Starting phenix.real_space_refine on Sat Feb 17 09:57:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nak_24272/02_2024/7nak_24272_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nak_24272/02_2024/7nak_24272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nak_24272/02_2024/7nak_24272.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nak_24272/02_2024/7nak_24272.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nak_24272/02_2024/7nak_24272_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nak_24272/02_2024/7nak_24272_trim_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians I 8 10.91 5 P 16 5.49 5 S 48 5.16 5 C 5976 2.51 5 N 1544 2.21 5 O 1744 1.98 5 H 8967 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 596": "OE1" <-> "OE2" Residue "C GLU 686": "OE1" <-> "OE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 693": "OE1" <-> "OE2" Residue "F GLU 604": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18303 Number of models: 1 Model: "" Number of chains: 16 Chain: "D" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2243 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "C" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2242 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "G" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2241 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "B" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2243 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "A" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2242 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "E" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2241 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "F" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2242 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "H" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2241 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1QD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1QD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1QD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1QD': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1QD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1QD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1QD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1QD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.91, per 1000 atoms: 0.43 Number of scatterers: 18303 At special positions: 0 Unit cell: (81.45, 80.364, 157.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) I 8 52.95 S 48 16.00 P 16 15.00 O 1744 8.00 N 1544 7.00 C 5976 6.00 H 8967 1.00 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: 13.51 Conformation dependent library (CDL) restraints added in 1.7 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 10 sheets defined 40.8% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'D' and resid 574 through 587 removed outlier: 3.681A pdb=" N HIS D 587 " --> pdb=" O HIS D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 597 No H-bonds generated for 'chain 'D' and resid 594 through 597' Processing helix chain 'D' and resid 604 through 612 removed outlier: 3.542A pdb=" N ILE D 608 " --> pdb=" O GLU D 604 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN D 609 " --> pdb=" O ASP D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 649 removed outlier: 3.555A pdb=" N THR D 645 " --> pdb=" O LYS D 641 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA D 646 " --> pdb=" O GLU D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 677 removed outlier: 3.502A pdb=" N GLN D 673 " --> pdb=" O GLU D 670 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ALA D 674 " --> pdb=" O ASP D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 698 removed outlier: 3.755A pdb=" N GLU D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 587 Processing helix chain 'C' and resid 594 through 597 No H-bonds generated for 'chain 'C' and resid 594 through 597' Processing helix chain 'C' and resid 604 through 612 removed outlier: 3.755A pdb=" N GLN C 609 " --> pdb=" O ASP C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 649 removed outlier: 3.568A pdb=" N GLU C 642 " --> pdb=" O TRP C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 667 No H-bonds generated for 'chain 'C' and resid 665 through 667' Processing helix chain 'C' and resid 674 through 677 Processing helix chain 'C' and resid 688 through 698 Processing helix chain 'G' and resid 574 through 587 removed outlier: 4.007A pdb=" N LEU G 586 " --> pdb=" O VAL G 582 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS G 587 " --> pdb=" O HIS G 583 " (cutoff:3.500A) Processing helix chain 'G' and resid 594 through 597 No H-bonds generated for 'chain 'G' and resid 594 through 597' Processing helix chain 'G' and resid 604 through 613 removed outlier: 4.039A pdb=" N MET G 612 " --> pdb=" O ILE G 608 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 648 removed outlier: 3.542A pdb=" N ILE G 643 " --> pdb=" O VAL G 639 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR G 645 " --> pdb=" O LYS G 641 " (cutoff:3.500A) Processing helix chain 'G' and resid 673 through 675 No H-bonds generated for 'chain 'G' and resid 673 through 675' Processing helix chain 'G' and resid 688 through 698 Processing helix chain 'B' and resid 574 through 587 removed outlier: 3.661A pdb=" N HIS B 587 " --> pdb=" O HIS B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 No H-bonds generated for 'chain 'B' and resid 594 through 597' Processing helix chain 'B' and resid 603 through 613 Processing helix chain 'B' and resid 638 through 648 removed outlier: 3.638A pdb=" N THR B 645 " --> pdb=" O LYS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 667 No H-bonds generated for 'chain 'B' and resid 665 through 667' Processing helix chain 'B' and resid 670 through 677 removed outlier: 3.677A pdb=" N GLN B 673 " --> pdb=" O GLU B 670 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ALA B 674 " --> pdb=" O ASP B 671 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL B 675 " --> pdb=" O MET B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 698 Processing helix chain 'A' and resid 574 through 587 removed outlier: 3.600A pdb=" N LEU A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS A 587 " --> pdb=" O HIS A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 597 No H-bonds generated for 'chain 'A' and resid 594 through 597' Processing helix chain 'A' and resid 603 through 611 removed outlier: 3.943A pdb=" N ILE A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 629 No H-bonds generated for 'chain 'A' and resid 627 through 629' Processing helix chain 'A' and resid 638 through 649 removed outlier: 3.620A pdb=" N THR A 645 " --> pdb=" O LYS A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 677 removed outlier: 3.627A pdb=" N LEU A 676 " --> pdb=" O GLN A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 698 removed outlier: 3.550A pdb=" N GLU A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 587 removed outlier: 3.745A pdb=" N HIS E 587 " --> pdb=" O HIS E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 597 No H-bonds generated for 'chain 'E' and resid 594 through 597' Processing helix chain 'E' and resid 604 through 613 removed outlier: 3.687A pdb=" N ILE E 608 " --> pdb=" O GLU E 604 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN E 609 " --> pdb=" O ASP E 605 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N MET E 612 " --> pdb=" O ILE E 608 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY E 613 " --> pdb=" O GLN E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 640 through 648 removed outlier: 3.636A pdb=" N THR E 645 " --> pdb=" O LYS E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 665 through 667 No H-bonds generated for 'chain 'E' and resid 665 through 667' Processing helix chain 'E' and resid 673 through 675 No H-bonds generated for 'chain 'E' and resid 673 through 675' Processing helix chain 'E' and resid 688 through 698 Processing helix chain 'F' and resid 574 through 586 removed outlier: 3.557A pdb=" N VAL F 582 " --> pdb=" O SER F 578 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS F 583 " --> pdb=" O LEU F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 597 No H-bonds generated for 'chain 'F' and resid 594 through 597' Processing helix chain 'F' and resid 604 through 613 removed outlier: 3.658A pdb=" N ILE F 608 " --> pdb=" O GLU F 604 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 648 Processing helix chain 'F' and resid 671 through 677 removed outlier: 4.078A pdb=" N ALA F 674 " --> pdb=" O ASP F 671 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR F 677 " --> pdb=" O ALA F 674 " (cutoff:3.500A) Processing helix chain 'F' and resid 688 through 698 removed outlier: 3.559A pdb=" N GLU F 693 " --> pdb=" O GLU F 689 " (cutoff:3.500A) Processing helix chain 'H' and resid 574 through 587 removed outlier: 3.775A pdb=" N HIS H 583 " --> pdb=" O LEU H 579 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU H 584 " --> pdb=" O LEU H 580 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN H 585 " --> pdb=" O LYS H 581 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS H 587 " --> pdb=" O HIS H 583 " (cutoff:3.500A) Processing helix chain 'H' and resid 594 through 596 No H-bonds generated for 'chain 'H' and resid 594 through 596' Processing helix chain 'H' and resid 604 through 611 removed outlier: 4.165A pdb=" N GLN H 609 " --> pdb=" O ASP H 605 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL H 611 " --> pdb=" O LEU H 607 " (cutoff:3.500A) Processing helix chain 'H' and resid 627 through 629 No H-bonds generated for 'chain 'H' and resid 627 through 629' Processing helix chain 'H' and resid 638 through 649 removed outlier: 3.660A pdb=" N ILE H 643 " --> pdb=" O VAL H 639 " (cutoff:3.500A) Processing helix chain 'H' and resid 670 through 677 removed outlier: 4.726A pdb=" N ALA H 674 " --> pdb=" O ASP H 671 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL H 675 " --> pdb=" O MET H 672 " (cutoff:3.500A) Processing helix chain 'H' and resid 688 through 698 Processing sheet with id= A, first strand: chain 'D' and resid 616 through 622 removed outlier: 6.341A pdb=" N ASN D 652 " --> pdb=" O PHE D 617 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU D 619 " --> pdb=" O ASN D 652 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL D 654 " --> pdb=" O LEU D 619 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU D 621 " --> pdb=" O VAL D 654 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE D 656 " --> pdb=" O LEU D 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 564 through 567 removed outlier: 6.895A pdb=" N ASN C 616 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N SER C 567 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL C 618 " --> pdb=" O SER C 567 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASN C 652 " --> pdb=" O PHE C 617 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU C 619 " --> pdb=" O ASN C 652 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL C 654 " --> pdb=" O LEU C 619 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU C 621 " --> pdb=" O VAL C 654 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE C 656 " --> pdb=" O LEU C 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'G' and resid 564 through 567 removed outlier: 6.917A pdb=" N ASN G 616 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N SER G 567 " --> pdb=" O ASN G 616 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL G 618 " --> pdb=" O SER G 567 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'G' and resid 620 through 622 removed outlier: 5.969A pdb=" N ILE G 656 " --> pdb=" O LEU G 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 564 through 567 removed outlier: 7.090A pdb=" N ASN B 616 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N SER B 567 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 618 " --> pdb=" O SER B 567 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ASN B 652 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU B 619 " --> pdb=" O ASN B 652 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL B 654 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU B 621 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE B 656 " --> pdb=" O LEU B 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 616 through 622 removed outlier: 5.742A pdb=" N ASN A 652 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU A 619 " --> pdb=" O ASN A 652 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 654 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU A 621 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE A 656 " --> pdb=" O LEU A 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'E' and resid 564 through 567 removed outlier: 7.141A pdb=" N ASN E 616 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N SER E 567 " --> pdb=" O ASN E 616 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL E 618 " --> pdb=" O SER E 567 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASN E 652 " --> pdb=" O PHE E 617 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU E 619 " --> pdb=" O ASN E 652 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 654 " --> pdb=" O LEU E 619 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU E 621 " --> pdb=" O VAL E 654 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE E 656 " --> pdb=" O LEU E 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'F' and resid 564 through 567 removed outlier: 6.629A pdb=" N ASN F 616 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N SER F 567 " --> pdb=" O ASN F 616 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL F 618 " --> pdb=" O SER F 567 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'H' and resid 564 through 567 removed outlier: 6.502A pdb=" N ASN H 616 " --> pdb=" O PHE H 565 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N SER H 567 " --> pdb=" O ASN H 616 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL H 618 " --> pdb=" O SER H 567 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'H' and resid 620 through 622 removed outlier: 6.614A pdb=" N ILE H 656 " --> pdb=" O LEU H 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= J 212 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.24 Time building geometry restraints manager: 14.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 2.40: 18550 2.40 - 3.96: 0 3.96 - 5.52: 0 5.52 - 7.08: 0 7.08 - 8.64: 1 Warning: very large bond lengths. Bond restraints: 18551 Sorted by residual: bond pdb=" OH TYR H 687 " pdb=" HH TYR H 687 " ideal model delta sigma weight residual 0.840 8.641 -7.801 2.00e-02 2.50e+03 1.52e+05 bond pdb=" C26 1QD E 801 " pdb=" N27 1QD E 801 " ideal model delta sigma weight residual 1.334 1.459 -0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" C26 1QD A 801 " pdb=" N27 1QD A 801 " ideal model delta sigma weight residual 1.334 1.459 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C26 1QD H 801 " pdb=" N27 1QD H 801 " ideal model delta sigma weight residual 1.334 1.459 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C26 1QD G 801 " pdb=" N27 1QD G 801 " ideal model delta sigma weight residual 1.334 1.458 -0.124 2.00e-02 2.50e+03 3.82e+01 ... (remaining 18546 not shown) Histogram of bond angle deviations from ideal: 98.51 - 105.88: 217 105.88 - 113.24: 22058 113.24 - 120.61: 6459 120.61 - 127.97: 4678 127.97 - 135.33: 138 Bond angle restraints: 33550 Sorted by residual: angle pdb=" O08 1QD B 801 " pdb=" P09 1QD B 801 " pdb=" O11 1QD B 801 " ideal model delta sigma weight residual 93.31 110.09 -16.78 3.00e+00 1.11e-01 3.13e+01 angle pdb=" O08 1QD H 801 " pdb=" P09 1QD H 801 " pdb=" O11 1QD H 801 " ideal model delta sigma weight residual 93.31 109.87 -16.56 3.00e+00 1.11e-01 3.05e+01 angle pdb=" O08 1QD A 801 " pdb=" P09 1QD A 801 " pdb=" O11 1QD A 801 " ideal model delta sigma weight residual 93.31 109.84 -16.53 3.00e+00 1.11e-01 3.04e+01 angle pdb=" O08 1QD D 801 " pdb=" P09 1QD D 801 " pdb=" O11 1QD D 801 " ideal model delta sigma weight residual 93.31 109.33 -16.02 3.00e+00 1.11e-01 2.85e+01 angle pdb=" O08 1QD E 801 " pdb=" P09 1QD E 801 " pdb=" O11 1QD E 801 " ideal model delta sigma weight residual 93.31 109.32 -16.01 3.00e+00 1.11e-01 2.85e+01 ... (remaining 33545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.04: 8512 34.04 - 68.08: 366 68.08 - 102.12: 53 102.12 - 136.16: 10 136.16 - 170.20: 2 Dihedral angle restraints: 8943 sinusoidal: 5048 harmonic: 3895 Sorted by residual: dihedral pdb=" C14 1QD F 801 " pdb=" C12 1QD F 801 " pdb=" C13 1QD F 801 " pdb=" O11 1QD F 801 " ideal model delta sinusoidal sigma weight residual 179.65 -10.15 -170.20 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C12 1QD B 801 " pdb=" O11 1QD B 801 " pdb=" P09 1QD B 801 " pdb=" O30 1QD B 801 " ideal model delta sinusoidal sigma weight residual 85.52 -55.37 140.89 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" C12 1QD B 801 " pdb=" O11 1QD B 801 " pdb=" P09 1QD B 801 " pdb=" O08 1QD B 801 " ideal model delta sinusoidal sigma weight residual 197.89 64.52 133.37 1 3.00e+01 1.11e-03 1.80e+01 ... (remaining 8940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1212 0.062 - 0.123: 201 0.123 - 0.185: 18 0.185 - 0.246: 10 0.246 - 0.308: 7 Chirality restraints: 1448 Sorted by residual: chirality pdb=" C01 1QD H 801 " pdb=" C02 1QD H 801 " pdb=" N36 1QD H 801 " pdb=" O33 1QD H 801 " both_signs ideal model delta sigma weight residual False 2.38 2.69 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C01 1QD D 801 " pdb=" C02 1QD D 801 " pdb=" N36 1QD D 801 " pdb=" O33 1QD D 801 " both_signs ideal model delta sigma weight residual False 2.38 2.68 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C01 1QD F 801 " pdb=" C02 1QD F 801 " pdb=" N36 1QD F 801 " pdb=" O33 1QD F 801 " both_signs ideal model delta sigma weight residual False 2.38 2.68 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1445 not shown) Planarity restraints: 2664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN H 688 " -0.196 2.00e-02 2.50e+03 2.23e-01 7.44e+02 pdb=" CD GLN H 688 " 0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN H 688 " 0.192 2.00e-02 2.50e+03 pdb=" NE2 GLN H 688 " -0.006 2.00e-02 2.50e+03 pdb="HE21 GLN H 688 " 0.329 2.00e-02 2.50e+03 pdb="HE22 GLN H 688 " -0.337 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN H 609 " 0.190 2.00e-02 2.50e+03 2.15e-01 6.94e+02 pdb=" CD GLN H 609 " -0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN H 609 " -0.186 2.00e-02 2.50e+03 pdb=" NE2 GLN H 609 " 0.007 2.00e-02 2.50e+03 pdb="HE21 GLN H 609 " -0.318 2.00e-02 2.50e+03 pdb="HE22 GLN H 609 " 0.324 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 616 " -0.120 2.00e-02 2.50e+03 1.27e-01 2.42e+02 pdb=" CG ASN G 616 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN G 616 " 0.112 2.00e-02 2.50e+03 pdb=" ND2 ASN G 616 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN G 616 " 0.181 2.00e-02 2.50e+03 pdb="HD22 ASN G 616 " -0.191 2.00e-02 2.50e+03 ... (remaining 2661 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.27: 2981 2.27 - 2.95: 46189 2.95 - 3.62: 56981 3.62 - 4.29: 88505 4.29 - 4.96: 139744 Nonbonded interactions: 334400 Sorted by model distance: nonbonded pdb=" O SER F 574 " pdb=" HG SER F 578 " model vdw 1.602 1.850 nonbonded pdb=" HH TYR C 687 " pdb=" O LYS B 682 " model vdw 1.603 1.850 nonbonded pdb=" O SER E 574 " pdb=" HG SER E 578 " model vdw 1.608 1.850 nonbonded pdb="HH21 ARG H 569 " pdb=" O ALA H 625 " model vdw 1.625 1.850 nonbonded pdb=" HZ1 LYS D 581 " pdb=" OE1 GLN D 585 " model vdw 1.631 1.850 ... (remaining 334395 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 561 through 586 or (resid 587 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 588 through 700 or resid 801)) selection = (chain 'B' and (resid 561 through 586 or (resid 587 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 588 through 639 or (resid 640 and (name N or name CA or name C or name O or \ name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or \ name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid \ 641 through 700 or resid 801)) selection = (chain 'C' and (resid 561 through 586 or (resid 587 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 588 through 639 or (resid 640 and (name N or name CA or name C or name O or \ name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or \ name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid \ 641 through 700 or resid 801)) selection = (chain 'D' and (resid 561 through 586 or (resid 587 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 588 through 639 or (resid 640 and (name N or name CA or name C or name O or \ name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or \ name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid \ 641 through 700 or resid 801)) selection = (chain 'E' and (resid 561 through 586 or (resid 587 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 588 through 700 or resid 801)) selection = (chain 'F' and (resid 561 through 586 or (resid 587 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 588 through 700 or resid 801)) selection = (chain 'G' and (resid 561 through 586 or (resid 587 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 588 through 700 or resid 801)) selection = (chain 'H' and (resid 561 through 586 or (resid 587 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 588 through 700 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=0.00 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.250 Extract box with map and model: 6.440 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 59.270 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.130 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 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 : 0.008 0.125 9584 Z= 0.510 Angle : 1.032 16.783 13040 Z= 0.455 Chirality : 0.052 0.308 1448 Planarity : 0.003 0.036 1600 Dihedral : 19.829 170.196 3840 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -0.76 (0.26), residues: 1104 helix: -0.98 (0.25), residues: 392 sheet: -0.36 (0.42), residues: 152 loop : 0.01 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 638 HIS 0.006 0.001 HIS B 583 PHE 0.016 0.001 PHE B 660 TYR 0.009 0.001 TYR B 687 ARG 0.002 0.000 ARG C 697 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 664 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6612 (tm-30) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 2.5893 time to fit residues: 539.1341 Evaluate side-chains 156 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.0980 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 0.0870 chunk 101 optimal weight: 0.6980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 587 HIS G 616 ASN B 673 GLN H 575 GLN H 688 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9584 Z= 0.166 Angle : 0.532 5.430 13040 Z= 0.266 Chirality : 0.041 0.139 1448 Planarity : 0.004 0.058 1600 Dihedral : 17.940 170.357 1624 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.00 % Allowed : 11.10 % Favored : 87.90 % 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: 0.14 (0.26), residues: 1104 helix: 0.36 (0.26), residues: 392 sheet: -0.06 (0.42), residues: 152 loop : 0.11 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 638 HIS 0.007 0.001 HIS C 587 PHE 0.009 0.001 PHE B 660 TYR 0.021 0.001 TYR H 687 ARG 0.007 0.000 ARG E 615 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 172 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 643 ILE cc_start: 0.6531 (mm) cc_final: 0.6011 (mt) REVERT: G 596 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.6006 (tt0) REVERT: G 676 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7422 (pt) outliers start: 10 outliers final: 6 residues processed: 175 average time/residue: 2.5600 time to fit residues: 480.0257 Evaluate side-chains 165 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 157 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain G residue 596 GLU Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain F residue 622 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 0.0970 chunk 110 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9584 Z= 0.200 Angle : 0.515 5.657 13040 Z= 0.258 Chirality : 0.041 0.149 1448 Planarity : 0.003 0.051 1600 Dihedral : 16.010 169.209 1624 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.40 % Allowed : 13.20 % Favored : 85.40 % 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: 0.38 (0.26), residues: 1104 helix: 0.52 (0.26), residues: 416 sheet: -0.04 (0.42), residues: 152 loop : 0.32 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 638 HIS 0.005 0.001 HIS C 583 PHE 0.013 0.001 PHE B 660 TYR 0.008 0.001 TYR H 687 ARG 0.008 0.000 ARG E 615 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 596 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.6002 (tt0) outliers start: 14 outliers final: 8 residues processed: 169 average time/residue: 2.5359 time to fit residues: 458.5951 Evaluate side-chains 167 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 158 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain G residue 596 GLU Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain F residue 622 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 0.0470 chunk 96 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9584 Z= 0.160 Angle : 0.485 7.911 13040 Z= 0.241 Chirality : 0.040 0.140 1448 Planarity : 0.003 0.062 1600 Dihedral : 14.672 172.888 1624 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.60 % Allowed : 13.80 % Favored : 84.60 % 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: 0.60 (0.26), residues: 1104 helix: 0.72 (0.26), residues: 432 sheet: 0.13 (0.42), residues: 152 loop : 0.40 (0.30), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 638 HIS 0.003 0.001 HIS C 583 PHE 0.020 0.001 PHE E 603 TYR 0.006 0.001 TYR B 687 ARG 0.011 0.000 ARG E 615 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 689 GLU cc_start: 0.6847 (pm20) cc_final: 0.6628 (pm20) outliers start: 16 outliers final: 10 residues processed: 167 average time/residue: 2.5640 time to fit residues: 457.9500 Evaluate side-chains 165 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 155 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain E residue 622 SER Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain F residue 622 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 chunk 97 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9584 Z= 0.207 Angle : 0.507 4.905 13040 Z= 0.255 Chirality : 0.041 0.152 1448 Planarity : 0.004 0.068 1600 Dihedral : 14.780 178.997 1624 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.90 % Allowed : 15.70 % Favored : 82.40 % 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: 0.51 (0.26), residues: 1104 helix: 0.71 (0.26), residues: 432 sheet: 0.03 (0.42), residues: 152 loop : 0.30 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 638 HIS 0.005 0.001 HIS C 583 PHE 0.013 0.001 PHE B 660 TYR 0.008 0.002 TYR B 687 ARG 0.013 0.000 ARG E 615 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 612 MET cc_start: 0.7608 (mmm) cc_final: 0.7084 (mpm) outliers start: 19 outliers final: 12 residues processed: 169 average time/residue: 2.6317 time to fit residues: 475.5799 Evaluate side-chains 172 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 160 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain E residue 622 SER Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain F residue 622 SER Chi-restraints excluded: chain H residue 585 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 666 GLN C 571 ASN B 688 GLN ** H 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9584 Z= 0.360 Angle : 0.627 6.801 13040 Z= 0.315 Chirality : 0.044 0.171 1448 Planarity : 0.005 0.082 1600 Dihedral : 15.746 175.647 1624 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.00 % Allowed : 17.10 % Favored : 80.90 % 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: -0.16 (0.25), residues: 1104 helix: 0.14 (0.25), residues: 424 sheet: -0.32 (0.41), residues: 152 loop : -0.08 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP D 638 HIS 0.009 0.001 HIS C 583 PHE 0.019 0.002 PHE B 660 TYR 0.014 0.003 TYR H 568 ARG 0.017 0.001 ARG E 615 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 689 GLU cc_start: 0.6976 (pm20) cc_final: 0.6667 (pm20) REVERT: F 612 MET cc_start: 0.7358 (mmm) cc_final: 0.6963 (mpm) outliers start: 20 outliers final: 16 residues processed: 173 average time/residue: 2.5890 time to fit residues: 480.5097 Evaluate side-chains 179 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain E residue 622 SER Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain F residue 622 SER Chi-restraints excluded: chain H residue 640 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9584 Z= 0.215 Angle : 0.533 5.685 13040 Z= 0.268 Chirality : 0.041 0.151 1448 Planarity : 0.004 0.092 1600 Dihedral : 14.953 169.150 1624 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.20 % Allowed : 18.40 % Favored : 79.40 % 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: 0.09 (0.26), residues: 1104 helix: 0.41 (0.26), residues: 424 sheet: -0.19 (0.41), residues: 152 loop : 0.01 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 638 HIS 0.004 0.001 HIS C 583 PHE 0.020 0.001 PHE E 603 TYR 0.011 0.002 TYR H 687 ARG 0.016 0.001 ARG E 615 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 SER cc_start: 0.7898 (OUTLIER) cc_final: 0.7510 (m) outliers start: 22 outliers final: 11 residues processed: 169 average time/residue: 2.6321 time to fit residues: 475.7222 Evaluate side-chains 171 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain F residue 622 SER Chi-restraints excluded: chain H residue 640 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 700 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9584 Z= 0.252 Angle : 0.562 8.101 13040 Z= 0.281 Chirality : 0.042 0.154 1448 Planarity : 0.004 0.100 1600 Dihedral : 14.836 163.039 1624 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.50 % Allowed : 18.80 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1104 helix: 0.39 (0.26), residues: 424 sheet: -0.25 (0.42), residues: 152 loop : -0.03 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 638 HIS 0.005 0.001 HIS C 583 PHE 0.018 0.002 PHE E 603 TYR 0.011 0.002 TYR H 687 ARG 0.018 0.001 ARG E 615 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 162 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 571 ASN cc_start: 0.8029 (p0) cc_final: 0.7817 (p0) REVERT: B 574 SER cc_start: 0.7926 (OUTLIER) cc_final: 0.7513 (m) outliers start: 15 outliers final: 10 residues processed: 170 average time/residue: 2.6179 time to fit residues: 477.6017 Evaluate side-chains 170 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain F residue 622 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9584 Z= 0.227 Angle : 0.555 8.174 13040 Z= 0.276 Chirality : 0.041 0.149 1448 Planarity : 0.004 0.106 1600 Dihedral : 14.581 158.526 1624 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.20 % Allowed : 19.80 % Favored : 79.00 % 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: 0.14 (0.26), residues: 1104 helix: 0.51 (0.26), residues: 424 sheet: -0.20 (0.42), residues: 152 loop : 0.00 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 638 HIS 0.004 0.001 HIS C 583 PHE 0.015 0.001 PHE E 603 TYR 0.011 0.002 TYR H 687 ARG 0.019 0.001 ARG E 615 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 571 ASN cc_start: 0.7994 (p0) cc_final: 0.7732 (p0) REVERT: B 574 SER cc_start: 0.7908 (OUTLIER) cc_final: 0.7512 (m) outliers start: 12 outliers final: 11 residues processed: 170 average time/residue: 2.5791 time to fit residues: 468.9754 Evaluate side-chains 171 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain F residue 622 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 94 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9584 Z= 0.188 Angle : 0.533 9.105 13040 Z= 0.264 Chirality : 0.041 0.140 1448 Planarity : 0.004 0.111 1600 Dihedral : 14.172 154.562 1624 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.10 % Allowed : 19.60 % Favored : 79.30 % 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: 0.35 (0.26), residues: 1104 helix: 0.63 (0.26), residues: 432 sheet: -0.06 (0.42), residues: 152 loop : 0.15 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 638 HIS 0.003 0.001 HIS C 583 PHE 0.016 0.001 PHE E 603 TYR 0.008 0.001 TYR H 687 ARG 0.021 0.001 ARG E 615 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 163 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 571 ASN cc_start: 0.7975 (p0) cc_final: 0.7713 (p0) REVERT: B 574 SER cc_start: 0.7733 (OUTLIER) cc_final: 0.7397 (m) outliers start: 11 outliers final: 8 residues processed: 168 average time/residue: 2.5610 time to fit residues: 460.0570 Evaluate side-chains 169 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain F residue 622 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.0070 chunk 88 optimal weight: 0.5980 chunk 37 optimal weight: 0.0570 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.209898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.179038 restraints weight = 17581.189| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 1.30 r_work: 0.4099 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.4006 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9584 Z= 0.151 Angle : 0.513 9.129 13040 Z= 0.254 Chirality : 0.040 0.130 1448 Planarity : 0.004 0.109 1600 Dihedral : 13.628 150.653 1624 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.90 % Allowed : 20.40 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.27), residues: 1104 helix: 0.95 (0.26), residues: 432 sheet: 0.21 (0.43), residues: 152 loop : 0.33 (0.30), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 638 HIS 0.003 0.001 HIS D 640 PHE 0.013 0.001 PHE E 603 TYR 0.006 0.001 TYR B 687 ARG 0.021 0.001 ARG E 615 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8131.87 seconds wall clock time: 142 minutes 42.88 seconds (8562.88 seconds total)