Starting phenix.real_space_refine on Sun Mar 17 13:46:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5e_24187/03_2024/7n5e_24187_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5e_24187/03_2024/7n5e_24187.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/7n5e_24187/03_2024/7n5e_24187.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5e_24187/03_2024/7n5e_24187.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5e_24187/03_2024/7n5e_24187_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5e_24187/03_2024/7n5e_24187_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= 0.001 sd= 0.025 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 77 5.16 5 C 11784 2.51 5 N 2960 2.21 5 O 3094 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 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: 17915 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2579 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 7, 'TRANS': 308} Chain breaks: 2 Chain: "B" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "C" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "D" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "E" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "F" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "G" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 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: 9.49, per 1000 atoms: 0.53 Number of scatterers: 17915 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 77 16.00 O 3094 8.00 N 2960 7.00 C 11784 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: 6.84 Conformation dependent library (CDL) restraints added in 3.3 seconds 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4224 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 14 sheets defined 56.3% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... 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 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 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 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 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 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 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) 1132 hydrogen bonds defined for protein. 3093 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: 5.47 Time building geometry restraints manager: 7.44 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: 3350 1.31 - 1.44: 4632 1.44 - 1.56: 10105 1.56 - 1.69: 59 1.69 - 1.81: 133 Bond restraints: 18279 Sorted by residual: 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 bond pdb=" CD2 TRP B 507 " pdb=" CE3 TRP B 507 " ideal model delta sigma weight residual 1.398 1.503 -0.105 1.60e-02 3.91e+03 4.28e+01 bond pdb=" CZ2 TRP C 507 " pdb=" CH2 TRP C 507 " ideal model delta sigma weight residual 1.368 1.486 -0.118 1.90e-02 2.77e+03 3.82e+01 bond pdb=" CZ2 TRP E 507 " pdb=" CH2 TRP E 507 " ideal model delta sigma weight residual 1.368 1.483 -0.115 1.90e-02 2.77e+03 3.64e+01 ... (remaining 18274 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.71: 327 105.71 - 112.90: 9671 112.90 - 120.09: 7770 120.09 - 127.27: 6750 127.27 - 134.46: 198 Bond angle restraints: 24716 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 24711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 10586 17.71 - 35.42: 253 35.42 - 53.13: 50 53.13 - 70.84: 30 70.84 - 88.54: 12 Dihedral angle restraints: 10931 sinusoidal: 4511 harmonic: 6420 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 10928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2091 0.092 - 0.185: 712 0.185 - 0.277: 110 0.277 - 0.370: 17 0.370 - 0.462: 1 Chirality restraints: 2931 Sorted by residual: chirality pdb=" CA THR C 557 " pdb=" N THR C 557 " pdb=" C THR C 557 " pdb=" CB THR C 557 " both_signs ideal model delta sigma weight residual False 2.53 2.06 0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" CA TRP B 304 " pdb=" N TRP B 304 " pdb=" C TRP B 304 " pdb=" CB TRP B 304 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA THR G 557 " pdb=" N THR G 557 " pdb=" C THR G 557 " pdb=" CB THR G 557 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 2928 not shown) Planarity restraints: 3023 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 3020 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 6744 2.88 - 3.39: 18223 3.39 - 3.89: 30379 3.89 - 4.40: 35025 4.40 - 4.90: 56056 Nonbonded interactions: 146427 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 146422 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 294 through 354 or resid 507 through 751 or resid 801)) selection = (chain 'B' and (resid 294 through 751 or resid 801)) selection = (chain 'C' and (resid 294 through 751 or resid 801)) selection = (chain 'D' and (resid 294 through 751 or resid 801)) selection = (chain 'E' and (resid 294 through 751 or resid 801)) selection = (chain 'F' and (resid 294 through 751 or resid 801)) selection = (chain 'G' and (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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.470 Check model and map are aligned: 0.240 Set scattering table: 0.130 Process input model: 47.440 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 0.132 18279 Z= 1.471 Angle : 1.544 8.842 24716 Z= 1.056 Chirality : 0.090 0.462 2931 Planarity : 0.008 0.043 3023 Dihedral : 10.255 88.544 6707 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 0.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 1.87 (0.17), residues: 2146 helix: 1.62 (0.13), residues: 1206 sheet: 0.56 (0.31), residues: 290 loop : 1.09 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.010 TRP E 683 HIS 0.010 0.002 HIS A 331 PHE 0.059 0.006 PHE A 335 TYR 0.044 0.009 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) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 585 time to evaluate : 2.281 Fit side-chains revert: symmetry clash REVERT: A 541 ILE cc_start: 0.8735 (mt) cc_final: 0.8435 (mt) REVERT: B 563 LEU cc_start: 0.8000 (tp) cc_final: 0.7773 (mm) REVERT: B 624 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7783 (mmtm) REVERT: C 526 LYS cc_start: 0.6893 (mttt) cc_final: 0.5990 (tptp) REVERT: C 595 ASP cc_start: 0.7265 (m-30) cc_final: 0.7001 (m-30) REVERT: D 701 LYS cc_start: 0.8572 (mmtp) cc_final: 0.8330 (mmtp) REVERT: E 632 SER cc_start: 0.8136 (p) cc_final: 0.7909 (p) REVERT: E 717 GLU cc_start: 0.7571 (tp30) cc_final: 0.7356 (tp30) REVERT: E 737 ASP cc_start: 0.7125 (t0) cc_final: 0.6892 (t0) REVERT: G 324 LYS cc_start: 0.8490 (mttm) cc_final: 0.8271 (mttm) REVERT: G 525 ASN cc_start: 0.6814 (m-40) cc_final: 0.6601 (t0) REVERT: G 581 ILE cc_start: 0.8434 (mt) cc_final: 0.8105 (mt) REVERT: G 748 SER cc_start: 0.8818 (t) cc_final: 0.8614 (p) outliers start: 0 outliers final: 1 residues processed: 585 average time/residue: 1.3185 time to fit residues: 853.9445 Evaluate side-chains 508 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 507 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 547 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 197 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN A 741 ASN C 531 GLN C 648 GLN C 688 ASN C 698 ASN D 533 ASN D 698 ASN D 713 GLN E 531 GLN E 648 GLN E 698 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN F 576 ASN G 719 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18279 Z= 0.243 Angle : 0.570 7.436 24716 Z= 0.312 Chirality : 0.044 0.192 2931 Planarity : 0.004 0.029 3023 Dihedral : 7.506 58.186 2367 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.54 % Allowed : 9.68 % Favored : 87.78 % 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: 2.65 (0.18), residues: 2146 helix: 2.64 (0.14), residues: 1190 sheet: 0.49 (0.27), residues: 329 loop : 0.82 (0.28), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 316 HIS 0.006 0.001 HIS A 331 PHE 0.025 0.002 PHE A 335 TYR 0.009 0.001 TYR D 740 ARG 0.005 0.000 ARG F 599 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 527 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 LYS cc_start: 0.7689 (tttm) cc_final: 0.7391 (tttm) REVERT: A 632 SER cc_start: 0.8726 (p) cc_final: 0.8513 (p) REVERT: B 624 LYS cc_start: 0.8202 (mmtm) cc_final: 0.7952 (mmtm) REVERT: B 669 LYS cc_start: 0.8403 (mtpm) cc_final: 0.8136 (mtpm) REVERT: B 748 SER cc_start: 0.8398 (t) cc_final: 0.8157 (p) REVERT: C 526 LYS cc_start: 0.6745 (mttt) cc_final: 0.6121 (ttpp) REVERT: C 544 MET cc_start: 0.5029 (OUTLIER) cc_final: 0.4761 (mmp) REVERT: C 669 LYS cc_start: 0.8128 (ttmm) cc_final: 0.7927 (mttm) REVERT: D 531 GLN cc_start: 0.7002 (mt0) cc_final: 0.6784 (mt0) REVERT: D 644 ARG cc_start: 0.8499 (mtt180) cc_final: 0.8168 (mtt180) REVERT: D 650 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7932 (t0) REVERT: E 720 ARG cc_start: 0.7462 (ttp-110) cc_final: 0.7255 (ttm-80) REVERT: F 671 ARG cc_start: 0.8335 (mmm-85) cc_final: 0.8071 (mmm160) REVERT: F 717 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7788 (mm-30) REVERT: G 324 LYS cc_start: 0.8491 (mttm) cc_final: 0.8265 (mttm) outliers start: 51 outliers final: 18 residues processed: 539 average time/residue: 1.2210 time to fit residues: 734.2158 Evaluate side-chains 532 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 512 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 718 LYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain G residue 309 VAL Chi-restraints excluded: chain G residue 568 VAL Chi-restraints excluded: chain G residue 580 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 197 optimal weight: 0.6980 chunk 213 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 195 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 686 GLN B 698 ASN C 531 GLN D 686 GLN E 531 GLN E 576 ASN E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 681 ASN G 531 GLN G 681 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18279 Z= 0.245 Angle : 0.505 6.241 24716 Z= 0.276 Chirality : 0.042 0.139 2931 Planarity : 0.004 0.055 3023 Dihedral : 7.428 59.803 2367 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.04 % Allowed : 12.02 % Favored : 84.94 % 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: 2.68 (0.19), residues: 2146 helix: 2.77 (0.14), residues: 1190 sheet: 0.49 (0.27), residues: 329 loop : 0.62 (0.29), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 304 HIS 0.006 0.001 HIS F 684 PHE 0.022 0.002 PHE G 301 TYR 0.015 0.002 TYR E 740 ARG 0.006 0.000 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 523 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 LYS cc_start: 0.7655 (tttm) cc_final: 0.7385 (tttm) REVERT: B 669 LYS cc_start: 0.8445 (mtpm) cc_final: 0.8153 (ttmm) REVERT: B 673 LYS cc_start: 0.8738 (tttm) cc_final: 0.8536 (tttm) REVERT: C 544 MET cc_start: 0.5207 (OUTLIER) cc_final: 0.4878 (mmp) REVERT: D 531 GLN cc_start: 0.7019 (mt0) cc_final: 0.6762 (mt0) REVERT: D 650 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7869 (t0) REVERT: D 710 ILE cc_start: 0.7820 (pt) cc_final: 0.7611 (pt) REVERT: E 737 ASP cc_start: 0.6990 (t0) cc_final: 0.6584 (t0) REVERT: F 653 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7753 (mt-10) REVERT: G 324 LYS cc_start: 0.8532 (mttm) cc_final: 0.8310 (mttm) outliers start: 61 outliers final: 29 residues processed: 530 average time/residue: 1.3264 time to fit residues: 783.7191 Evaluate side-chains 539 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 507 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 693 GLU Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 635 CYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 718 LYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 653 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain G residue 568 VAL Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 583 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 0.5980 chunk 148 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 198 optimal weight: 0.7980 chunk 209 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN E 648 GLN G 531 GLN G 681 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18279 Z= 0.218 Angle : 0.476 7.281 24716 Z= 0.258 Chirality : 0.041 0.162 2931 Planarity : 0.003 0.027 3023 Dihedral : 7.162 59.732 2367 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.54 % Allowed : 12.62 % Favored : 83.84 % 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: 2.74 (0.19), residues: 2146 helix: 2.90 (0.14), residues: 1190 sheet: 0.43 (0.27), residues: 329 loop : 0.50 (0.29), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 304 HIS 0.005 0.001 HIS F 684 PHE 0.022 0.001 PHE G 574 TYR 0.008 0.001 TYR B 740 ARG 0.004 0.000 ARG F 671 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 516 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 LYS cc_start: 0.7711 (tttm) cc_final: 0.7367 (tttm) REVERT: A 688 ASN cc_start: 0.7984 (OUTLIER) cc_final: 0.7739 (m-40) REVERT: A 717 GLU cc_start: 0.7065 (tp30) cc_final: 0.6829 (tp30) REVERT: B 669 LYS cc_start: 0.8442 (mtpm) cc_final: 0.8156 (ttmm) REVERT: B 717 GLU cc_start: 0.7342 (tp30) cc_final: 0.7058 (tp30) REVERT: C 301 PHE cc_start: 0.6607 (t80) cc_final: 0.6225 (t80) REVERT: D 531 GLN cc_start: 0.7099 (mt0) cc_final: 0.6840 (mt0) REVERT: F 653 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: F 671 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.8096 (mmm160) REVERT: F 692 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8119 (mtmt) REVERT: F 718 LYS cc_start: 0.8302 (tttm) cc_final: 0.8025 (ptmt) REVERT: G 324 LYS cc_start: 0.8536 (mttm) cc_final: 0.8306 (mttm) REVERT: G 717 GLU cc_start: 0.7460 (tp30) cc_final: 0.7127 (tp30) outliers start: 71 outliers final: 35 residues processed: 531 average time/residue: 1.3097 time to fit residues: 771.8563 Evaluate side-chains 542 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 504 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 586 ILE Chi-restraints excluded: chain D residue 606 LYS Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 653 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 692 LYS Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 545 ILE Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain G residue 583 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 686 GLN E 531 GLN E 648 GLN ** F 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 531 GLN G 681 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18279 Z= 0.236 Angle : 0.479 9.083 24716 Z= 0.258 Chirality : 0.041 0.198 2931 Planarity : 0.003 0.028 3023 Dihedral : 7.112 59.217 2367 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.14 % Allowed : 13.52 % Favored : 83.34 % 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: 2.74 (0.19), residues: 2146 helix: 2.97 (0.14), residues: 1190 sheet: 0.35 (0.27), residues: 329 loop : 0.40 (0.29), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 304 HIS 0.005 0.001 HIS F 684 PHE 0.018 0.001 PHE D 301 TYR 0.010 0.001 TYR E 740 ARG 0.003 0.000 ARG F 671 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 517 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 LYS cc_start: 0.7762 (tttm) cc_final: 0.7508 (tttm) REVERT: A 688 ASN cc_start: 0.8008 (OUTLIER) cc_final: 0.7754 (m-40) REVERT: A 737 ASP cc_start: 0.7738 (t0) cc_final: 0.7520 (t0) REVERT: B 669 LYS cc_start: 0.8451 (mtpm) cc_final: 0.8175 (ttmm) REVERT: B 717 GLU cc_start: 0.7365 (tp30) cc_final: 0.7092 (tp30) REVERT: C 301 PHE cc_start: 0.6569 (t80) cc_final: 0.6202 (t80) REVERT: D 531 GLN cc_start: 0.7143 (mt0) cc_final: 0.6856 (mt0) REVERT: F 612 MET cc_start: 0.8390 (mtp) cc_final: 0.8111 (ttm) REVERT: F 718 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8045 (ptmt) REVERT: G 324 LYS cc_start: 0.8527 (mttm) cc_final: 0.8300 (mttm) outliers start: 63 outliers final: 36 residues processed: 529 average time/residue: 1.2966 time to fit residues: 761.0812 Evaluate side-chains 546 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 508 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 586 ILE Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 667 ASP Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 718 LYS Chi-restraints excluded: chain G residue 545 ILE Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 583 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 6.9990 chunk 188 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 209 optimal weight: 0.4980 chunk 174 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 69 optimal weight: 30.0000 chunk 110 optimal weight: 0.8980 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 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN E 648 GLN ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18279 Z= 0.198 Angle : 0.465 8.485 24716 Z= 0.249 Chirality : 0.040 0.206 2931 Planarity : 0.003 0.028 3023 Dihedral : 7.002 59.809 2365 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.04 % Allowed : 14.11 % Favored : 82.84 % 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: 2.85 (0.19), residues: 2146 helix: 3.08 (0.14), residues: 1185 sheet: 0.24 (0.29), residues: 299 loop : 0.49 (0.28), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 304 HIS 0.004 0.001 HIS E 708 PHE 0.016 0.001 PHE D 301 TYR 0.009 0.001 TYR E 740 ARG 0.003 0.000 ARG F 671 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 518 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 LYS cc_start: 0.7739 (tttm) cc_final: 0.7496 (tttm) REVERT: A 688 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7752 (m-40) REVERT: A 737 ASP cc_start: 0.7728 (t0) cc_final: 0.7441 (t0) REVERT: B 629 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.7785 (t80) REVERT: B 669 LYS cc_start: 0.8441 (mtpm) cc_final: 0.8185 (ttmm) REVERT: C 301 PHE cc_start: 0.6546 (t80) cc_final: 0.6204 (t80) REVERT: D 531 GLN cc_start: 0.7128 (mt0) cc_final: 0.6837 (mt0) REVERT: E 737 ASP cc_start: 0.7107 (t0) cc_final: 0.6859 (t0) REVERT: F 653 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7959 (mt-10) REVERT: F 692 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8156 (mtmt) REVERT: F 718 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8038 (ptmt) REVERT: G 324 LYS cc_start: 0.8538 (mttm) cc_final: 0.8310 (mttm) REVERT: G 717 GLU cc_start: 0.7400 (tp30) cc_final: 0.7017 (tp30) outliers start: 61 outliers final: 32 residues processed: 533 average time/residue: 1.3128 time to fit residues: 775.0997 Evaluate side-chains 549 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 512 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 693 GLU Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 586 ILE Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain E residue 718 LYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 653 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 692 LYS Chi-restraints excluded: chain F residue 718 LYS Chi-restraints excluded: chain G residue 545 ILE Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 621 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 209 optimal weight: 0.9990 chunk 130 optimal weight: 30.0000 chunk 127 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 686 GLN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN E 648 GLN G 681 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18279 Z= 0.213 Angle : 0.480 9.459 24716 Z= 0.255 Chirality : 0.040 0.170 2931 Planarity : 0.003 0.027 3023 Dihedral : 7.031 59.189 2365 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.14 % Allowed : 14.61 % Favored : 82.24 % 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: 2.84 (0.19), residues: 2146 helix: 3.08 (0.14), residues: 1185 sheet: 0.17 (0.29), residues: 299 loop : 0.51 (0.28), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 304 HIS 0.005 0.001 HIS E 708 PHE 0.016 0.001 PHE E 574 TYR 0.016 0.001 TYR D 740 ARG 0.005 0.000 ARG F 599 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 502 time to evaluate : 2.082 Fit side-chains revert: symmetry clash REVERT: A 579 LYS cc_start: 0.7751 (tttm) cc_final: 0.7531 (tttm) REVERT: A 688 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7750 (m-40) REVERT: A 717 GLU cc_start: 0.6859 (tp30) cc_final: 0.6546 (tp30) REVERT: A 737 ASP cc_start: 0.7743 (t0) cc_final: 0.7354 (t0) REVERT: B 629 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.8002 (t80) REVERT: B 669 LYS cc_start: 0.8466 (mtpm) cc_final: 0.8177 (ttmm) REVERT: C 301 PHE cc_start: 0.6545 (t80) cc_final: 0.6185 (t80) REVERT: D 531 GLN cc_start: 0.7127 (mt0) cc_final: 0.6848 (mt0) REVERT: E 737 ASP cc_start: 0.7076 (t0) cc_final: 0.6825 (t0) REVERT: F 718 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8037 (ptmt) REVERT: G 324 LYS cc_start: 0.8566 (mttm) cc_final: 0.8336 (mttm) REVERT: G 717 GLU cc_start: 0.7421 (tp30) cc_final: 0.7030 (tp30) outliers start: 63 outliers final: 38 residues processed: 521 average time/residue: 1.3366 time to fit residues: 770.5686 Evaluate side-chains 535 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 494 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 693 GLU Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain E residue 718 LYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 718 LYS Chi-restraints excluded: chain G residue 319 LYS Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain G residue 583 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 0.0770 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 164 optimal weight: 1.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 681 ASN ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18279 Z= 0.199 Angle : 0.480 8.651 24716 Z= 0.254 Chirality : 0.040 0.152 2931 Planarity : 0.003 0.028 3023 Dihedral : 6.902 57.888 2365 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.84 % Allowed : 15.26 % Favored : 81.90 % 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: 2.86 (0.19), residues: 2146 helix: 3.11 (0.14), residues: 1186 sheet: 0.15 (0.29), residues: 299 loop : 0.51 (0.28), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 304 HIS 0.005 0.001 HIS E 708 PHE 0.013 0.001 PHE D 301 TYR 0.016 0.001 TYR D 740 ARG 0.002 0.000 ARG G 599 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 507 time to evaluate : 2.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 LYS cc_start: 0.7753 (tttm) cc_final: 0.7550 (tttm) REVERT: A 688 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7749 (m-40) REVERT: A 737 ASP cc_start: 0.7749 (t0) cc_final: 0.7319 (t0) REVERT: B 629 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7983 (t80) REVERT: B 669 LYS cc_start: 0.8460 (mtpm) cc_final: 0.8168 (ttmm) REVERT: C 301 PHE cc_start: 0.6533 (t80) cc_final: 0.6192 (t80) REVERT: D 531 GLN cc_start: 0.7130 (mt0) cc_final: 0.6847 (mt0) REVERT: E 737 ASP cc_start: 0.7146 (t0) cc_final: 0.6927 (t0) REVERT: F 718 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.8016 (ptmt) REVERT: G 717 GLU cc_start: 0.7385 (tp30) cc_final: 0.6985 (tp30) outliers start: 57 outliers final: 40 residues processed: 520 average time/residue: 1.3089 time to fit residues: 754.1228 Evaluate side-chains 552 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 509 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 688 ASN Chi-restraints excluded: chain B residue 693 GLU Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 534 LYS Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain E residue 718 LYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 667 ASP Chi-restraints excluded: chain F residue 698 ASN Chi-restraints excluded: chain F residue 718 LYS Chi-restraints excluded: chain G residue 319 LYS Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 650 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 3.9990 chunk 200 optimal weight: 0.5980 chunk 182 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 117 optimal weight: 0.0570 chunk 84 optimal weight: 0.4980 chunk 153 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 176 optimal weight: 2.9990 chunk 184 optimal weight: 0.4980 chunk 127 optimal weight: 0.9980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 GLN B 515 GLN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 576 ASN G 681 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18279 Z= 0.155 Angle : 0.465 9.332 24716 Z= 0.247 Chirality : 0.040 0.147 2931 Planarity : 0.003 0.027 3023 Dihedral : 6.813 58.669 2365 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.34 % Allowed : 16.01 % Favored : 81.65 % 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: 2.87 (0.19), residues: 2146 helix: 3.13 (0.14), residues: 1192 sheet: 0.14 (0.29), residues: 299 loop : 0.47 (0.29), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 304 HIS 0.004 0.000 HIS E 708 PHE 0.022 0.001 PHE D 574 TYR 0.013 0.001 TYR D 740 ARG 0.002 0.000 ARG G 599 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 502 time to evaluate : 1.787 Fit side-chains revert: symmetry clash REVERT: A 579 LYS cc_start: 0.7738 (tttm) cc_final: 0.7504 (tttm) REVERT: A 688 ASN cc_start: 0.7978 (OUTLIER) cc_final: 0.7739 (m-40) REVERT: A 717 GLU cc_start: 0.6684 (tp30) cc_final: 0.6466 (tp30) REVERT: A 737 ASP cc_start: 0.7734 (t0) cc_final: 0.7297 (t0) REVERT: B 629 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7959 (t80) REVERT: B 669 LYS cc_start: 0.8434 (mtpm) cc_final: 0.8156 (ttmm) REVERT: B 731 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8412 (ttpp) REVERT: C 301 PHE cc_start: 0.6506 (t80) cc_final: 0.6175 (t80) REVERT: D 531 GLN cc_start: 0.7105 (mt0) cc_final: 0.6832 (mt0) REVERT: F 671 ARG cc_start: 0.8303 (mmm-85) cc_final: 0.8066 (mmm160) REVERT: G 717 GLU cc_start: 0.7245 (tp30) cc_final: 0.6891 (tp30) outliers start: 47 outliers final: 37 residues processed: 511 average time/residue: 1.3355 time to fit residues: 755.9441 Evaluate side-chains 538 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 499 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 693 GLU Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 534 LYS Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 586 ILE Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain E residue 718 LYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 667 ASP Chi-restraints excluded: chain F residue 698 ASN Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain G residue 319 LYS Chi-restraints excluded: chain G residue 545 ILE Chi-restraints excluded: chain G residue 577 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 143 optimal weight: 0.6980 chunk 216 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 686 GLN B 613 ASN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 613 ASN G 698 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18279 Z= 0.323 Angle : 0.541 9.000 24716 Z= 0.285 Chirality : 0.042 0.159 2931 Planarity : 0.003 0.031 3023 Dihedral : 7.013 59.744 2365 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.69 % Allowed : 15.81 % Favored : 81.50 % 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: 2.62 (0.19), residues: 2146 helix: 2.94 (0.14), residues: 1191 sheet: 0.11 (0.29), residues: 294 loop : 0.29 (0.28), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 683 HIS 0.007 0.001 HIS E 708 PHE 0.016 0.002 PHE F 572 TYR 0.020 0.002 TYR D 740 ARG 0.004 0.000 ARG F 599 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 504 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 LYS cc_start: 0.7771 (tttm) cc_final: 0.7538 (tttm) REVERT: A 688 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7775 (m-40) REVERT: A 737 ASP cc_start: 0.7775 (t0) cc_final: 0.7340 (t0) REVERT: B 629 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.8086 (t80) REVERT: B 717 GLU cc_start: 0.7444 (tp30) cc_final: 0.7184 (tp30) REVERT: C 301 PHE cc_start: 0.6532 (t80) cc_final: 0.6195 (t80) REVERT: D 531 GLN cc_start: 0.7199 (mt0) cc_final: 0.6960 (mt0) REVERT: F 717 GLU cc_start: 0.7512 (tp30) cc_final: 0.7261 (tp30) outliers start: 54 outliers final: 41 residues processed: 516 average time/residue: 1.3565 time to fit residues: 774.0756 Evaluate side-chains 538 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 495 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 693 GLU Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 695 GLU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 534 LYS Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain E residue 718 LYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 698 ASN Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain G residue 545 ILE Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 680 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 158 optimal weight: 8.9990 chunk 25 optimal weight: 0.0670 chunk 47 optimal weight: 0.6980 chunk 172 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 177 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 151 optimal weight: 0.4980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 GLN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN F 531 GLN ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.164552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129286 restraints weight = 25206.084| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.73 r_work: 0.3427 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18279 Z= 0.177 Angle : 0.485 11.270 24716 Z= 0.256 Chirality : 0.040 0.152 2931 Planarity : 0.003 0.028 3023 Dihedral : 6.839 58.455 2365 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.39 % Allowed : 16.76 % Favored : 80.85 % 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: 2.81 (0.19), residues: 2146 helix: 3.09 (0.14), residues: 1186 sheet: 0.07 (0.29), residues: 299 loop : 0.48 (0.28), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 304 HIS 0.005 0.001 HIS E 708 PHE 0.028 0.001 PHE D 574 TYR 0.016 0.001 TYR D 740 ARG 0.007 0.000 ARG A 599 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10326.83 seconds wall clock time: 180 minutes 55.25 seconds (10855.25 seconds total)