Starting phenix.real_space_refine on Mon Mar 18 10:21:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/03_2024/7n5d_24186_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/03_2024/7n5d_24186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/03_2024/7n5d_24186.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/03_2024/7n5d_24186.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/03_2024/7n5d_24186_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/03_2024/7n5d_24186_updated.pdb" } resolution = 2.8 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= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 13516 2.51 5 N 3419 2.21 5 O 3574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 598": "OD1" <-> "OD2" Residue "C PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 625": "OE1" <-> "OE2" Residue "D TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 746": "OE1" <-> "OE2" Residue "E PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 611": "OE1" <-> "OE2" Residue "G PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 695": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20593 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3019 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 7, 'TRANS': 378} Chain breaks: 5 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "F" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "G" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.72, per 1000 atoms: 0.52 Number of scatterers: 20593 At special positions: 0 Unit cell: (147.29, 144.2, 140.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3574 8.00 N 3419 7.00 C 13516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.98 Conformation dependent library (CDL) restraints added in 3.4 seconds 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5066 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 14 sheets defined 60.9% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.92 Creating SS restraints... Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 191 through 201 Processing helix chain 'A' and resid 223 through 243 removed outlier: 4.232A pdb=" N LEU A 226 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU A 234 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 282 removed outlier: 5.237A pdb=" N THR A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 332 removed outlier: 4.266A pdb=" N HIS A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 352 Processing helix chain 'A' and resid 504 through 551 Processing helix chain 'A' and resid 557 through 573 removed outlier: 3.585A pdb=" N PHE A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 589 Processing helix chain 'A' and resid 631 through 636 removed outlier: 4.907A pdb=" N THR A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 678 Processing helix chain 'A' and resid 715 through 736 Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 236 through 240 Processing helix chain 'B' and resid 265 through 284 Processing helix chain 'B' and resid 296 through 330 removed outlier: 3.906A pdb=" N SER B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 350 removed outlier: 5.032A pdb=" N ASP B 337 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 349 " --> pdb=" O HIS B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 551 removed outlier: 4.134A pdb=" N ASN B 525 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS B 526 " --> pdb=" O LEU B 522 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 527 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ALA B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL B 529 " --> pdb=" O ASN B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 589 removed outlier: 5.467A pdb=" N ASN B 576 " --> pdb=" O PHE B 572 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 636 removed outlier: 4.664A pdb=" N THR B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 677 Processing helix chain 'B' and resid 715 through 735 Processing helix chain 'C' and resid 187 through 202 Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'C' and resid 265 through 284 Processing helix chain 'C' and resid 296 through 330 removed outlier: 3.892A pdb=" N SER C 329 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 351 removed outlier: 5.010A pdb=" N ASP C 337 " --> pdb=" O ARG C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 551 removed outlier: 4.129A pdb=" N ASN C 525 " --> pdb=" O ALA C 521 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS C 526 " --> pdb=" O LEU C 522 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR C 527 " --> pdb=" O ASN C 523 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ALA C 528 " --> pdb=" O ASP C 524 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL C 529 " --> pdb=" O ASN C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 589 removed outlier: 5.551A pdb=" N ASN C 576 " --> pdb=" O PHE C 572 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 636 removed outlier: 4.970A pdb=" N THR C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 677 Processing helix chain 'C' and resid 715 through 736 Processing helix chain 'D' and resid 187 through 202 Processing helix chain 'D' and resid 223 through 231 Processing helix chain 'D' and resid 235 through 241 Processing helix chain 'D' and resid 265 through 284 Processing helix chain 'D' and resid 296 through 330 removed outlier: 3.709A pdb=" N SER D 328 " --> pdb=" O LYS D 324 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER D 329 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 351 removed outlier: 5.086A pdb=" N ASP D 337 " --> pdb=" O ARG D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 551 removed outlier: 4.146A pdb=" N ASN D 525 " --> pdb=" O ALA D 521 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS D 526 " --> pdb=" O LEU D 522 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR D 527 " --> pdb=" O ASN D 523 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA D 528 " --> pdb=" O ASP D 524 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL D 529 " --> pdb=" O ASN D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 589 removed outlier: 5.586A pdb=" N ASN D 576 " --> pdb=" O PHE D 572 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N THR D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 636 removed outlier: 5.031A pdb=" N THR D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 679 Processing helix chain 'D' and resid 715 through 736 Processing helix chain 'E' and resid 187 through 202 Processing helix chain 'E' and resid 223 through 231 Processing helix chain 'E' and resid 235 through 241 Processing helix chain 'E' and resid 265 through 284 Processing helix chain 'E' and resid 296 through 330 removed outlier: 3.648A pdb=" N SER E 328 " --> pdb=" O LYS E 324 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER E 329 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 351 removed outlier: 5.103A pdb=" N ASP E 337 " --> pdb=" O ARG E 334 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU E 341 " --> pdb=" O ARG E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 523 Processing helix chain 'E' and resid 527 through 551 Processing helix chain 'E' and resid 557 through 589 removed outlier: 5.669A pdb=" N ASN E 576 " --> pdb=" O PHE E 572 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR E 577 " --> pdb=" O ILE E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 636 removed outlier: 4.850A pdb=" N THR E 636 " --> pdb=" O SER E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 662 through 677 Processing helix chain 'E' and resid 715 through 735 Processing helix chain 'F' and resid 187 through 202 Processing helix chain 'F' and resid 223 through 231 Processing helix chain 'F' and resid 236 through 240 Processing helix chain 'F' and resid 265 through 284 Processing helix chain 'F' and resid 296 through 330 removed outlier: 3.985A pdb=" N SER F 329 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE F 330 " --> pdb=" O LEU F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 351 removed outlier: 5.041A pdb=" N ASP F 337 " --> pdb=" O ARG F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 525 removed outlier: 4.147A pdb=" N ASN F 525 " --> pdb=" O ALA F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 551 Processing helix chain 'F' and resid 557 through 589 removed outlier: 5.688A pdb=" N ASN F 576 " --> pdb=" O PHE F 572 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR F 577 " --> pdb=" O ILE F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 636 removed outlier: 5.218A pdb=" N THR F 636 " --> pdb=" O SER F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 678 Processing helix chain 'F' and resid 715 through 736 Processing helix chain 'G' and resid 187 through 202 Processing helix chain 'G' and resid 223 through 230 Processing helix chain 'G' and resid 236 through 241 Processing helix chain 'G' and resid 265 through 284 Processing helix chain 'G' and resid 296 through 330 removed outlier: 3.906A pdb=" N SER G 329 " --> pdb=" O ILE G 325 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE G 330 " --> pdb=" O LEU G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 351 removed outlier: 5.016A pdb=" N ASP G 337 " --> pdb=" O ARG G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 525 removed outlier: 4.328A pdb=" N ASN G 525 " --> pdb=" O ALA G 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 527 through 551 Processing helix chain 'G' and resid 557 through 589 removed outlier: 5.688A pdb=" N ASN G 576 " --> pdb=" O PHE G 572 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N THR G 577 " --> pdb=" O ILE G 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 631 through 636 removed outlier: 5.129A pdb=" N THR G 636 " --> pdb=" O SER G 632 " (cutoff:3.500A) Processing helix chain 'G' and resid 662 through 678 Processing helix chain 'G' and resid 715 through 735 Processing sheet with id= A, first strand: chain 'A' and resid 639 through 641 removed outlier: 6.640A pdb=" N VAL A 618 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N MET A 612 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N THR A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 649 through 657 removed outlier: 6.783A pdb=" N ALA A 703 " --> pdb=" O VAL A 691 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL A 691 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE A 705 " --> pdb=" O MET A 689 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N MET A 689 " --> pdb=" O PHE A 705 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASN A 707 " --> pdb=" O HIS A 687 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N HIS A 687 " --> pdb=" O ASN A 707 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 639 through 641 removed outlier: 6.843A pdb=" N VAL B 618 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N MET B 612 " --> pdb=" O THR B 616 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR B 616 " --> pdb=" O MET B 612 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 649 through 657 removed outlier: 6.749A pdb=" N ALA B 703 " --> pdb=" O VAL B 691 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL B 691 " --> pdb=" O ALA B 703 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE B 705 " --> pdb=" O MET B 689 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N MET B 689 " --> pdb=" O PHE B 705 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 639 through 641 removed outlier: 6.833A pdb=" N VAL C 618 " --> pdb=" O GLU C 610 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N MET C 612 " --> pdb=" O THR C 616 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR C 616 " --> pdb=" O MET C 612 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 649 through 657 removed outlier: 6.743A pdb=" N ALA C 703 " --> pdb=" O VAL C 691 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL C 691 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N PHE C 705 " --> pdb=" O MET C 689 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N MET C 689 " --> pdb=" O PHE C 705 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ASN C 707 " --> pdb=" O HIS C 687 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N HIS C 687 " --> pdb=" O ASN C 707 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 639 through 641 removed outlier: 6.513A pdb=" N VAL D 618 " --> pdb=" O GLU D 610 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N MET D 612 " --> pdb=" O THR D 616 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR D 616 " --> pdb=" O MET D 612 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 649 through 657 removed outlier: 6.772A pdb=" N ALA D 703 " --> pdb=" O VAL D 691 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL D 691 " --> pdb=" O ALA D 703 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N PHE D 705 " --> pdb=" O MET D 689 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N MET D 689 " --> pdb=" O PHE D 705 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 639 through 641 removed outlier: 6.665A pdb=" N VAL E 618 " --> pdb=" O GLU E 610 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N MET E 612 " --> pdb=" O THR E 616 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR E 616 " --> pdb=" O MET E 612 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 649 through 657 removed outlier: 6.774A pdb=" N ALA E 703 " --> pdb=" O VAL E 691 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL E 691 " --> pdb=" O ALA E 703 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE E 705 " --> pdb=" O MET E 689 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N MET E 689 " --> pdb=" O PHE E 705 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 639 through 641 removed outlier: 6.799A pdb=" N VAL F 618 " --> pdb=" O GLU F 610 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 649 through 657 removed outlier: 6.713A pdb=" N ALA F 703 " --> pdb=" O VAL F 691 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL F 691 " --> pdb=" O ALA F 703 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE F 705 " --> pdb=" O MET F 689 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N MET F 689 " --> pdb=" O PHE F 705 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASN F 707 " --> pdb=" O HIS F 687 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N HIS F 687 " --> pdb=" O ASN F 707 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 599 through 602 removed outlier: 6.667A pdb=" N VAL G 618 " --> pdb=" O GLU G 610 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N MET G 612 " --> pdb=" O THR G 616 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR G 616 " --> pdb=" O MET G 612 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 649 through 657 removed outlier: 6.782A pdb=" N ALA G 703 " --> pdb=" O VAL G 691 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL G 691 " --> pdb=" O ALA G 703 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE G 705 " --> pdb=" O MET G 689 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N MET G 689 " --> pdb=" O PHE G 705 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASN G 707 " --> pdb=" O HIS G 687 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N HIS G 687 " --> pdb=" O ASN G 707 " (cutoff:3.500A) 1386 hydrogen bonds defined for protein. 3771 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: 6.65 Time building geometry restraints manager: 8.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3829 1.31 - 1.44: 5375 1.44 - 1.56: 11510 1.56 - 1.69: 113 1.69 - 1.82: 147 Bond restraints: 20974 Sorted by residual: bond pdb=" CB ILE E 285 " pdb=" CG1 ILE E 285 " ideal model delta sigma weight residual 1.530 1.672 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" CB ILE F 285 " pdb=" CG1 ILE F 285 " ideal model delta sigma weight residual 1.530 1.671 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" CB ILE G 285 " pdb=" CG1 ILE G 285 " ideal model delta sigma weight residual 1.530 1.667 -0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" CB HIS A 331 " pdb=" CG HIS A 331 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.47e+01 bond pdb=" CD2 TRP D 507 " pdb=" CE3 TRP D 507 " ideal model delta sigma weight residual 1.398 1.505 -0.107 1.60e-02 3.91e+03 4.46e+01 ... (remaining 20969 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.71: 335 105.71 - 112.90: 11316 112.90 - 120.09: 8686 120.09 - 127.27: 7847 127.27 - 134.46: 240 Bond angle restraints: 28424 Sorted by residual: angle pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " pdb=" CG PHE A 335 " ideal model delta sigma weight residual 113.80 122.08 -8.28 1.00e+00 1.00e+00 6.86e+01 angle pdb=" C GLN G 291 " pdb=" N PRO G 292 " pdb=" CA PRO G 292 " ideal model delta sigma weight residual 119.47 128.27 -8.80 1.16e+00 7.43e-01 5.76e+01 angle pdb=" C GLN C 291 " pdb=" N PRO C 292 " pdb=" CA PRO C 292 " ideal model delta sigma weight residual 119.56 127.00 -7.44 1.02e+00 9.61e-01 5.32e+01 angle pdb=" N THR C 557 " pdb=" CA THR C 557 " pdb=" C THR C 557 " ideal model delta sigma weight residual 112.89 121.73 -8.84 1.24e+00 6.50e-01 5.08e+01 angle pdb=" C HIS E 592 " pdb=" N PRO E 593 " pdb=" CA PRO E 593 " ideal model delta sigma weight residual 119.56 126.71 -7.15 1.01e+00 9.80e-01 5.02e+01 ... (remaining 28419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 12108 17.71 - 35.42: 257 35.42 - 53.13: 50 53.13 - 70.84: 30 70.84 - 88.54: 12 Dihedral angle restraints: 12457 sinusoidal: 4779 harmonic: 7678 Sorted by residual: dihedral pdb=" N PHE A 335 " pdb=" C PHE A 335 " pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " ideal model delta harmonic sigma weight residual 122.80 130.99 -8.19 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" N ARG A 296 " pdb=" C ARG A 296 " pdb=" CA ARG A 296 " pdb=" CB ARG A 296 " ideal model delta harmonic sigma weight residual 122.80 114.64 8.16 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" CB GLU A 611 " pdb=" CG GLU A 611 " pdb=" CD GLU A 611 " pdb=" OE1 GLU A 611 " ideal model delta sinusoidal sigma weight residual 0.00 -88.54 88.54 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 12454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2784 0.110 - 0.220: 601 0.220 - 0.330: 46 0.330 - 0.440: 9 0.440 - 0.550: 12 Chirality restraints: 3452 Sorted by residual: chirality pdb=" CG LEU C 264 " pdb=" CB LEU C 264 " pdb=" CD1 LEU C 264 " pdb=" CD2 LEU C 264 " both_signs ideal model delta sigma weight residual False -2.59 -3.14 0.55 2.00e-01 2.50e+01 7.56e+00 chirality pdb=" CB ILE A 285 " pdb=" CA ILE A 285 " pdb=" CG1 ILE A 285 " pdb=" CG2 ILE A 285 " both_signs ideal model delta sigma weight residual False 2.64 3.18 -0.53 2.00e-01 2.50e+01 7.15e+00 chirality pdb=" CG LEU A 258 " pdb=" CB LEU A 258 " pdb=" CD1 LEU A 258 " pdb=" CD2 LEU A 258 " both_signs ideal model delta sigma weight residual False -2.59 -3.12 0.53 2.00e-01 2.50e+01 7.03e+00 ... (remaining 3449 not shown) Planarity restraints: 3469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 335 " -0.059 2.00e-02 2.50e+03 3.66e-02 2.35e+01 pdb=" CG PHE A 335 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE A 335 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 335 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE A 335 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 335 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 335 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 291 " 0.022 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C GLN E 291 " -0.074 2.00e-02 2.50e+03 pdb=" O GLN E 291 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO E 292 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 675 " 0.044 2.00e-02 2.50e+03 2.53e-02 1.28e+01 pdb=" CG TYR E 675 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR E 675 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR E 675 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR E 675 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR E 675 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR E 675 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR E 675 " 0.042 2.00e-02 2.50e+03 ... (remaining 3466 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 7802 2.88 - 3.39: 21299 3.39 - 3.89: 34724 3.89 - 4.40: 40068 4.40 - 4.90: 62902 Nonbonded interactions: 166795 Sorted by model distance: nonbonded pdb=" OD1 ASP F 737 " pdb=" NZ LYS F 739 " model vdw 2.378 2.520 nonbonded pdb=" OD1 ASP G 737 " pdb=" NZ LYS G 739 " model vdw 2.385 2.520 nonbonded pdb=" OD1 ASP B 737 " pdb=" NZ LYS B 739 " model vdw 2.386 2.520 nonbonded pdb=" OD1 ASP D 737 " pdb=" NZ LYS D 739 " model vdw 2.399 2.520 nonbonded pdb=" OD1 ASP E 737 " pdb=" NZ LYS E 739 " model vdw 2.399 2.520 ... (remaining 166790 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 186 through 203 or resid 222 through 242 or resid 264 thro \ ugh 354 or resid 507 through 751 or resid 801)) selection = (chain 'B' and (resid 186 through 285 or resid 294 through 751 or resid 801)) selection = (chain 'C' and (resid 186 through 285 or resid 294 through 751 or resid 801)) selection = (chain 'D' and (resid 186 through 285 or resid 294 through 751 or resid 801)) selection = (chain 'E' and (resid 186 through 285 or resid 294 through 751 or resid 801)) selection = (chain 'F' and (resid 186 through 285 or resid 294 through 751 or resid 801)) selection = (chain 'G' and (resid 186 through 285 or resid 294 through 751 or resid 801)) } 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: 2.150 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: 0.020 Extract box with map and model: 5.780 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 53.950 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.090 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:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 0.023 0.142 20974 Z= 1.478 Angle : 1.521 8.842 28424 Z= 1.044 Chirality : 0.093 0.550 3452 Planarity : 0.008 0.043 3469 Dihedral : 9.909 88.544 7391 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 0.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.83 (0.15), residues: 2540 helix: 1.53 (0.11), residues: 1580 sheet: 0.56 (0.31), residues: 290 loop : 1.05 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.008 TRP E 683 HIS 0.010 0.002 HIS A 331 PHE 0.059 0.005 PHE A 335 TYR 0.044 0.008 TYR E 675 ARG 0.006 0.001 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 794 time to evaluate : 2.495 Fit side-chains REVERT: A 311 ILE cc_start: 0.8728 (mt) cc_final: 0.8502 (mm) REVERT: A 325 ILE cc_start: 0.8581 (mt) cc_final: 0.8294 (mt) REVERT: A 525 ASN cc_start: 0.7725 (t0) cc_final: 0.7345 (t0) REVERT: B 300 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7184 (mp0) REVERT: B 526 LYS cc_start: 0.8486 (mttt) cc_final: 0.7916 (mtpp) REVERT: C 304 TRP cc_start: 0.8104 (m100) cc_final: 0.7693 (m100) REVERT: C 525 ASN cc_start: 0.7029 (t0) cc_final: 0.5993 (t0) REVERT: C 526 LYS cc_start: 0.7602 (mttt) cc_final: 0.7398 (mmmm) REVERT: C 595 ASP cc_start: 0.7585 (m-30) cc_final: 0.7253 (m-30) REVERT: D 314 PHE cc_start: 0.8224 (t80) cc_final: 0.7703 (t80) REVERT: D 329 SER cc_start: 0.8520 (m) cc_final: 0.7877 (p) REVERT: D 526 LYS cc_start: 0.8635 (mttt) cc_final: 0.8422 (mmtm) REVERT: D 621 LYS cc_start: 0.8070 (mtmt) cc_final: 0.7421 (mtmt) REVERT: D 625 GLU cc_start: 0.7377 (tt0) cc_final: 0.6938 (tt0) REVERT: F 671 ARG cc_start: 0.8620 (mmm-85) cc_final: 0.8246 (mmm-85) REVERT: F 717 GLU cc_start: 0.8625 (tp30) cc_final: 0.8381 (mm-30) REVERT: F 735 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7350 (mt-10) REVERT: G 282 VAL cc_start: 0.7420 (m) cc_final: 0.7153 (p) REVERT: G 526 LYS cc_start: 0.8236 (mttt) cc_final: 0.8028 (mptt) REVERT: G 748 SER cc_start: 0.8856 (t) cc_final: 0.8640 (p) outliers start: 0 outliers final: 6 residues processed: 794 average time/residue: 1.2247 time to fit residues: 1102.4163 Evaluate side-chains 646 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 640 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain F residue 539 ILE Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 560 ILE Chi-restraints excluded: chain G residue 311 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 0.7980 chunk 197 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 203 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 236 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN C 648 GLN D 525 ASN D 576 ASN ** D 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 HIS D 713 GLN E 533 ASN E 648 GLN E 698 ASN F 525 ASN F 648 GLN G 533 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20974 Z= 0.257 Angle : 0.602 8.993 28424 Z= 0.323 Chirality : 0.043 0.288 3452 Planarity : 0.004 0.030 3469 Dihedral : 7.003 59.371 2793 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 3.66 % Allowed : 14.14 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.46 (0.16), residues: 2540 helix: 2.32 (0.12), residues: 1600 sheet: 0.48 (0.28), residues: 329 loop : 0.55 (0.27), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 281 HIS 0.007 0.001 HIS A 592 PHE 0.027 0.002 PHE A 335 TYR 0.010 0.002 TYR A 259 ARG 0.005 0.000 ARG F 599 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 682 time to evaluate : 2.032 Fit side-chains revert: symmetry clash REVERT: A 300 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7832 (mt-10) REVERT: A 302 VAL cc_start: 0.8603 (t) cc_final: 0.8321 (m) REVERT: A 330 PHE cc_start: 0.7484 (t80) cc_final: 0.7161 (t80) REVERT: A 576 ASN cc_start: 0.7242 (t0) cc_final: 0.6872 (t0) REVERT: B 273 TRP cc_start: 0.7971 (t60) cc_final: 0.7744 (t60) REVERT: B 324 LYS cc_start: 0.8277 (mmtt) cc_final: 0.8071 (mmtt) REVERT: B 328 SER cc_start: 0.8706 (OUTLIER) cc_final: 0.8427 (t) REVERT: B 583 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7596 (mt-10) REVERT: B 686 GLN cc_start: 0.8060 (mp-120) cc_final: 0.7833 (mp10) REVERT: C 304 TRP cc_start: 0.7839 (m100) cc_final: 0.7624 (m100) REVERT: C 595 ASP cc_start: 0.7529 (m-30) cc_final: 0.7302 (m-30) REVERT: C 655 SER cc_start: 0.8518 (p) cc_final: 0.8266 (m) REVERT: C 689 MET cc_start: 0.8436 (ttp) cc_final: 0.8221 (ttp) REVERT: D 297 LYS cc_start: 0.7139 (tttt) cc_final: 0.6920 (mmpt) REVERT: D 314 PHE cc_start: 0.7977 (t80) cc_final: 0.7724 (t80) REVERT: D 695 GLU cc_start: 0.6506 (tt0) cc_final: 0.6279 (tt0) REVERT: F 526 LYS cc_start: 0.8202 (mttt) cc_final: 0.8000 (mttp) REVERT: F 548 TRP cc_start: 0.8216 (t60) cc_final: 0.7804 (t60) REVERT: F 653 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7771 (mt-10) REVERT: F 671 ARG cc_start: 0.8638 (mmm-85) cc_final: 0.8179 (mmm-85) REVERT: F 735 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7488 (mt-10) REVERT: G 715 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7676 (m-80) outliers start: 79 outliers final: 26 residues processed: 706 average time/residue: 1.1278 time to fit residues: 907.5768 Evaluate side-chains 692 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 663 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain F residue 653 GLU Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain G residue 568 VAL Chi-restraints excluded: chain G residue 626 LYS Chi-restraints excluded: chain G residue 715 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 196 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 chunk 255 optimal weight: 0.7980 chunk 210 optimal weight: 0.0870 chunk 234 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 189 optimal weight: 0.0370 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 HIS A 533 ASN A 686 GLN B 576 ASN B 686 GLN C 648 GLN D 648 GLN D 686 GLN D 688 ASN E 576 ASN E 648 GLN G 525 ASN G 576 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20974 Z= 0.172 Angle : 0.521 8.577 28424 Z= 0.273 Chirality : 0.041 0.234 3452 Planarity : 0.003 0.026 3469 Dihedral : 6.726 59.480 2783 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 4.03 % Allowed : 17.20 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.34 (0.17), residues: 2540 helix: 2.30 (0.12), residues: 1606 sheet: 0.26 (0.28), residues: 341 loop : 0.35 (0.28), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 548 HIS 0.006 0.001 HIS A 592 PHE 0.025 0.001 PHE F 301 TYR 0.009 0.001 TYR E 740 ARG 0.004 0.000 ARG C 720 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 660 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7823 (mt-10) REVERT: A 302 VAL cc_start: 0.8489 (t) cc_final: 0.8287 (m) REVERT: A 576 ASN cc_start: 0.7330 (t0) cc_final: 0.6725 (t0) REVERT: A 717 GLU cc_start: 0.6792 (tp30) cc_final: 0.6581 (tp30) REVERT: B 583 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7427 (mt-10) REVERT: B 686 GLN cc_start: 0.8079 (mp10) cc_final: 0.7863 (mp10) REVERT: C 300 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7388 (mp0) REVERT: C 595 ASP cc_start: 0.7580 (m-30) cc_final: 0.7380 (m-30) REVERT: C 689 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8249 (ttp) REVERT: D 282 VAL cc_start: 0.7802 (p) cc_final: 0.7597 (m) REVERT: D 314 PHE cc_start: 0.7917 (t80) cc_final: 0.7704 (t80) REVERT: E 325 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8578 (pp) REVERT: E 739 LYS cc_start: 0.8556 (mttp) cc_final: 0.8296 (mttp) REVERT: F 671 ARG cc_start: 0.8570 (mmm-85) cc_final: 0.8254 (mmm-85) REVERT: F 735 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7286 (mt-10) REVERT: G 715 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7479 (m-80) outliers start: 87 outliers final: 39 residues processed: 692 average time/residue: 1.1778 time to fit residues: 926.5885 Evaluate side-chains 685 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 643 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 673 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain C residue 689 MET Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 539 ILE Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 545 ILE Chi-restraints excluded: chain F residue 547 ILE Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 739 LYS Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 551 VAL Chi-restraints excluded: chain G residue 565 SER Chi-restraints excluded: chain G residue 715 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 112 optimal weight: 8.9990 chunk 158 optimal weight: 0.8980 chunk 237 optimal weight: 0.9980 chunk 251 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN A 605 ASN A 686 GLN C 576 ASN C 648 GLN C 698 ASN D 531 GLN D 576 ASN D 648 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 688 ASN D 698 ASN E 531 GLN E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 576 ASN F 688 ASN G 525 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20974 Z= 0.203 Angle : 0.520 7.977 28424 Z= 0.268 Chirality : 0.041 0.188 3452 Planarity : 0.003 0.028 3469 Dihedral : 6.500 57.190 2781 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.71 % Allowed : 18.59 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.41 (0.17), residues: 2540 helix: 2.35 (0.12), residues: 1606 sheet: 0.45 (0.28), residues: 319 loop : 0.25 (0.28), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 316 HIS 0.004 0.001 HIS E 708 PHE 0.023 0.001 PHE D 301 TYR 0.012 0.001 TYR F 740 ARG 0.004 0.000 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 647 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7813 (mt-10) REVERT: A 576 ASN cc_start: 0.7361 (t0) cc_final: 0.6993 (t0) REVERT: A 717 GLU cc_start: 0.6813 (tp30) cc_final: 0.6596 (tp30) REVERT: A 737 ASP cc_start: 0.7782 (t0) cc_final: 0.7319 (t0) REVERT: A 739 LYS cc_start: 0.8188 (ptpp) cc_final: 0.7977 (pttm) REVERT: B 686 GLN cc_start: 0.8064 (mp10) cc_final: 0.7862 (mp10) REVERT: C 300 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7158 (mp0) REVERT: E 325 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8546 (pp) REVERT: F 671 ARG cc_start: 0.8576 (mmm-85) cc_final: 0.8263 (mmm-85) REVERT: F 735 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7344 (mt-10) REVERT: G 715 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7512 (m-80) outliers start: 80 outliers final: 35 residues processed: 672 average time/residue: 1.1881 time to fit residues: 905.0000 Evaluate side-chains 671 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 634 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 545 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain G residue 324 LYS Chi-restraints excluded: chain G residue 715 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 214 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 0.4980 chunk 225 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN C 525 ASN C 648 GLN C 698 ASN D 531 GLN D 648 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 698 ASN E 531 GLN E 648 GLN E 688 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN G 525 ASN G 576 ASN G 681 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20974 Z= 0.237 Angle : 0.519 8.574 28424 Z= 0.269 Chirality : 0.041 0.228 3452 Planarity : 0.003 0.025 3469 Dihedral : 6.408 58.545 2781 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.80 % Allowed : 19.56 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.17), residues: 2540 helix: 2.37 (0.12), residues: 1606 sheet: 0.46 (0.27), residues: 319 loop : 0.19 (0.28), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 316 HIS 0.006 0.001 HIS E 708 PHE 0.026 0.001 PHE G 301 TYR 0.011 0.001 TYR F 740 ARG 0.003 0.000 ARG D 296 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 638 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7793 (mt-10) REVERT: A 323 LEU cc_start: 0.8305 (mt) cc_final: 0.8010 (tm) REVERT: A 576 ASN cc_start: 0.7401 (t0) cc_final: 0.7056 (t0) REVERT: A 717 GLU cc_start: 0.6750 (tp30) cc_final: 0.6529 (tp30) REVERT: A 737 ASP cc_start: 0.7854 (t0) cc_final: 0.7363 (t0) REVERT: A 739 LYS cc_start: 0.8252 (ptpp) cc_final: 0.8041 (pttm) REVERT: B 583 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7584 (mt-10) REVERT: B 686 GLN cc_start: 0.8075 (mp10) cc_final: 0.7863 (mp10) REVERT: C 300 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7167 (mt-10) REVERT: E 325 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8562 (pp) REVERT: G 715 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7622 (m-80) outliers start: 82 outliers final: 47 residues processed: 667 average time/residue: 1.2267 time to fit residues: 926.9053 Evaluate side-chains 679 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 630 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 545 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain G residue 688 ASN Chi-restraints excluded: chain G residue 715 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 251 optimal weight: 0.9990 chunk 208 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN A 525 ASN A 533 ASN A 686 GLN C 525 ASN C 648 GLN D 531 GLN D 648 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 688 ASN E 531 GLN E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN G 525 ASN G 576 ASN G 681 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20974 Z= 0.211 Angle : 0.520 10.224 28424 Z= 0.266 Chirality : 0.041 0.206 3452 Planarity : 0.003 0.026 3469 Dihedral : 6.287 58.955 2781 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.03 % Allowed : 19.70 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.46 (0.17), residues: 2540 helix: 2.46 (0.12), residues: 1606 sheet: 0.39 (0.27), residues: 319 loop : 0.14 (0.28), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 316 HIS 0.005 0.001 HIS A 592 PHE 0.022 0.001 PHE A 271 TYR 0.010 0.001 TYR F 740 ARG 0.004 0.000 ARG D 296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 649 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7781 (mt-10) REVERT: A 323 LEU cc_start: 0.8307 (mt) cc_final: 0.8018 (tm) REVERT: A 576 ASN cc_start: 0.7441 (t0) cc_final: 0.7102 (t0) REVERT: A 737 ASP cc_start: 0.7870 (t0) cc_final: 0.7339 (t0) REVERT: A 739 LYS cc_start: 0.8288 (ptpp) cc_final: 0.8055 (pttm) REVERT: B 300 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6979 (mp0) REVERT: B 629 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.7852 (t80) REVERT: B 686 GLN cc_start: 0.8090 (mp10) cc_final: 0.7885 (mp10) REVERT: C 300 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7191 (mt-10) REVERT: E 300 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7487 (mp0) REVERT: E 325 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8570 (pp) REVERT: F 300 GLU cc_start: 0.7571 (tm-30) cc_final: 0.6869 (mt-10) REVERT: F 671 ARG cc_start: 0.8542 (mmm-85) cc_final: 0.8294 (mmm-85) REVERT: G 715 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7621 (m-80) outliers start: 87 outliers final: 52 residues processed: 677 average time/residue: 1.2202 time to fit residues: 935.6997 Evaluate side-chains 686 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 631 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 635 CYS Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain F residue 304 TRP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 545 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain G residue 680 LEU Chi-restraints excluded: chain G residue 688 ASN Chi-restraints excluded: chain G residue 715 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 183 optimal weight: 0.1980 chunk 142 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 140 optimal weight: 0.0000 chunk 250 optimal weight: 0.7980 chunk 156 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 513 ASN A 525 ASN A 686 GLN C 525 ASN C 648 GLN D 686 GLN D 688 ASN ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN G 525 ASN G 681 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20974 Z= 0.154 Angle : 0.500 9.376 28424 Z= 0.256 Chirality : 0.040 0.187 3452 Planarity : 0.003 0.026 3469 Dihedral : 6.134 59.198 2781 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.99 % Allowed : 19.89 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.56 (0.17), residues: 2540 helix: 2.55 (0.12), residues: 1606 sheet: 0.41 (0.26), residues: 329 loop : 0.14 (0.28), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 316 HIS 0.004 0.001 HIS E 708 PHE 0.025 0.001 PHE F 301 TYR 0.008 0.001 TYR F 740 ARG 0.006 0.000 ARG D 296 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 644 time to evaluate : 2.395 Fit side-chains revert: symmetry clash REVERT: A 300 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7852 (mt-10) REVERT: A 323 LEU cc_start: 0.8286 (mt) cc_final: 0.7999 (tm) REVERT: A 576 ASN cc_start: 0.7398 (t0) cc_final: 0.6999 (t0) REVERT: A 737 ASP cc_start: 0.7886 (t0) cc_final: 0.7309 (t0) REVERT: A 739 LYS cc_start: 0.8252 (ptpp) cc_final: 0.8014 (pttm) REVERT: B 300 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6976 (mp0) REVERT: B 567 LEU cc_start: 0.8359 (tm) cc_final: 0.8125 (tt) REVERT: B 583 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7608 (mt-10) REVERT: B 629 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.7833 (t80) REVERT: C 300 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7196 (mt-10) REVERT: C 689 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8238 (ttp) REVERT: D 548 TRP cc_start: 0.7565 (t60) cc_final: 0.7088 (t60) REVERT: E 300 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7487 (mt-10) REVERT: E 325 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8569 (pp) REVERT: F 671 ARG cc_start: 0.8491 (mmm-85) cc_final: 0.8093 (mmm-85) REVERT: G 715 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7511 (m-80) outliers start: 86 outliers final: 52 residues processed: 676 average time/residue: 1.2040 time to fit residues: 921.2488 Evaluate side-chains 686 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 630 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 566 GLN Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 689 MET Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 734 GLU Chi-restraints excluded: chain F residue 304 TRP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 680 LEU Chi-restraints excluded: chain G residue 688 ASN Chi-restraints excluded: chain G residue 715 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 159 optimal weight: 0.5980 chunk 170 optimal weight: 0.0270 chunk 123 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 196 optimal weight: 0.3980 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 513 ASN A 525 ASN A 686 GLN C 525 ASN C 648 GLN D 531 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 688 ASN E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN G 525 ASN G 681 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20974 Z= 0.199 Angle : 0.525 9.982 28424 Z= 0.267 Chirality : 0.040 0.181 3452 Planarity : 0.003 0.027 3469 Dihedral : 6.118 58.718 2781 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.38 % Allowed : 21.28 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.54 (0.17), residues: 2540 helix: 2.53 (0.12), residues: 1606 sheet: 0.41 (0.26), residues: 329 loop : 0.13 (0.28), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 316 HIS 0.006 0.001 HIS A 592 PHE 0.028 0.001 PHE G 301 TYR 0.009 0.001 TYR F 740 ARG 0.002 0.000 ARG G 296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 628 time to evaluate : 2.325 Fit side-chains revert: symmetry clash REVERT: A 296 ARG cc_start: 0.6955 (pmt170) cc_final: 0.6626 (pmt170) REVERT: A 300 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 323 LEU cc_start: 0.8288 (mt) cc_final: 0.8026 (tm) REVERT: A 576 ASN cc_start: 0.7526 (t0) cc_final: 0.7202 (t0) REVERT: A 671 ARG cc_start: 0.8738 (mmm-85) cc_final: 0.8510 (mmm-85) REVERT: A 737 ASP cc_start: 0.7895 (t0) cc_final: 0.7270 (t0) REVERT: A 739 LYS cc_start: 0.8281 (ptpp) cc_final: 0.8024 (pttm) REVERT: B 283 MET cc_start: 0.4796 (mmm) cc_final: 0.4530 (mmm) REVERT: B 300 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6974 (mp0) REVERT: B 301 PHE cc_start: 0.7355 (t80) cc_final: 0.7052 (t80) REVERT: B 629 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7834 (t80) REVERT: C 300 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7167 (mt-10) REVERT: E 300 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7468 (mt-10) REVERT: E 325 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8577 (pp) REVERT: F 300 GLU cc_start: 0.7548 (tm-30) cc_final: 0.6852 (mt-10) REVERT: F 671 ARG cc_start: 0.8500 (mmm-85) cc_final: 0.8070 (mmm-85) REVERT: G 715 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7547 (m-80) outliers start: 73 outliers final: 48 residues processed: 658 average time/residue: 1.2097 time to fit residues: 906.5455 Evaluate side-chains 680 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 629 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 547 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 680 LEU Chi-restraints excluded: chain G residue 688 ASN Chi-restraints excluded: chain G residue 715 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 chunk 219 optimal weight: 0.2980 chunk 233 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 71 optimal weight: 0.3980 chunk 211 optimal weight: 0.4980 chunk 220 optimal weight: 0.5980 chunk 232 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN A 686 GLN C 525 ASN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 688 ASN E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN G 525 ASN G 681 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20974 Z= 0.157 Angle : 0.525 10.532 28424 Z= 0.266 Chirality : 0.040 0.183 3452 Planarity : 0.003 0.026 3469 Dihedral : 5.985 56.346 2781 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.11 % Allowed : 22.02 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.58 (0.17), residues: 2540 helix: 2.58 (0.13), residues: 1606 sheet: 0.39 (0.26), residues: 329 loop : 0.13 (0.29), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 316 HIS 0.003 0.001 HIS E 708 PHE 0.027 0.001 PHE F 301 TYR 0.010 0.001 TYR D 740 ARG 0.002 0.000 ARG F 599 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 621 time to evaluate : 2.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 ARG cc_start: 0.6907 (pmt170) cc_final: 0.6599 (pmt170) REVERT: A 300 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7840 (mt-10) REVERT: A 323 LEU cc_start: 0.8285 (mt) cc_final: 0.8008 (tm) REVERT: A 576 ASN cc_start: 0.7447 (t0) cc_final: 0.7125 (t0) REVERT: A 671 ARG cc_start: 0.8712 (mmm-85) cc_final: 0.8488 (mmm-85) REVERT: A 737 ASP cc_start: 0.7863 (t0) cc_final: 0.7224 (t0) REVERT: A 739 LYS cc_start: 0.8258 (ptpp) cc_final: 0.7959 (pttm) REVERT: B 306 ILE cc_start: 0.8238 (mp) cc_final: 0.8035 (mt) REVERT: B 629 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.7804 (t80) REVERT: C 300 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7189 (mt-10) REVERT: C 689 MET cc_start: 0.8472 (ttp) cc_final: 0.8217 (ttp) REVERT: D 548 TRP cc_start: 0.7534 (t60) cc_final: 0.7086 (t60) REVERT: E 300 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7466 (mt-10) REVERT: E 325 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8580 (pp) REVERT: F 300 GLU cc_start: 0.7550 (tm-30) cc_final: 0.6903 (mt-10) REVERT: F 671 ARG cc_start: 0.8467 (mmm-85) cc_final: 0.8213 (mmm-85) REVERT: G 715 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7495 (m-80) outliers start: 67 outliers final: 48 residues processed: 646 average time/residue: 1.2112 time to fit residues: 886.8646 Evaluate side-chains 672 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 621 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain F residue 304 TRP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 545 ILE Chi-restraints excluded: chain F residue 547 ILE Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 300 GLU Chi-restraints excluded: chain G residue 680 LEU Chi-restraints excluded: chain G residue 688 ASN Chi-restraints excluded: chain G residue 715 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 3.9990 chunk 246 optimal weight: 0.6980 chunk 150 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 159 optimal weight: 0.0010 chunk 126 optimal weight: 0.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN A 686 GLN C 525 ASN C 678 GLN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 525 ASN G 681 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20974 Z= 0.189 Angle : 0.542 10.652 28424 Z= 0.273 Chirality : 0.041 0.171 3452 Planarity : 0.003 0.028 3469 Dihedral : 5.967 56.756 2781 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.83 % Allowed : 22.86 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.49 (0.17), residues: 2540 helix: 2.54 (0.13), residues: 1606 sheet: 0.12 (0.27), residues: 341 loop : 0.16 (0.29), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 316 HIS 0.006 0.001 HIS A 592 PHE 0.026 0.001 PHE A 271 TYR 0.010 0.001 TYR D 740 ARG 0.002 0.000 ARG G 296 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 622 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 ARG cc_start: 0.6926 (pmt170) cc_final: 0.6590 (pmt170) REVERT: A 300 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7839 (mt-10) REVERT: A 323 LEU cc_start: 0.8300 (mt) cc_final: 0.8026 (tm) REVERT: A 737 ASP cc_start: 0.7875 (t0) cc_final: 0.7219 (t0) REVERT: A 739 LYS cc_start: 0.8269 (ptpp) cc_final: 0.7973 (pttm) REVERT: B 629 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7849 (t80) REVERT: C 300 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7136 (mt-10) REVERT: D 283 MET cc_start: 0.4386 (mmm) cc_final: 0.3943 (mmm) REVERT: D 548 TRP cc_start: 0.7623 (t60) cc_final: 0.7193 (t60) REVERT: E 300 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7467 (mt-10) REVERT: E 325 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8582 (pp) REVERT: F 671 ARG cc_start: 0.8492 (mmm-85) cc_final: 0.8216 (mmm-85) REVERT: G 715 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7486 (m-80) outliers start: 61 outliers final: 49 residues processed: 644 average time/residue: 1.2320 time to fit residues: 897.5411 Evaluate side-chains 673 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 621 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 566 GLN Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 545 ILE Chi-restraints excluded: chain F residue 547 ILE Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 560 ILE Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain G residue 680 LEU Chi-restraints excluded: chain G residue 688 ASN Chi-restraints excluded: chain G residue 715 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 1.9990 chunk 219 optimal weight: 0.0980 chunk 63 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 chunk 212 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN A 686 GLN B 515 GLN C 525 ASN C 678 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 525 ASN G 681 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.135334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.107884 restraints weight = 33029.913| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.94 r_work: 0.3333 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20974 Z= 0.189 Angle : 0.541 11.326 28424 Z= 0.276 Chirality : 0.041 0.168 3452 Planarity : 0.003 0.026 3469 Dihedral : 5.926 57.650 2781 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.87 % Allowed : 23.09 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.55 (0.17), residues: 2540 helix: 2.54 (0.13), residues: 1606 sheet: 0.38 (0.27), residues: 329 loop : 0.15 (0.29), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 316 HIS 0.005 0.001 HIS E 708 PHE 0.029 0.001 PHE G 301 TYR 0.010 0.001 TYR D 740 ARG 0.002 0.000 ARG A 334 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12215.48 seconds wall clock time: 213 minutes 45.10 seconds (12825.10 seconds total)