 258 removed outlier: 3.888A pdb=" N TYR D 241 " --> pdb=" O PHE D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 326 through 340 Processing helix chain 'D' and resid 340 through 351 Processing helix chain 'D' and resid 362 through 385 removed outlier: 3.912A pdb=" N SER D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 426 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 427 through 432 Processing helix chain 'D' and resid 435 through 460 Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 473 through 492 Processing helix chain 'D' and resid 493 through 500 removed outlier: 3.782A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 540 removed outlier: 4.102A pdb=" N LEU D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE D 522 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 567 through 580 removed outlier: 3.695A pdb=" N VAL D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE D 580 " --> pdb=" O PHE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 588 removed outlier: 3.635A pdb=" N VAL D 587 " --> pdb=" O ASN D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 613 Processing helix chain 'D' and resid 614 through 633 removed outlier: 3.812A pdb=" N ASN D 618 " --> pdb=" O VAL D 614 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN D 629 " --> pdb=" O ASN D 625 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 630 " --> pdb=" O ASN D 626 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D 631 " --> pdb=" O SER D 627 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP D 633 " --> pdb=" O GLN D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 650 removed outlier: 3.701A pdb=" N TYR D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 731 Processing helix chain 'D' and resid 740 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.149A pdb=" N VAL B 166 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 removed outlier: 4.148A pdb=" N VAL A 166 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 18 through 20 removed outlier: 4.148A pdb=" N VAL C 166 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 18 through 20 removed outlier: 4.149A pdb=" N VAL D 166 " --> pdb=" O LEU C 20 " (cutoff:3.500A) 1432 hydrogen bonds defined for protein. 4200 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: 7.07 Time building geometry restraints manager: 6.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3500 1.32 - 1.44: 6112 1.44 - 1.57: 12960 1.57 - 1.69: 16 1.69 - 1.81: 188 Bond restraints: 22776 Sorted by residual: bond pdb=" C12 YZY D 806 " pdb=" C13 YZY D 806 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C12 YZY A 806 " pdb=" C13 YZY A 806 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C12 YZY C 806 " pdb=" C13 YZY C 806 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C12 YZY B 806 " pdb=" C13 YZY B 806 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C28 YZY B 806 " pdb=" C29 YZY B 806 " ideal model delta sigma weight residual 1.332 1.504 -0.172 2.00e-02 2.50e+03 7.40e+01 ... (remaining 22771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.11: 30604 4.11 - 8.22: 128 8.22 - 12.32: 36 12.32 - 16.43: 12 16.43 - 20.54: 4 Bond angle restraints: 30784 Sorted by residual: angle pdb=" C27 YZY D 806 " pdb=" C28 YZY D 806 " pdb=" C29 YZY D 806 " ideal model delta sigma weight residual 128.13 107.59 20.54 3.00e+00 1.11e-01 4.69e+01 angle pdb=" C27 YZY A 806 " pdb=" C28 YZY A 806 " pdb=" C29 YZY A 806 " ideal model delta sigma weight residual 128.13 107.62 20.51 3.00e+00 1.11e-01 4.68e+01 angle pdb=" C27 YZY C 806 " pdb=" C28 YZY C 806 " pdb=" C29 YZY C 806 " ideal model delta sigma weight residual 128.13 107.64 20.49 3.00e+00 1.11e-01 4.67e+01 angle pdb=" C27 YZY B 806 " pdb=" C28 YZY B 806 " pdb=" C29 YZY B 806 " ideal model delta sigma weight residual 128.13 107.65 20.48 3.00e+00 1.11e-01 4.66e+01 angle pdb=" C21 YZY C 806 " pdb=" C20 YZY C 806 " pdb=" O4 YZY C 806 " ideal model delta sigma weight residual 111.77 126.25 -14.48 3.00e+00 1.11e-01 2.33e+01 ... (remaining 30779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 13623 34.84 - 69.68: 236 69.68 - 104.52: 16 104.52 - 139.36: 8 139.36 - 174.21: 12 Dihedral angle restraints: 13895 sinusoidal: 6031 harmonic: 7864 Sorted by residual: dihedral pdb=" C26 YZY B 806 " pdb=" C27 YZY B 806 " pdb=" C28 YZY B 806 " pdb=" C29 YZY B 806 " ideal model delta sinusoidal sigma weight residual 119.11 -66.68 -174.21 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C26 YZY A 806 " pdb=" C27 YZY A 806 " pdb=" C28 YZY A 806 " pdb=" C29 YZY A 806 " ideal model delta sinusoidal sigma weight residual 119.11 -66.70 -174.19 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C26 YZY C 806 " pdb=" C27 YZY C 806 " pdb=" C28 YZY C 806 " pdb=" C29 YZY C 806 " ideal model delta sinusoidal sigma weight residual 119.11 -66.70 -174.19 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 13892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2832 0.046 - 0.092: 520 0.092 - 0.138: 76 0.138 - 0.185: 8 0.185 - 0.231: 8 Chirality restraints: 3444 Sorted by residual: chirality pdb=" CBI Y01 A 803 " pdb=" CAU Y01 A 803 " pdb=" CBE Y01 A 803 " pdb=" CBG Y01 A 803 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CBI Y01 B 803 " pdb=" CAU Y01 B 803 " pdb=" CBE Y01 B 803 " pdb=" CBG Y01 B 803 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CBI Y01 C 803 " pdb=" CAU Y01 C 803 " pdb=" CBE Y01 C 803 " pdb=" CBG Y01 C 803 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 3441 not shown) Planarity restraints: 3784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 573 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C GLN C 573 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN C 573 " 0.008 2.00e-02 2.50e+03 pdb=" N SER C 574 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 573 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C GLN B 573 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN B 573 " 0.008 2.00e-02 2.50e+03 pdb=" N SER B 574 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 573 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C GLN D 573 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN D 573 " 0.008 2.00e-02 2.50e+03 pdb=" N SER D 574 " 0.007 2.00e-02 2.50e+03 ... (remaining 3781 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 148 2.60 - 3.18: 18816 3.18 - 3.75: 35361 3.75 - 4.33: 48589 4.33 - 4.90: 81463 Nonbonded interactions: 184377 Sorted by model distance: nonbonded pdb=" SG CYS C 553 " pdb=" SG CYS C 558 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS B 553 " pdb=" SG CYS B 558 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS D 553 " pdb=" SG CYS D 558 " model vdw 2.031 3.760 nonbonded pdb=" OG1 THR B 140 " pdb=" OD1 ASP B 142 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR D 140 " pdb=" OD1 ASP D 142 " model vdw 2.279 3.040 ... (remaining 184372 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.120 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: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 54.800 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 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 : 0.007 0.204 22776 Z= 0.438 Angle : 0.786 20.541 30784 Z= 0.323 Chirality : 0.036 0.231 3444 Planarity : 0.003 0.029 3784 Dihedral : 14.086 174.205 8772 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.01 % Allowed : 3.21 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.77 (0.15), residues: 2608 helix: 0.88 (0.11), residues: 1948 sheet: None (None), residues: 0 loop : -0.35 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 639 HIS 0.001 0.000 HIS A 370 PHE 0.014 0.001 PHE D 341 TYR 0.010 0.001 TYR A 524 ARG 0.003 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 484 time to evaluate : 2.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.6611 (mt-10) cc_final: 0.6372 (mt-10) REVERT: A 42 LYS cc_start: 0.6697 (mtmt) cc_final: 0.6411 (mmtt) REVERT: A 54 GLU cc_start: 0.6850 (tt0) cc_final: 0.5948 (tm-30) REVERT: A 56 GLU cc_start: 0.6000 (mt-10) cc_final: 0.5578 (tm-30) REVERT: A 75 LEU cc_start: 0.5852 (mp) cc_final: 0.5484 (mp) REVERT: A 79 GLU cc_start: 0.7629 (tt0) cc_final: 0.7005 (mp0) REVERT: A 170 ARG cc_start: 0.6102 (mtp180) cc_final: 0.5362 (ptp90) REVERT: A 191 ARG cc_start: 0.6848 (ttm-80) cc_final: 0.5850 (tpp-160) REVERT: A 214 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7482 (mp0) REVERT: A 237 PHE cc_start: 0.6873 (m-80) cc_final: 0.6649 (m-80) REVERT: A 337 ILE cc_start: 0.6925 (mm) cc_final: 0.6716 (mt) REVERT: A 393 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6514 (mp) REVERT: A 422 MET cc_start: 0.6625 (tpt) cc_final: 0.6289 (ttp) REVERT: A 512 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7546 (mmm160) REVERT: A 551 ASN cc_start: 0.8531 (t0) cc_final: 0.8065 (t0) REVERT: A 634 HIS cc_start: 0.6683 (m90) cc_final: 0.6454 (m170) REVERT: A 653 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7349 (pm20) REVERT: A 715 GLU cc_start: 0.6827 (tt0) cc_final: 0.6614 (pt0) REVERT: B 33 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6608 (mt-10) REVERT: B 42 LYS cc_start: 0.6699 (mtmt) cc_final: 0.6412 (mmtt) REVERT: B 54 GLU cc_start: 0.6809 (tt0) cc_final: 0.5907 (tm-30) REVERT: B 56 GLU cc_start: 0.5994 (mt-10) cc_final: 0.5574 (tm-30) REVERT: B 75 LEU cc_start: 0.5855 (mp) cc_final: 0.5476 (OUTLIER) REVERT: B 79 GLU cc_start: 0.7598 (tt0) cc_final: 0.6986 (mp0) REVERT: B 87 GLU cc_start: 0.7564 (tt0) cc_final: 0.6832 (tp30) REVERT: B 91 ASN cc_start: 0.8098 (m-40) cc_final: 0.7646 (m-40) REVERT: B 170 ARG cc_start: 0.6104 (mtp180) cc_final: 0.5366 (ptp90) REVERT: B 191 ARG cc_start: 0.6849 (ttm-80) cc_final: 0.5848 (tpp-160) REVERT: B 214 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7484 (mp0) REVERT: B 237 PHE cc_start: 0.6873 (m-80) cc_final: 0.6648 (m-80) REVERT: B 337 ILE cc_start: 0.6925 (mm) cc_final: 0.6715 (mt) REVERT: B 393 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6470 (mt) REVERT: B 422 MET cc_start: 0.6619 (tpt) cc_final: 0.6285 (ttp) REVERT: B 512 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7547 (mmm160) REVERT: B 551 ASN cc_start: 0.8531 (t0) cc_final: 0.8063 (t0) REVERT: B 634 HIS cc_start: 0.6681 (m90) cc_final: 0.6454 (m170) REVERT: B 653 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7367 (pm20) REVERT: B 715 GLU cc_start: 0.6841 (tt0) cc_final: 0.6551 (pt0) REVERT: C 33 GLU cc_start: 0.6617 (mt-10) cc_final: 0.6379 (mt-10) REVERT: C 42 LYS cc_start: 0.6707 (mtmt) cc_final: 0.6417 (mmtt) REVERT: C 54 GLU cc_start: 0.6771 (tt0) cc_final: 0.5880 (tm-30) REVERT: C 56 GLU cc_start: 0.5993 (mt-10) cc_final: 0.5553 (tm-30) REVERT: C 75 LEU cc_start: 0.5854 (mp) cc_final: 0.5476 (OUTLIER) REVERT: C 79 GLU cc_start: 0.7597 (tt0) cc_final: 0.6986 (mp0) REVERT: C 170 ARG cc_start: 0.5949 (mtp180) cc_final: 0.5236 (ptp90) REVERT: C 191 ARG cc_start: 0.6845 (ttm-80) cc_final: 0.5844 (tpp-160) REVERT: C 214 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7397 (mp0) REVERT: C 237 PHE cc_start: 0.6909 (m-80) cc_final: 0.6693 (m-80) REVERT: C 337 ILE cc_start: 0.6929 (mm) cc_final: 0.6720 (mt) REVERT: C 393 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6399 (mt) REVERT: C 422 MET cc_start: 0.6558 (tpt) cc_final: 0.6256 (ttp) REVERT: C 512 ARG cc_start: 0.7790 (mmm-85) cc_final: 0.7541 (mmm160) REVERT: C 551 ASN cc_start: 0.8513 (t0) cc_final: 0.8032 (t0) REVERT: C 634 HIS cc_start: 0.6670 (m90) cc_final: 0.6440 (m170) REVERT: C 653 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7403 (pm20) REVERT: C 715 GLU cc_start: 0.6825 (tt0) cc_final: 0.6615 (pt0) REVERT: D 33 GLU cc_start: 0.6610 (mt-10) cc_final: 0.6372 (mt-10) REVERT: D 42 LYS cc_start: 0.6708 (mtmt) cc_final: 0.6418 (mmtt) REVERT: D 54 GLU cc_start: 0.6825 (tt0) cc_final: 0.5917 (tm-30) REVERT: D 56 GLU cc_start: 0.5997 (mt-10) cc_final: 0.5575 (tm-30) REVERT: D 75 LEU cc_start: 0.5851 (mp) cc_final: 0.5474 (OUTLIER) REVERT: D 79 GLU cc_start: 0.7597 (tt0) cc_final: 0.6984 (mp0) REVERT: D 170 ARG cc_start: 0.6120 (mtp180) cc_final: 0.5389 (ptp90) REVERT: D 191 ARG cc_start: 0.6844 (ttm-80) cc_final: 0.5845 (tpp-160) REVERT: D 214 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7397 (mp0) REVERT: D 237 PHE cc_start: 0.6870 (m-80) cc_final: 0.6651 (m-80) REVERT: D 359 PHE cc_start: 0.7325 (t80) cc_final: 0.6778 (t80) REVERT: D 393 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6412 (mt) REVERT: D 422 MET cc_start: 0.6562 (tpt) cc_final: 0.6253 (ttp) REVERT: D 512 ARG cc_start: 0.7795 (mmm-85) cc_final: 0.7541 (mmm160) REVERT: D 551 ASN cc_start: 0.8502 (t0) cc_final: 0.8020 (t0) REVERT: D 593 ARG cc_start: 0.7985 (mtp180) cc_final: 0.7634 (mtp-110) REVERT: D 595 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6432 (mp0) REVERT: D 634 HIS cc_start: 0.6694 (m90) cc_final: 0.6463 (m170) REVERT: D 653 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7347 (pm20) REVERT: D 715 GLU cc_start: 0.6825 (tt0) cc_final: 0.6616 (pt0) outliers start: 24 outliers final: 10 residues processed: 500 average time/residue: 1.4140 time to fit residues: 798.5939 Evaluate side-chains 294 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 283 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 631 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 239 optimal weight: 0.0000 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN A 609 ASN ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN B 609 ASN ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 GLN C 609 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN D 609 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 22776 Z= 0.308 Angle : 0.562 7.415 30784 Z= 0.281 Chirality : 0.038 0.148 3444 Planarity : 0.004 0.034 3784 Dihedral : 14.448 178.433 3569 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.76 % Allowed : 10.05 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.89 (0.16), residues: 2608 helix: 1.62 (0.11), residues: 1952 sheet: None (None), residues: 0 loop : 0.32 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 315 HIS 0.004 0.001 HIS B 712 PHE 0.020 0.002 PHE D 341 TYR 0.013 0.002 TYR A 539 ARG 0.003 0.000 ARG B 754 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 296 time to evaluate : 2.515 Fit side-chains REVERT: A 42 LYS cc_start: 0.6930 (mtmt) cc_final: 0.6587 (mmtt) REVERT: A 56 GLU cc_start: 0.5900 (mt-10) cc_final: 0.5569 (tm-30) REVERT: A 79 GLU cc_start: 0.7518 (tt0) cc_final: 0.6894 (mp0) REVERT: A 87 GLU cc_start: 0.7491 (tt0) cc_final: 0.6896 (tp30) REVERT: A 170 ARG cc_start: 0.6595 (mtp180) cc_final: 0.5603 (ptp90) REVERT: A 214 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7552 (mp0) REVERT: A 332 LEU cc_start: 0.7138 (tt) cc_final: 0.6809 (mt) REVERT: A 335 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.6091 (mpt) REVERT: A 356 LEU cc_start: 0.7248 (mt) cc_final: 0.6984 (tp) REVERT: A 393 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6516 (mp) REVERT: A 512 ARG cc_start: 0.7859 (mmm-85) cc_final: 0.7655 (mmm160) REVERT: A 520 PHE cc_start: 0.6990 (OUTLIER) cc_final: 0.6067 (t80) REVERT: A 551 ASN cc_start: 0.8486 (t0) cc_final: 0.7955 (t0) REVERT: A 595 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6530 (mp0) REVERT: A 653 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7201 (pm20) REVERT: A 715 GLU cc_start: 0.7243 (tt0) cc_final: 0.6902 (pt0) REVERT: B 42 LYS cc_start: 0.6908 (mtmt) cc_final: 0.6568 (mmtt) REVERT: B 56 GLU cc_start: 0.5905 (mt-10) cc_final: 0.5588 (tm-30) REVERT: B 79 GLU cc_start: 0.7518 (tt0) cc_final: 0.6895 (mp0) REVERT: B 87 GLU cc_start: 0.7495 (tt0) cc_final: 0.6849 (tp30) REVERT: B 91 ASN cc_start: 0.7887 (m-40) cc_final: 0.7469 (m-40) REVERT: B 170 ARG cc_start: 0.6594 (mtp180) cc_final: 0.5605 (ptp90) REVERT: B 214 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7553 (mp0) REVERT: B 332 LEU cc_start: 0.7163 (tt) cc_final: 0.6824 (mt) REVERT: B 335 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6458 (mpt) REVERT: B 356 LEU cc_start: 0.7252 (mt) cc_final: 0.6980 (tp) REVERT: B 393 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6563 (mt) REVERT: B 520 PHE cc_start: 0.7001 (OUTLIER) cc_final: 0.6083 (t80) REVERT: B 551 ASN cc_start: 0.8525 (t0) cc_final: 0.7976 (t0) REVERT: B 595 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6530 (mp0) REVERT: B 653 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7210 (pm20) REVERT: B 715 GLU cc_start: 0.7243 (tt0) cc_final: 0.6902 (pt0) REVERT: C 42 LYS cc_start: 0.6960 (mtmt) cc_final: 0.6609 (mmtt) REVERT: C 56 GLU cc_start: 0.5889 (mt-10) cc_final: 0.5589 (tm-30) REVERT: C 79 GLU cc_start: 0.7518 (tt0) cc_final: 0.6895 (mp0) REVERT: C 87 GLU cc_start: 0.7490 (tt0) cc_final: 0.6902 (tp30) REVERT: C 170 ARG cc_start: 0.6418 (mtp180) cc_final: 0.5456 (ptp90) REVERT: C 214 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7564 (mp0) REVERT: C 332 LEU cc_start: 0.7165 (tt) cc_final: 0.6832 (mt) REVERT: C 356 LEU cc_start: 0.7256 (mt) cc_final: 0.6986 (tp) REVERT: C 393 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6444 (mt) REVERT: C 520 PHE cc_start: 0.7011 (OUTLIER) cc_final: 0.6091 (t80) REVERT: C 551 ASN cc_start: 0.8523 (t0) cc_final: 0.7966 (t0) REVERT: C 595 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6492 (mp0) REVERT: C 653 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7218 (pm20) REVERT: C 715 GLU cc_start: 0.7243 (tt0) cc_final: 0.6904 (pt0) REVERT: D 42 LYS cc_start: 0.6960 (mtmt) cc_final: 0.6610 (mmtt) REVERT: D 56 GLU cc_start: 0.5895 (mt-10) cc_final: 0.5591 (tm-30) REVERT: D 79 GLU cc_start: 0.7518 (tt0) cc_final: 0.6894 (mp0) REVERT: D 87 GLU cc_start: 0.7492 (tt0) cc_final: 0.6903 (tp30) REVERT: D 170 ARG cc_start: 0.6562 (mtp180) cc_final: 0.5594 (ptp90) REVERT: D 214 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7564 (mp0) REVERT: D 332 LEU cc_start: 0.7136 (tt) cc_final: 0.6809 (mt) REVERT: D 335 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6563 (mpt) REVERT: D 356 LEU cc_start: 0.7258 (mt) cc_final: 0.6999 (tp) REVERT: D 393 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6454 (mt) REVERT: D 520 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.6096 (t80) REVERT: D 551 ASN cc_start: 0.8524 (t0) cc_final: 0.7976 (t0) REVERT: D 552 ASN cc_start: 0.7410 (m-40) cc_final: 0.7091 (t0) REVERT: D 593 ARG cc_start: 0.7933 (mtp180) cc_final: 0.7608 (mtp-110) REVERT: D 595 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6498 (mp0) REVERT: D 653 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7222 (pm20) REVERT: D 715 GLU cc_start: 0.7242 (tt0) cc_final: 0.6905 (pt0) outliers start: 89 outliers final: 40 residues processed: 340 average time/residue: 1.2778 time to fit residues: 497.6450 Evaluate side-chains 315 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 264 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 520 PHE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 520 PHE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 750 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 10.0000 chunk 74 optimal weight: 0.3980 chunk 199 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 238 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 192 optimal weight: 0.4980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 192 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22776 Z= 0.213 Angle : 0.469 7.013 30784 Z= 0.239 Chirality : 0.036 0.149 3444 Planarity : 0.004 0.035 3784 Dihedral : 14.140 174.923 3560 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.05 % Allowed : 11.49 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 2.32 (0.16), residues: 2608 helix: 1.97 (0.11), residues: 1952 sheet: None (None), residues: 0 loop : 0.34 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 315 HIS 0.003 0.001 HIS A 92 PHE 0.021 0.001 PHE D 341 TYR 0.010 0.001 TYR B 524 ARG 0.001 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 294 time to evaluate : 2.479 Fit side-chains REVERT: A 42 LYS cc_start: 0.7022 (mtmt) cc_final: 0.6640 (mmtt) REVERT: A 54 GLU cc_start: 0.6508 (mp0) cc_final: 0.5577 (tm-30) REVERT: A 79 GLU cc_start: 0.7435 (tt0) cc_final: 0.6801 (mp0) REVERT: A 87 GLU cc_start: 0.7453 (tt0) cc_final: 0.6832 (tp30) REVERT: A 170 ARG cc_start: 0.6561 (mtp180) cc_final: 0.5487 (ptp90) REVERT: A 214 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7532 (mp0) REVERT: A 332 LEU cc_start: 0.7090 (tt) cc_final: 0.6786 (mt) REVERT: A 335 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.6148 (mpt) REVERT: A 356 LEU cc_start: 0.7286 (mt) cc_final: 0.7022 (tp) REVERT: A 393 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6712 (mp) REVERT: A 520 PHE cc_start: 0.7010 (OUTLIER) cc_final: 0.6121 (t80) REVERT: A 551 ASN cc_start: 0.8490 (t0) cc_final: 0.7949 (t0) REVERT: A 570 GLU cc_start: 0.7053 (tp30) cc_final: 0.6663 (mm-30) REVERT: A 595 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6516 (mp0) REVERT: A 653 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7260 (pm20) REVERT: A 715 GLU cc_start: 0.7230 (tt0) cc_final: 0.6898 (pt0) REVERT: B 42 LYS cc_start: 0.7025 (mtmt) cc_final: 0.6641 (mmtt) REVERT: B 54 GLU cc_start: 0.6506 (mp0) cc_final: 0.5579 (tm-30) REVERT: B 79 GLU cc_start: 0.7435 (tt0) cc_final: 0.6801 (mp0) REVERT: B 87 GLU cc_start: 0.7454 (tt0) cc_final: 0.6805 (tp30) REVERT: B 91 ASN cc_start: 0.7916 (m-40) cc_final: 0.7523 (m-40) REVERT: B 170 ARG cc_start: 0.6585 (mtp180) cc_final: 0.5519 (ptp90) REVERT: B 214 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7533 (mp0) REVERT: B 332 LEU cc_start: 0.7079 (tt) cc_final: 0.6766 (mt) REVERT: B 356 LEU cc_start: 0.7246 (mt) cc_final: 0.6972 (tp) REVERT: B 393 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6610 (mp) REVERT: B 520 PHE cc_start: 0.6993 (OUTLIER) cc_final: 0.6089 (t80) REVERT: B 551 ASN cc_start: 0.8517 (t0) cc_final: 0.7960 (t0) REVERT: B 570 GLU cc_start: 0.7041 (tp30) cc_final: 0.6652 (mm-30) REVERT: B 595 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6508 (mp0) REVERT: B 653 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7261 (pm20) REVERT: B 715 GLU cc_start: 0.7228 (tt0) cc_final: 0.6897 (pt0) REVERT: C 42 LYS cc_start: 0.7025 (mtmt) cc_final: 0.6637 (mmtt) REVERT: C 54 GLU cc_start: 0.6505 (mp0) cc_final: 0.5546 (tm-30) REVERT: C 79 GLU cc_start: 0.7311 (tt0) cc_final: 0.6739 (mp0) REVERT: C 87 GLU cc_start: 0.7460 (tt0) cc_final: 0.6855 (tp30) REVERT: C 170 ARG cc_start: 0.6557 (mtp180) cc_final: 0.5498 (ptp90) REVERT: C 214 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7507 (mp0) REVERT: C 332 LEU cc_start: 0.7088 (tt) cc_final: 0.6787 (mt) REVERT: C 335 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6547 (mpt) REVERT: C 356 LEU cc_start: 0.7253 (mt) cc_final: 0.6986 (tp) REVERT: C 393 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6518 (mp) REVERT: C 520 PHE cc_start: 0.7010 (OUTLIER) cc_final: 0.6111 (t80) REVERT: C 551 ASN cc_start: 0.8524 (t0) cc_final: 0.7955 (t0) REVERT: C 570 GLU cc_start: 0.7047 (tp30) cc_final: 0.6664 (mm-30) REVERT: C 595 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6493 (mp0) REVERT: C 653 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7265 (pm20) REVERT: C 715 GLU cc_start: 0.7247 (tt0) cc_final: 0.6907 (pt0) REVERT: D 42 LYS cc_start: 0.7022 (mtmt) cc_final: 0.6638 (mmtt) REVERT: D 54 GLU cc_start: 0.6506 (mp0) cc_final: 0.5576 (tm-30) REVERT: D 79 GLU cc_start: 0.7335 (tt0) cc_final: 0.6757 (mp0) REVERT: D 87 GLU cc_start: 0.7465 (tt0) cc_final: 0.6856 (tp30) REVERT: D 170 ARG cc_start: 0.6561 (mtp180) cc_final: 0.5498 (ptp90) REVERT: D 214 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7507 (mp0) REVERT: D 332 LEU cc_start: 0.7094 (tt) cc_final: 0.6797 (mt) REVERT: D 356 LEU cc_start: 0.7289 (mt) cc_final: 0.7033 (tp) REVERT: D 393 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6592 (mp) REVERT: D 520 PHE cc_start: 0.7002 (OUTLIER) cc_final: 0.6120 (t80) REVERT: D 551 ASN cc_start: 0.8523 (t0) cc_final: 0.7944 (t0) REVERT: D 570 GLU cc_start: 0.7049 (tp30) cc_final: 0.6659 (mm-30) REVERT: D 593 ARG cc_start: 0.8010 (mtp180) cc_final: 0.7669 (mtp-110) REVERT: D 595 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6500 (mp0) REVERT: D 653 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7266 (pm20) REVERT: D 715 GLU cc_start: 0.7209 (tt0) cc_final: 0.6862 (pt0) outliers start: 96 outliers final: 26 residues processed: 342 average time/residue: 1.2082 time to fit residues: 476.7749 Evaluate side-chains 293 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 257 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 520 PHE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 520 PHE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 750 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 241 optimal weight: 0.8980 chunk 255 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 228 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22776 Z= 0.247 Angle : 0.494 6.944 30784 Z= 0.249 Chirality : 0.037 0.148 3444 Planarity : 0.004 0.038 3784 Dihedral : 14.014 166.313 3554 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.63 % Allowed : 12.75 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 2.40 (0.16), residues: 2608 helix: 2.04 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.32 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 315 HIS 0.003 0.001 HIS C 326 PHE 0.022 0.002 PHE C 341 TYR 0.010 0.001 TYR A 539 ARG 0.003 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 282 time to evaluate : 3.021 Fit side-chains REVERT: A 42 LYS cc_start: 0.7057 (mtmt) cc_final: 0.6603 (mmtt) REVERT: A 79 GLU cc_start: 0.7324 (tt0) cc_final: 0.6745 (mp0) REVERT: A 87 GLU cc_start: 0.7483 (tt0) cc_final: 0.6811 (tp30) REVERT: A 170 ARG cc_start: 0.6709 (mtp180) cc_final: 0.5538 (ptp90) REVERT: A 214 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7495 (mp0) REVERT: A 332 LEU cc_start: 0.7028 (tt) cc_final: 0.6764 (mt) REVERT: A 356 LEU cc_start: 0.7257 (mt) cc_final: 0.7003 (tp) REVERT: A 393 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6686 (mp) REVERT: A 520 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.6134 (t80) REVERT: A 537 GLN cc_start: 0.7997 (tp40) cc_final: 0.7299 (tp40) REVERT: A 551 ASN cc_start: 0.8535 (t0) cc_final: 0.7991 (t0) REVERT: A 570 GLU cc_start: 0.7079 (tp30) cc_final: 0.6681 (mm-30) REVERT: A 595 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6517 (mp0) REVERT: A 653 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7242 (pm20) REVERT: A 715 GLU cc_start: 0.7101 (tt0) cc_final: 0.6756 (pt0) REVERT: B 42 LYS cc_start: 0.7059 (mtmt) cc_final: 0.6603 (mmtt) REVERT: B 79 GLU cc_start: 0.7307 (tt0) cc_final: 0.6745 (mp0) REVERT: B 87 GLU cc_start: 0.7479 (tt0) cc_final: 0.6739 (tp30) REVERT: B 91 ASN cc_start: 0.7950 (m-40) cc_final: 0.7351 (m-40) REVERT: B 115 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7069 (mm) REVERT: B 170 ARG cc_start: 0.6630 (mtp180) cc_final: 0.5446 (ptp90) REVERT: B 214 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7493 (mp0) REVERT: B 332 LEU cc_start: 0.7025 (tt) cc_final: 0.6759 (mt) REVERT: B 335 MET cc_start: 0.6861 (OUTLIER) cc_final: 0.6631 (mpt) REVERT: B 356 LEU cc_start: 0.7210 (mt) cc_final: 0.6950 (tp) REVERT: B 520 PHE cc_start: 0.6986 (OUTLIER) cc_final: 0.6093 (t80) REVERT: B 537 GLN cc_start: 0.7965 (tp40) cc_final: 0.7235 (tp40) REVERT: B 551 ASN cc_start: 0.8557 (t0) cc_final: 0.7978 (t0) REVERT: B 552 ASN cc_start: 0.7443 (m-40) cc_final: 0.7144 (t0) REVERT: B 553 CYS cc_start: 0.8154 (t) cc_final: 0.7762 (t) REVERT: B 570 GLU cc_start: 0.7078 (tp30) cc_final: 0.6682 (mm-30) REVERT: B 595 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6511 (mp0) REVERT: B 653 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7230 (pm20) REVERT: B 715 GLU cc_start: 0.7101 (tt0) cc_final: 0.6755 (pt0) REVERT: C 42 LYS cc_start: 0.7060 (mtmt) cc_final: 0.6601 (mmtt) REVERT: C 79 GLU cc_start: 0.7308 (tt0) cc_final: 0.6745 (mp0) REVERT: C 87 GLU cc_start: 0.7486 (tt0) cc_final: 0.6816 (tp30) REVERT: C 170 ARG cc_start: 0.6629 (mtp180) cc_final: 0.5450 (ptp90) REVERT: C 214 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7497 (mp0) REVERT: C 332 LEU cc_start: 0.7017 (tt) cc_final: 0.6753 (mt) REVERT: C 335 MET cc_start: 0.6873 (OUTLIER) cc_final: 0.6651 (mpt) REVERT: C 356 LEU cc_start: 0.7317 (mt) cc_final: 0.7054 (tp) REVERT: C 520 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6112 (t80) REVERT: C 537 GLN cc_start: 0.7961 (tp40) cc_final: 0.7237 (tp40) REVERT: C 551 ASN cc_start: 0.8550 (t0) cc_final: 0.7963 (t0) REVERT: C 552 ASN cc_start: 0.7465 (m-40) cc_final: 0.7155 (t0) REVERT: C 553 CYS cc_start: 0.8297 (t) cc_final: 0.8011 (t) REVERT: C 570 GLU cc_start: 0.7080 (tp30) cc_final: 0.6684 (mm-30) REVERT: C 595 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6524 (mp0) REVERT: C 653 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7231 (pm20) REVERT: C 715 GLU cc_start: 0.7100 (tt0) cc_final: 0.6756 (pt0) REVERT: D 42 LYS cc_start: 0.7072 (mtmt) cc_final: 0.6618 (mmtt) REVERT: D 79 GLU cc_start: 0.7323 (tt0) cc_final: 0.6744 (mp0) REVERT: D 87 GLU cc_start: 0.7491 (tt0) cc_final: 0.6820 (tp30) REVERT: D 170 ARG cc_start: 0.6631 (mtp180) cc_final: 0.5447 (ptp90) REVERT: D 214 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7496 (mp0) REVERT: D 332 LEU cc_start: 0.7017 (tt) cc_final: 0.6755 (mt) REVERT: D 335 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.6660 (mpt) REVERT: D 356 LEU cc_start: 0.7278 (mt) cc_final: 0.7017 (tp) REVERT: D 520 PHE cc_start: 0.7070 (OUTLIER) cc_final: 0.6124 (t80) REVERT: D 537 GLN cc_start: 0.7953 (tp40) cc_final: 0.7251 (tp40) REVERT: D 551 ASN cc_start: 0.8565 (t0) cc_final: 0.7998 (t0) REVERT: D 552 ASN cc_start: 0.7465 (m-40) cc_final: 0.7154 (t0) REVERT: D 553 CYS cc_start: 0.8221 (t) cc_final: 0.7859 (t) REVERT: D 570 GLU cc_start: 0.7082 (tp30) cc_final: 0.6686 (mm-30) REVERT: D 593 ARG cc_start: 0.8057 (mtp180) cc_final: 0.7708 (mtp-110) REVERT: D 595 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6537 (mp0) REVERT: D 653 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7230 (pm20) REVERT: D 715 GLU cc_start: 0.7099 (tt0) cc_final: 0.6756 (pt0) outliers start: 86 outliers final: 44 residues processed: 325 average time/residue: 1.3475 time to fit residues: 499.1622 Evaluate side-chains 316 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 263 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 520 PHE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 520 PHE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 750 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 190 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 217 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22776 Z= 0.312 Angle : 0.523 10.121 30784 Z= 0.265 Chirality : 0.038 0.150 3444 Planarity : 0.004 0.040 3784 Dihedral : 14.049 171.344 3546 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.59 % Allowed : 14.02 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.16), residues: 2608 helix: 1.97 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.19 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 315 HIS 0.004 0.001 HIS D 473 PHE 0.024 0.002 PHE D 341 TYR 0.010 0.001 TYR D 539 ARG 0.003 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 276 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7151 (mtmt) cc_final: 0.6615 (mmtt) REVERT: A 79 GLU cc_start: 0.7318 (tt0) cc_final: 0.6761 (mp0) REVERT: A 87 GLU cc_start: 0.7422 (tt0) cc_final: 0.6785 (tp30) REVERT: A 115 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7130 (mm) REVERT: A 170 ARG cc_start: 0.6837 (mtp180) cc_final: 0.5442 (ptp90) REVERT: A 214 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7438 (mp0) REVERT: A 332 LEU cc_start: 0.7059 (tt) cc_final: 0.6844 (mt) REVERT: A 335 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6619 (mpt) REVERT: A 356 LEU cc_start: 0.7240 (mt) cc_final: 0.6995 (tp) REVERT: A 520 PHE cc_start: 0.6855 (OUTLIER) cc_final: 0.6017 (t80) REVERT: A 537 GLN cc_start: 0.8010 (tp40) cc_final: 0.7391 (tp40) REVERT: A 551 ASN cc_start: 0.8610 (t0) cc_final: 0.8012 (t0) REVERT: A 570 GLU cc_start: 0.7071 (tp30) cc_final: 0.6658 (mm-30) REVERT: A 595 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6513 (mp0) REVERT: A 653 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7207 (pm20) REVERT: A 715 GLU cc_start: 0.7124 (tt0) cc_final: 0.6731 (pt0) REVERT: B 42 LYS cc_start: 0.7152 (mtmt) cc_final: 0.6614 (mmtt) REVERT: B 79 GLU cc_start: 0.7318 (tt0) cc_final: 0.6762 (mp0) REVERT: B 87 GLU cc_start: 0.7419 (tt0) cc_final: 0.6801 (tp30) REVERT: B 91 ASN cc_start: 0.8016 (m-40) cc_final: 0.7568 (m-40) REVERT: B 115 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7181 (mm) REVERT: B 170 ARG cc_start: 0.6838 (mtp180) cc_final: 0.5445 (ptp90) REVERT: B 214 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7439 (mp0) REVERT: B 332 LEU cc_start: 0.7068 (tt) cc_final: 0.6846 (mt) REVERT: B 356 LEU cc_start: 0.7208 (mt) cc_final: 0.6930 (tp) REVERT: B 393 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6658 (mp) REVERT: B 520 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.6024 (t80) REVERT: B 537 GLN cc_start: 0.8010 (tp40) cc_final: 0.7314 (tp40) REVERT: B 551 ASN cc_start: 0.8629 (t0) cc_final: 0.8022 (t0) REVERT: B 552 ASN cc_start: 0.7584 (m-40) cc_final: 0.7203 (t0) REVERT: B 553 CYS cc_start: 0.8247 (t) cc_final: 0.7723 (t) REVERT: B 570 GLU cc_start: 0.7098 (tp30) cc_final: 0.6694 (mm-30) REVERT: B 595 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6519 (mp0) REVERT: B 653 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7201 (pm20) REVERT: B 715 GLU cc_start: 0.7124 (tt0) cc_final: 0.6730 (pt0) REVERT: C 42 LYS cc_start: 0.7155 (mtmt) cc_final: 0.6614 (mmtt) REVERT: C 79 GLU cc_start: 0.7319 (tt0) cc_final: 0.6762 (mp0) REVERT: C 87 GLU cc_start: 0.7426 (tt0) cc_final: 0.6788 (tp30) REVERT: C 115 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7095 (mm) REVERT: C 170 ARG cc_start: 0.6837 (mtp180) cc_final: 0.5447 (ptp90) REVERT: C 214 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7441 (mp0) REVERT: C 332 LEU cc_start: 0.7051 (tt) cc_final: 0.6835 (mt) REVERT: C 335 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6714 (mpt) REVERT: C 356 LEU cc_start: 0.7247 (mt) cc_final: 0.6991 (tp) REVERT: C 393 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6642 (mp) REVERT: C 520 PHE cc_start: 0.6854 (OUTLIER) cc_final: 0.6010 (t80) REVERT: C 537 GLN cc_start: 0.8006 (tp40) cc_final: 0.7388 (tp40) REVERT: C 551 ASN cc_start: 0.8633 (t0) cc_final: 0.8037 (t0) REVERT: C 552 ASN cc_start: 0.7596 (m-40) cc_final: 0.7203 (t0) REVERT: C 553 CYS cc_start: 0.8236 (t) cc_final: 0.7715 (t) REVERT: C 570 GLU cc_start: 0.7104 (tp30) cc_final: 0.6701 (mm-30) REVERT: C 595 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6527 (mp0) REVERT: C 653 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7232 (pm20) REVERT: C 715 GLU cc_start: 0.7133 (tt0) cc_final: 0.6734 (pt0) REVERT: D 42 LYS cc_start: 0.7153 (mtmt) cc_final: 0.6615 (mmtt) REVERT: D 79 GLU cc_start: 0.7318 (tt0) cc_final: 0.6762 (mp0) REVERT: D 87 GLU cc_start: 0.7432 (tt0) cc_final: 0.6793 (tp30) REVERT: D 115 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7094 (mm) REVERT: D 170 ARG cc_start: 0.6836 (mtp180) cc_final: 0.5445 (ptp90) REVERT: D 214 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7435 (mp0) REVERT: D 332 LEU cc_start: 0.7059 (tt) cc_final: 0.6840 (mt) REVERT: D 356 LEU cc_start: 0.7242 (mt) cc_final: 0.6989 (tp) REVERT: D 393 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6647 (mp) REVERT: D 520 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.6044 (t80) REVERT: D 537 GLN cc_start: 0.8008 (tp40) cc_final: 0.7392 (tp40) REVERT: D 551 ASN cc_start: 0.8625 (t0) cc_final: 0.8025 (t0) REVERT: D 552 ASN cc_start: 0.7580 (m-40) cc_final: 0.7210 (t0) REVERT: D 553 CYS cc_start: 0.8230 (t) cc_final: 0.7719 (t) REVERT: D 570 GLU cc_start: 0.7066 (tp30) cc_final: 0.6653 (mm-30) REVERT: D 593 ARG cc_start: 0.8093 (mtp180) cc_final: 0.7752 (mtp-110) REVERT: D 595 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6527 (mp0) REVERT: D 623 MET cc_start: 0.7088 (mtp) cc_final: 0.6835 (mtm) REVERT: D 653 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7233 (pm20) REVERT: D 715 GLU cc_start: 0.7133 (tt0) cc_final: 0.6734 (pt0) outliers start: 85 outliers final: 34 residues processed: 325 average time/residue: 1.1938 time to fit residues: 447.6808 Evaluate side-chains 316 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 269 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 520 PHE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 520 PHE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 750 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 255 optimal weight: 0.4980 chunk 212 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS C 192 HIS C 326 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22776 Z= 0.141 Angle : 0.441 6.822 30784 Z= 0.226 Chirality : 0.035 0.142 3444 Planarity : 0.003 0.037 3784 Dihedral : 13.587 175.677 3544 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.91 % Allowed : 14.99 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 2.60 (0.16), residues: 2608 helix: 2.24 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.24 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 315 HIS 0.003 0.001 HIS D 92 PHE 0.022 0.001 PHE A 341 TYR 0.010 0.001 TYR D 200 ARG 0.002 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 303 time to evaluate : 2.543 Fit side-chains REVERT: A 42 LYS cc_start: 0.7126 (mtmt) cc_final: 0.6594 (mmtt) REVERT: A 79 GLU cc_start: 0.7297 (tt0) cc_final: 0.6723 (mp0) REVERT: A 87 GLU cc_start: 0.7435 (tt0) cc_final: 0.6780 (tp30) REVERT: A 170 ARG cc_start: 0.6900 (mtp180) cc_final: 0.5508 (ptp90) REVERT: A 214 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7442 (mp0) REVERT: A 332 LEU cc_start: 0.7047 (tt) cc_final: 0.6834 (mt) REVERT: A 356 LEU cc_start: 0.7208 (mt) cc_final: 0.6950 (tp) REVERT: A 393 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6687 (mp) REVERT: A 537 GLN cc_start: 0.7915 (tp40) cc_final: 0.7137 (tp40) REVERT: A 551 ASN cc_start: 0.8497 (t0) cc_final: 0.7888 (t0) REVERT: A 570 GLU cc_start: 0.7030 (tp30) cc_final: 0.6617 (mm-30) REVERT: A 595 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6505 (mp0) REVERT: A 715 GLU cc_start: 0.7004 (tt0) cc_final: 0.6629 (pt0) REVERT: B 42 LYS cc_start: 0.7129 (mtmt) cc_final: 0.6601 (mmtt) REVERT: B 79 GLU cc_start: 0.7298 (tt0) cc_final: 0.6730 (mp0) REVERT: B 87 GLU cc_start: 0.7488 (tt0) cc_final: 0.6850 (tp30) REVERT: B 91 ASN cc_start: 0.8010 (m-40) cc_final: 0.7580 (m-40) REVERT: B 170 ARG cc_start: 0.6850 (mtp180) cc_final: 0.5456 (ptp90) REVERT: B 214 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7438 (mp0) REVERT: B 356 LEU cc_start: 0.7229 (mt) cc_final: 0.6957 (tp) REVERT: B 393 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6622 (mt) REVERT: B 537 GLN cc_start: 0.7940 (tp40) cc_final: 0.7167 (tp40) REVERT: B 551 ASN cc_start: 0.8551 (t0) cc_final: 0.7978 (t0) REVERT: B 552 ASN cc_start: 0.7481 (m-40) cc_final: 0.7157 (t0) REVERT: B 553 CYS cc_start: 0.8115 (t) cc_final: 0.7740 (t) REVERT: B 570 GLU cc_start: 0.7018 (tp30) cc_final: 0.6604 (mm-30) REVERT: B 595 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6498 (mp0) REVERT: B 715 GLU cc_start: 0.7002 (tt0) cc_final: 0.6627 (pt0) REVERT: C 42 LYS cc_start: 0.7131 (mtmt) cc_final: 0.6600 (mmtt) REVERT: C 79 GLU cc_start: 0.7297 (tt0) cc_final: 0.6729 (mp0) REVERT: C 87 GLU cc_start: 0.7436 (tt0) cc_final: 0.6781 (tp30) REVERT: C 170 ARG cc_start: 0.6852 (mtp180) cc_final: 0.5460 (ptp90) REVERT: C 214 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7439 (mp0) REVERT: C 356 LEU cc_start: 0.7232 (mt) cc_final: 0.6975 (tp) REVERT: C 393 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6611 (mt) REVERT: C 537 GLN cc_start: 0.7985 (tp40) cc_final: 0.7203 (tp40) REVERT: C 551 ASN cc_start: 0.8544 (t0) cc_final: 0.7966 (t0) REVERT: C 552 ASN cc_start: 0.7494 (m-40) cc_final: 0.7155 (t0) REVERT: C 553 CYS cc_start: 0.8136 (t) cc_final: 0.7718 (t) REVERT: C 570 GLU cc_start: 0.7020 (tp30) cc_final: 0.6605 (mm-30) REVERT: C 595 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6500 (mp0) REVERT: C 715 GLU cc_start: 0.7002 (tt0) cc_final: 0.6627 (pt0) REVERT: D 42 LYS cc_start: 0.7129 (mtmt) cc_final: 0.6594 (mmtt) REVERT: D 79 GLU cc_start: 0.7229 (tt0) cc_final: 0.6660 (mp0) REVERT: D 87 GLU cc_start: 0.7443 (tt0) cc_final: 0.6787 (tp30) REVERT: D 115 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.7069 (mm) REVERT: D 170 ARG cc_start: 0.6853 (mtp180) cc_final: 0.5459 (ptp90) REVERT: D 214 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7396 (mp0) REVERT: D 332 LEU cc_start: 0.7039 (tt) cc_final: 0.6827 (mt) REVERT: D 356 LEU cc_start: 0.7327 (mt) cc_final: 0.7062 (tp) REVERT: D 393 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6609 (mt) REVERT: D 537 GLN cc_start: 0.7986 (tp40) cc_final: 0.7212 (tp40) REVERT: D 551 ASN cc_start: 0.8543 (t0) cc_final: 0.7988 (t0) REVERT: D 552 ASN cc_start: 0.7489 (m-40) cc_final: 0.7143 (t0) REVERT: D 553 CYS cc_start: 0.8131 (t) cc_final: 0.7717 (t) REVERT: D 570 GLU cc_start: 0.7023 (tp30) cc_final: 0.6607 (mm-30) REVERT: D 593 ARG cc_start: 0.8095 (mtp180) cc_final: 0.7742 (mtp-110) REVERT: D 595 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6502 (mp0) REVERT: D 715 GLU cc_start: 0.7003 (tt0) cc_final: 0.6628 (pt0) outliers start: 69 outliers final: 25 residues processed: 348 average time/residue: 1.2046 time to fit residues: 484.5577 Evaluate side-chains 297 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 267 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 750 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 186 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS ** D 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22776 Z= 0.273 Angle : 0.510 6.879 30784 Z= 0.258 Chirality : 0.037 0.153 3444 Planarity : 0.004 0.038 3784 Dihedral : 13.329 170.290 3544 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.42 % Allowed : 15.24 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 2.48 (0.16), residues: 2608 helix: 2.14 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.22 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 327 HIS 0.003 0.001 HIS D 326 PHE 0.024 0.002 PHE C 341 TYR 0.009 0.001 TYR A 539 ARG 0.002 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 272 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7093 (mtmt) cc_final: 0.6515 (mmtt) REVERT: A 79 GLU cc_start: 0.7160 (tt0) cc_final: 0.6590 (mp0) REVERT: A 87 GLU cc_start: 0.7420 (tt0) cc_final: 0.6769 (tp30) REVERT: A 115 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7079 (mm) REVERT: A 170 ARG cc_start: 0.6905 (mtp180) cc_final: 0.5541 (ptp90) REVERT: A 214 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7428 (mp0) REVERT: A 332 LEU cc_start: 0.7055 (tt) cc_final: 0.6853 (mt) REVERT: A 356 LEU cc_start: 0.7223 (mt) cc_final: 0.6973 (tp) REVERT: A 510 LEU cc_start: 0.6696 (tp) cc_final: 0.6471 (mp) REVERT: A 551 ASN cc_start: 0.8598 (t0) cc_final: 0.7992 (t0) REVERT: A 570 GLU cc_start: 0.7059 (tp30) cc_final: 0.6649 (mm-30) REVERT: A 595 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6510 (mp0) REVERT: A 715 GLU cc_start: 0.7009 (tt0) cc_final: 0.6609 (pt0) REVERT: B 42 LYS cc_start: 0.7171 (mtmt) cc_final: 0.6594 (mmtt) REVERT: B 79 GLU cc_start: 0.7269 (tt0) cc_final: 0.6675 (mp0) REVERT: B 87 GLU cc_start: 0.7411 (tt0) cc_final: 0.6788 (tp30) REVERT: B 91 ASN cc_start: 0.8057 (m-40) cc_final: 0.7608 (m-40) REVERT: B 115 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7159 (mm) REVERT: B 170 ARG cc_start: 0.6903 (mtp180) cc_final: 0.5514 (ptp90) REVERT: B 214 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7428 (mp0) REVERT: B 356 LEU cc_start: 0.7258 (mt) cc_final: 0.7011 (tp) REVERT: B 393 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6683 (mt) REVERT: B 552 ASN cc_start: 0.7585 (m-40) cc_final: 0.7193 (t0) REVERT: B 553 CYS cc_start: 0.8166 (t) cc_final: 0.7740 (t) REVERT: B 570 GLU cc_start: 0.7088 (tp30) cc_final: 0.6679 (mm-30) REVERT: B 595 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6513 (mp0) REVERT: B 715 GLU cc_start: 0.7010 (tt0) cc_final: 0.6608 (pt0) REVERT: C 42 LYS cc_start: 0.7146 (mtmt) cc_final: 0.6565 (mmtt) REVERT: C 79 GLU cc_start: 0.7269 (tt0) cc_final: 0.6675 (mp0) REVERT: C 87 GLU cc_start: 0.7421 (tt0) cc_final: 0.6772 (tp30) REVERT: C 170 ARG cc_start: 0.6902 (mtp180) cc_final: 0.5514 (ptp90) REVERT: C 214 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7431 (mp0) REVERT: C 356 LEU cc_start: 0.7334 (mt) cc_final: 0.7092 (tp) REVERT: C 393 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6677 (mp) REVERT: C 520 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.6164 (t80) REVERT: C 552 ASN cc_start: 0.7588 (m-40) cc_final: 0.7198 (t0) REVERT: C 553 CYS cc_start: 0.8166 (t) cc_final: 0.7740 (t) REVERT: C 570 GLU cc_start: 0.7086 (tp30) cc_final: 0.6675 (mm-30) REVERT: C 595 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6513 (mp0) REVERT: C 715 GLU cc_start: 0.7009 (tt0) cc_final: 0.6608 (pt0) REVERT: D 42 LYS cc_start: 0.7161 (mtmt) cc_final: 0.6583 (mmtt) REVERT: D 79 GLU cc_start: 0.7161 (tt0) cc_final: 0.6591 (mp0) REVERT: D 87 GLU cc_start: 0.7429 (tt0) cc_final: 0.6778 (tp30) REVERT: D 115 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7087 (mm) REVERT: D 170 ARG cc_start: 0.6906 (mtp180) cc_final: 0.5534 (ptp90) REVERT: D 214 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7428 (mp0) REVERT: D 332 LEU cc_start: 0.6978 (tt) cc_final: 0.6756 (mt) REVERT: D 356 LEU cc_start: 0.7203 (mt) cc_final: 0.6932 (tp) REVERT: D 393 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6670 (mt) REVERT: D 520 PHE cc_start: 0.6984 (OUTLIER) cc_final: 0.6176 (t80) REVERT: D 552 ASN cc_start: 0.7595 (m-40) cc_final: 0.7189 (t0) REVERT: D 553 CYS cc_start: 0.8175 (t) cc_final: 0.7708 (t) REVERT: D 570 GLU cc_start: 0.7088 (tp30) cc_final: 0.6678 (mm-30) REVERT: D 593 ARG cc_start: 0.8091 (mtp180) cc_final: 0.7740 (mtp-110) REVERT: D 595 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6509 (mp0) REVERT: D 715 GLU cc_start: 0.7009 (tt0) cc_final: 0.6609 (pt0) outliers start: 81 outliers final: 38 residues processed: 320 average time/residue: 1.2298 time to fit residues: 454.5205 Evaluate side-chains 305 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 259 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 520 PHE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 520 PHE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 728 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 231 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 748 GLN D 731 ASN D 748 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22776 Z= 0.209 Angle : 0.481 6.830 30784 Z= 0.244 Chirality : 0.036 0.147 3444 Planarity : 0.003 0.037 3784 Dihedral : 13.008 171.767 3544 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.67 % Allowed : 15.08 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.16), residues: 2608 helix: 2.19 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.19 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 327 HIS 0.002 0.001 HIS B 92 PHE 0.023 0.001 PHE C 341 TYR 0.009 0.001 TYR A 524 ARG 0.006 0.000 ARG D 323 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 269 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7013 (mtmt) cc_final: 0.6422 (mmtt) REVERT: A 79 GLU cc_start: 0.7246 (tt0) cc_final: 0.6668 (mp0) REVERT: A 87 GLU cc_start: 0.7419 (tt0) cc_final: 0.6767 (tp30) REVERT: A 115 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7170 (mm) REVERT: A 170 ARG cc_start: 0.6962 (mtp180) cc_final: 0.5699 (ptp-170) REVERT: A 214 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7408 (mp0) REVERT: A 332 LEU cc_start: 0.7046 (tt) cc_final: 0.6844 (mt) REVERT: A 356 LEU cc_start: 0.7312 (mt) cc_final: 0.7078 (tp) REVERT: A 393 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6698 (mt) REVERT: A 510 LEU cc_start: 0.6761 (tp) cc_final: 0.6534 (mp) REVERT: A 551 ASN cc_start: 0.8593 (t0) cc_final: 0.7977 (t0) REVERT: A 570 GLU cc_start: 0.7052 (tp30) cc_final: 0.6633 (mm-30) REVERT: A 595 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6505 (mp0) REVERT: A 715 GLU cc_start: 0.6970 (tt0) cc_final: 0.6577 (pt0) REVERT: B 42 LYS cc_start: 0.7105 (mtmt) cc_final: 0.6523 (mmtt) REVERT: B 79 GLU cc_start: 0.7235 (tt0) cc_final: 0.6678 (mp0) REVERT: B 87 GLU cc_start: 0.7410 (tt0) cc_final: 0.6764 (tp30) REVERT: B 91 ASN cc_start: 0.8051 (m-40) cc_final: 0.7582 (m-40) REVERT: B 115 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7179 (mm) REVERT: B 170 ARG cc_start: 0.6957 (mtp180) cc_final: 0.5686 (ptp-170) REVERT: B 214 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7407 (mp0) REVERT: B 356 LEU cc_start: 0.7279 (mt) cc_final: 0.6997 (tp) REVERT: B 393 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6645 (mt) REVERT: B 552 ASN cc_start: 0.7576 (m-40) cc_final: 0.7211 (t0) REVERT: B 553 CYS cc_start: 0.8141 (t) cc_final: 0.7733 (t) REVERT: B 570 GLU cc_start: 0.7047 (tp30) cc_final: 0.6629 (mm-30) REVERT: B 595 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6505 (mp0) REVERT: B 715 GLU cc_start: 0.6972 (tt0) cc_final: 0.6577 (pt0) REVERT: C 42 LYS cc_start: 0.7072 (mtmt) cc_final: 0.6549 (mmtt) REVERT: C 79 GLU cc_start: 0.7275 (tt0) cc_final: 0.6689 (mp0) REVERT: C 87 GLU cc_start: 0.7426 (tt0) cc_final: 0.6767 (tp30) REVERT: C 115 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7187 (mm) REVERT: C 170 ARG cc_start: 0.6953 (mtp180) cc_final: 0.5667 (ptp-170) REVERT: C 214 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7408 (mp0) REVERT: C 356 LEU cc_start: 0.7321 (mt) cc_final: 0.7075 (tp) REVERT: C 393 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6633 (mp) REVERT: C 552 ASN cc_start: 0.7587 (m-40) cc_final: 0.7209 (t0) REVERT: C 553 CYS cc_start: 0.8140 (t) cc_final: 0.7732 (t) REVERT: C 570 GLU cc_start: 0.7048 (tp30) cc_final: 0.6629 (mm-30) REVERT: C 595 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6505 (mp0) REVERT: C 715 GLU cc_start: 0.6972 (tt0) cc_final: 0.6577 (pt0) REVERT: D 42 LYS cc_start: 0.7015 (mtmt) cc_final: 0.6424 (mmtt) REVERT: D 79 GLU cc_start: 0.7248 (tt0) cc_final: 0.6669 (mp0) REVERT: D 87 GLU cc_start: 0.7432 (tt0) cc_final: 0.6773 (tp30) REVERT: D 115 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7166 (mm) REVERT: D 170 ARG cc_start: 0.6961 (mtp180) cc_final: 0.5689 (ptp-170) REVERT: D 214 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7406 (mp0) REVERT: D 356 LEU cc_start: 0.7180 (mt) cc_final: 0.6917 (tp) REVERT: D 393 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6627 (mt) REVERT: D 552 ASN cc_start: 0.7596 (m-40) cc_final: 0.7199 (t0) REVERT: D 553 CYS cc_start: 0.8137 (t) cc_final: 0.7727 (t) REVERT: D 570 GLU cc_start: 0.7050 (tp30) cc_final: 0.6630 (mm-30) REVERT: D 593 ARG cc_start: 0.8095 (mtp180) cc_final: 0.7743 (mtp-110) REVERT: D 595 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6505 (mp0) REVERT: D 715 GLU cc_start: 0.6944 (tt0) cc_final: 0.6545 (pt0) outliers start: 87 outliers final: 41 residues processed: 328 average time/residue: 1.1818 time to fit residues: 447.9449 Evaluate side-chains 305 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 256 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 5.9990 chunk 222 optimal weight: 0.0980 chunk 237 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 214 optimal weight: 0.7980 chunk 224 optimal weight: 0.8980 chunk 236 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN D 82 ASN D 731 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22776 Z= 0.310 Angle : 0.533 6.931 30784 Z= 0.272 Chirality : 0.038 0.149 3444 Planarity : 0.004 0.037 3784 Dihedral : 12.931 172.951 3544 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.59 % Allowed : 15.29 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 2.31 (0.16), residues: 2608 helix: 2.02 (0.11), residues: 1940 sheet: None (None), residues: 0 loop : 0.14 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP D 327 HIS 0.003 0.001 HIS A 473 PHE 0.027 0.002 PHE A 341 TYR 0.008 0.001 TYR C 539 ARG 0.004 0.000 ARG D 323 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 259 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7032 (mtmt) cc_final: 0.6535 (mmtt) REVERT: A 79 GLU cc_start: 0.7308 (tt0) cc_final: 0.6660 (mp0) REVERT: A 87 GLU cc_start: 0.7369 (tt0) cc_final: 0.6713 (tp30) REVERT: A 115 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7210 (mm) REVERT: A 170 ARG cc_start: 0.7014 (mtp180) cc_final: 0.5655 (ptp-170) REVERT: A 214 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7476 (mp0) REVERT: A 332 LEU cc_start: 0.7005 (tt) cc_final: 0.6805 (mt) REVERT: A 341 PHE cc_start: 0.6770 (OUTLIER) cc_final: 0.6045 (p90) REVERT: A 356 LEU cc_start: 0.7382 (mt) cc_final: 0.7123 (tp) REVERT: A 393 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6708 (mp) REVERT: A 510 LEU cc_start: 0.6744 (tp) cc_final: 0.6484 (mp) REVERT: A 520 PHE cc_start: 0.6945 (OUTLIER) cc_final: 0.6143 (t80) REVERT: A 551 ASN cc_start: 0.8605 (t0) cc_final: 0.7983 (t0) REVERT: A 570 GLU cc_start: 0.7092 (tp30) cc_final: 0.6682 (mm-30) REVERT: A 595 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6545 (mp0) REVERT: A 715 GLU cc_start: 0.6951 (tt0) cc_final: 0.6550 (pt0) REVERT: B 42 LYS cc_start: 0.7047 (mtmt) cc_final: 0.6552 (mmtt) REVERT: B 79 GLU cc_start: 0.7172 (tt0) cc_final: 0.6627 (mp0) REVERT: B 87 GLU cc_start: 0.7325 (tt0) cc_final: 0.6676 (tp30) REVERT: B 91 ASN cc_start: 0.8086 (m-40) cc_final: 0.7612 (m-40) REVERT: B 115 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7219 (mm) REVERT: B 170 ARG cc_start: 0.7012 (mtp180) cc_final: 0.5680 (ptp-170) REVERT: B 214 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7475 (mp0) REVERT: B 341 PHE cc_start: 0.6772 (OUTLIER) cc_final: 0.6052 (p90) REVERT: B 356 LEU cc_start: 0.7334 (mt) cc_final: 0.7057 (tp) REVERT: B 393 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6707 (mp) REVERT: B 552 ASN cc_start: 0.7603 (m-40) cc_final: 0.7186 (t0) REVERT: B 553 CYS cc_start: 0.8175 (t) cc_final: 0.7739 (t) REVERT: B 570 GLU cc_start: 0.7108 (tp30) cc_final: 0.6697 (mm-30) REVERT: B 595 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6514 (mp0) REVERT: B 715 GLU cc_start: 0.6949 (tt0) cc_final: 0.6549 (pt0) REVERT: C 42 LYS cc_start: 0.7048 (mtmt) cc_final: 0.6554 (mmtt) REVERT: C 79 GLU cc_start: 0.7171 (tt0) cc_final: 0.6627 (mp0) REVERT: C 87 GLU cc_start: 0.7372 (tt0) cc_final: 0.6719 (tp30) REVERT: C 115 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7228 (mm) REVERT: C 170 ARG cc_start: 0.7007 (mtp180) cc_final: 0.5549 (ptp90) REVERT: C 214 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7398 (mp0) REVERT: C 341 PHE cc_start: 0.6762 (OUTLIER) cc_final: 0.6048 (p90) REVERT: C 356 LEU cc_start: 0.7367 (mt) cc_final: 0.7081 (tp) REVERT: C 393 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6690 (mp) REVERT: C 552 ASN cc_start: 0.7617 (m-40) cc_final: 0.7181 (t0) REVERT: C 553 CYS cc_start: 0.8173 (t) cc_final: 0.7737 (t) REVERT: C 570 GLU cc_start: 0.7121 (tp30) cc_final: 0.6712 (mm-30) REVERT: C 595 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6503 (mp0) REVERT: C 715 GLU cc_start: 0.6942 (tt0) cc_final: 0.6532 (pt0) REVERT: D 42 LYS cc_start: 0.7035 (mtmt) cc_final: 0.6538 (mmtt) REVERT: D 79 GLU cc_start: 0.7310 (tt0) cc_final: 0.6661 (mp0) REVERT: D 87 GLU cc_start: 0.7379 (tt0) cc_final: 0.6725 (tp30) REVERT: D 115 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7188 (mm) REVERT: D 170 ARG cc_start: 0.7013 (mtp180) cc_final: 0.5681 (ptp-170) REVERT: D 214 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7395 (mp0) REVERT: D 341 PHE cc_start: 0.6775 (OUTLIER) cc_final: 0.6053 (p90) REVERT: D 356 LEU cc_start: 0.7348 (mt) cc_final: 0.7053 (tp) REVERT: D 393 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6691 (mp) REVERT: D 552 ASN cc_start: 0.7616 (m-40) cc_final: 0.7179 (t0) REVERT: D 553 CYS cc_start: 0.8171 (t) cc_final: 0.7735 (t) REVERT: D 570 GLU cc_start: 0.7090 (tp30) cc_final: 0.6680 (mm-30) REVERT: D 593 ARG cc_start: 0.8110 (mtp180) cc_final: 0.7757 (mtp-110) REVERT: D 595 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6500 (mp0) REVERT: D 715 GLU cc_start: 0.6942 (tt0) cc_final: 0.6532 (pt0) outliers start: 85 outliers final: 44 residues processed: 314 average time/residue: 1.2191 time to fit residues: 442.7404 Evaluate side-chains 309 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 252 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 653 GLU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 653 GLU Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 chunk 263 optimal weight: 5.9990 chunk 242 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 166 optimal weight: 0.0170 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 731 ASN B 625 ASN B 731 ASN C 731 ASN D 82 ASN D 731 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 22776 Z= 0.147 Angle : 0.480 9.880 30784 Z= 0.247 Chirality : 0.035 0.143 3444 Planarity : 0.003 0.036 3784 Dihedral : 12.362 174.945 3544 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.45 % Allowed : 16.68 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 2.57 (0.16), residues: 2608 helix: 2.23 (0.12), residues: 1944 sheet: None (None), residues: 0 loop : 0.18 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP D 327 HIS 0.002 0.000 HIS A 92 PHE 0.025 0.001 PHE C 341 TYR 0.009 0.001 TYR B 200 ARG 0.004 0.000 ARG D 323 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 284 time to evaluate : 2.650 Fit side-chains REVERT: A 42 LYS cc_start: 0.6942 (mtmt) cc_final: 0.6458 (mmtt) REVERT: A 71 ARG cc_start: 0.5337 (mtm110) cc_final: 0.5096 (mtm110) REVERT: A 79 GLU cc_start: 0.7282 (tt0) cc_final: 0.6629 (mp0) REVERT: A 87 GLU cc_start: 0.7355 (tt0) cc_final: 0.6679 (tp30) REVERT: A 115 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7173 (mm) REVERT: A 170 ARG cc_start: 0.7018 (mtp180) cc_final: 0.5551 (ptp90) REVERT: A 214 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7505 (mp0) REVERT: A 332 LEU cc_start: 0.7037 (tt) cc_final: 0.6835 (mt) REVERT: A 341 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.5986 (p90) REVERT: A 356 LEU cc_start: 0.7369 (mt) cc_final: 0.7103 (tp) REVERT: A 393 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6683 (mt) REVERT: A 510 LEU cc_start: 0.6859 (tp) cc_final: 0.6622 (mp) REVERT: A 528 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6991 (tp) REVERT: A 570 GLU cc_start: 0.7040 (tp30) cc_final: 0.6623 (mm-30) REVERT: A 595 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6497 (mp0) REVERT: A 623 MET cc_start: 0.6882 (mtp) cc_final: 0.6640 (mtm) REVERT: A 715 GLU cc_start: 0.6916 (tt0) cc_final: 0.6516 (pt0) REVERT: B 42 LYS cc_start: 0.6960 (mtmt) cc_final: 0.6477 (mmtt) REVERT: B 71 ARG cc_start: 0.5339 (mtm110) cc_final: 0.5086 (mtm110) REVERT: B 79 GLU cc_start: 0.7204 (tt0) cc_final: 0.6564 (mp0) REVERT: B 87 GLU cc_start: 0.7334 (tt0) cc_final: 0.6671 (tp30) REVERT: B 91 ASN cc_start: 0.8082 (m-40) cc_final: 0.7602 (m-40) REVERT: B 115 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7184 (mm) REVERT: B 170 ARG cc_start: 0.6973 (mtp180) cc_final: 0.5532 (ptp90) REVERT: B 214 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7506 (mp0) REVERT: B 341 PHE cc_start: 0.6639 (OUTLIER) cc_final: 0.5999 (p90) REVERT: B 356 LEU cc_start: 0.7323 (mt) cc_final: 0.7029 (tp) REVERT: B 393 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6668 (mp) REVERT: B 552 ASN cc_start: 0.7595 (m-40) cc_final: 0.7205 (t0) REVERT: B 553 CYS cc_start: 0.8119 (t) cc_final: 0.7721 (t) REVERT: B 570 GLU cc_start: 0.7087 (tp30) cc_final: 0.6671 (mm-30) REVERT: B 595 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6498 (mp0) REVERT: B 715 GLU cc_start: 0.6917 (tt0) cc_final: 0.6516 (pt0) REVERT: C 42 LYS cc_start: 0.6961 (mtmt) cc_final: 0.6478 (mmtt) REVERT: C 71 ARG cc_start: 0.5343 (mtm110) cc_final: 0.5098 (mtm110) REVERT: C 79 GLU cc_start: 0.7293 (tt0) cc_final: 0.6651 (mp0) REVERT: C 87 GLU cc_start: 0.7380 (tt0) cc_final: 0.6717 (tp30) REVERT: C 170 ARG cc_start: 0.6964 (mtp180) cc_final: 0.5626 (ptp-170) REVERT: C 214 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7423 (mp0) REVERT: C 341 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.6007 (p90) REVERT: C 356 LEU cc_start: 0.7295 (mt) cc_final: 0.7013 (tp) REVERT: C 393 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6638 (mt) REVERT: C 528 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6950 (tp) REVERT: C 552 ASN cc_start: 0.7607 (m-40) cc_final: 0.7202 (t0) REVERT: C 553 CYS cc_start: 0.8115 (t) cc_final: 0.7721 (t) REVERT: C 570 GLU cc_start: 0.7034 (tp30) cc_final: 0.6617 (mm-30) REVERT: C 595 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6500 (mp0) REVERT: C 715 GLU cc_start: 0.6916 (tt0) cc_final: 0.6516 (pt0) REVERT: D 42 LYS cc_start: 0.6944 (mtmt) cc_final: 0.6462 (mmtt) REVERT: D 71 ARG cc_start: 0.5355 (mtm110) cc_final: 0.5111 (mtm110) REVERT: D 79 GLU cc_start: 0.7284 (tt0) cc_final: 0.6639 (mp0) REVERT: D 87 GLU cc_start: 0.7383 (tt0) cc_final: 0.6716 (tp30) REVERT: D 170 ARG cc_start: 0.6992 (mtp180) cc_final: 0.5535 (ptp90) REVERT: D 214 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7422 (mp0) REVERT: D 341 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.5991 (p90) REVERT: D 356 LEU cc_start: 0.7319 (mt) cc_final: 0.7038 (tp) REVERT: D 393 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6647 (mt) REVERT: D 528 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6943 (tp) REVERT: D 552 ASN cc_start: 0.7607 (m-40) cc_final: 0.7198 (t0) REVERT: D 553 CYS cc_start: 0.8113 (t) cc_final: 0.7717 (t) REVERT: D 570 GLU cc_start: 0.7034 (tp30) cc_final: 0.6616 (mm-30) REVERT: D 593 ARG cc_start: 0.8125 (mtp180) cc_final: 0.7752 (mtp-110) REVERT: D 595 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6497 (mp0) REVERT: D 715 GLU cc_start: 0.6917 (tt0) cc_final: 0.6516 (pt0) outliers start: 58 outliers final: 34 residues processed: 331 average time/residue: 1.1523 time to fit residues: 442.9404 Evaluate side-chains 311 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 264 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 209 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 184 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 163 GLN A 551 ASN A 625 ASN A 731 ASN B 731 ASN C 192 HIS C 625 ASN C 731 ASN D 82 ASN D 163 GLN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.156174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.120249 restraints weight = 24559.503| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.59 r_work: 0.3251 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22776 Z= 0.153 Angle : 0.484 8.039 30784 Z= 0.249 Chirality : 0.036 0.142 3444 Planarity : 0.003 0.037 3784 Dihedral : 11.707 177.384 3544 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.12 % Allowed : 16.22 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 2.65 (0.16), residues: 2608 helix: 2.28 (0.11), residues: 1948 sheet: None (None), residues: 0 loop : 0.23 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP D 327 HIS 0.005 0.000 HIS D 326 PHE 0.025 0.001 PHE B 341 TYR 0.009 0.001 TYR B 200 ARG 0.004 0.000 ARG D 323 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7893.56 seconds wall clock time: 138 minutes 52.38 seconds (8332.38 seconds total)