Starting phenix.real_space_refine on Fri Mar 15 11:32:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a46_11629/03_2024/7a46_11629.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a46_11629/03_2024/7a46_11629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a46_11629/03_2024/7a46_11629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a46_11629/03_2024/7a46_11629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a46_11629/03_2024/7a46_11629.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a46_11629/03_2024/7a46_11629.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.094 sd= 2.381 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 28 5.16 5 C 7343 2.51 5 N 1967 2.21 5 O 2163 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 595": "NH1" <-> "NH2" Residue "A ARG 600": "NH1" <-> "NH2" Residue "A ARG 622": "NH1" <-> "NH2" Residue "A ASP 634": "OD1" <-> "OD2" Residue "A ARG 635": "NH1" <-> "NH2" Residue "A ARG 697": "NH1" <-> "NH2" Residue "B ARG 595": "NH1" <-> "NH2" Residue "B ARG 600": "NH1" <-> "NH2" Residue "B ARG 622": "NH1" <-> "NH2" Residue "B ASP 634": "OD1" <-> "OD2" Residue "B ARG 635": "NH1" <-> "NH2" Residue "B ARG 697": "NH1" <-> "NH2" Residue "C ARG 595": "NH1" <-> "NH2" Residue "C ARG 600": "NH1" <-> "NH2" Residue "C ARG 622": "NH1" <-> "NH2" Residue "C ASP 634": "OD1" <-> "OD2" Residue "C ARG 635": "NH1" <-> "NH2" Residue "C ARG 697": "NH1" <-> "NH2" Residue "D ARG 595": "NH1" <-> "NH2" Residue "D ARG 600": "NH1" <-> "NH2" Residue "D ARG 622": "NH1" <-> "NH2" Residue "D ASP 634": "OD1" <-> "OD2" Residue "D ARG 635": "NH1" <-> "NH2" Residue "D ARG 697": "NH1" <-> "NH2" Residue "E ARG 595": "NH1" <-> "NH2" Residue "E ARG 600": "NH1" <-> "NH2" Residue "E ARG 622": "NH1" <-> "NH2" Residue "E ASP 634": "OD1" <-> "OD2" Residue "E ARG 635": "NH1" <-> "NH2" Residue "E ARG 697": "NH1" <-> "NH2" Residue "F ARG 595": "NH1" <-> "NH2" Residue "F ARG 600": "NH1" <-> "NH2" Residue "F ARG 622": "NH1" <-> "NH2" Residue "F ASP 634": "OD1" <-> "OD2" Residue "F ARG 635": "NH1" <-> "NH2" Residue "F ARG 697": "NH1" <-> "NH2" Residue "G ARG 595": "NH1" <-> "NH2" Residue "G ARG 600": "NH1" <-> "NH2" Residue "G ARG 622": "NH1" <-> "NH2" Residue "G ASP 634": "OD1" <-> "OD2" Residue "G ARG 635": "NH1" <-> "NH2" Residue "G ARG 697": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11501 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1643 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1643 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1643 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1643 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1643 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1643 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1643 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 6.15, per 1000 atoms: 0.53 Number of scatterers: 11501 At special positions: 0 Unit cell: (104.223, 102.096, 125.493, 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 28 16.00 O 2163 8.00 N 1967 7.00 C 7343 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: 4.67 Conformation dependent library (CDL) restraints added in 2.4 seconds 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2856 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 8 sheets defined 54.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid -15 through 0 Processing helix chain 'A' and resid 518 through 533 Processing helix chain 'A' and resid 538 through 571 removed outlier: 5.641A pdb=" N THR A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 614 No H-bonds generated for 'chain 'A' and resid 612 through 614' Processing helix chain 'A' and resid 638 through 656 Processing helix chain 'A' and resid 656 through 661 removed outlier: 3.678A pdb=" N GLY A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 711 Processing helix chain 'B' and resid -14 through 0 Processing helix chain 'B' and resid 518 through 533 Processing helix chain 'B' and resid 538 through 571 removed outlier: 5.641A pdb=" N THR B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU B 558 " --> pdb=" O GLY B 554 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 638 through 656 Processing helix chain 'B' and resid 656 through 661 removed outlier: 3.678A pdb=" N GLY B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 711 Processing helix chain 'C' and resid -14 through 0 Processing helix chain 'C' and resid 518 through 533 Processing helix chain 'C' and resid 538 through 571 removed outlier: 5.641A pdb=" N THR C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU C 558 " --> pdb=" O GLY C 554 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL C 559 " --> pdb=" O SER C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 614 No H-bonds generated for 'chain 'C' and resid 612 through 614' Processing helix chain 'C' and resid 638 through 656 Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.679A pdb=" N GLY C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 711 Processing helix chain 'D' and resid -14 through 0 Processing helix chain 'D' and resid 518 through 533 Processing helix chain 'D' and resid 538 through 571 removed outlier: 5.640A pdb=" N THR D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU D 558 " --> pdb=" O GLY D 554 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 614 No H-bonds generated for 'chain 'D' and resid 612 through 614' Processing helix chain 'D' and resid 638 through 656 Processing helix chain 'D' and resid 656 through 661 removed outlier: 3.679A pdb=" N GLY D 661 " --> pdb=" O GLU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 711 Processing helix chain 'E' and resid -14 through 0 Processing helix chain 'E' and resid 518 through 533 Processing helix chain 'E' and resid 538 through 571 removed outlier: 5.641A pdb=" N THR E 557 " --> pdb=" O PHE E 553 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU E 558 " --> pdb=" O GLY E 554 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL E 559 " --> pdb=" O SER E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 614 No H-bonds generated for 'chain 'E' and resid 612 through 614' Processing helix chain 'E' and resid 638 through 656 Processing helix chain 'E' and resid 656 through 661 removed outlier: 3.679A pdb=" N GLY E 661 " --> pdb=" O GLU E 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 692 through 711 Processing helix chain 'F' and resid -14 through 0 Processing helix chain 'F' and resid 518 through 533 Processing helix chain 'F' and resid 538 through 571 removed outlier: 5.641A pdb=" N THR F 557 " --> pdb=" O PHE F 553 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU F 558 " --> pdb=" O GLY F 554 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL F 559 " --> pdb=" O SER F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 614 No H-bonds generated for 'chain 'F' and resid 612 through 614' Processing helix chain 'F' and resid 638 through 656 Processing helix chain 'F' and resid 656 through 661 removed outlier: 3.678A pdb=" N GLY F 661 " --> pdb=" O GLU F 657 " (cutoff:3.500A) Processing helix chain 'F' and resid 692 through 711 Processing helix chain 'G' and resid -14 through 0 Processing helix chain 'G' and resid 518 through 533 Processing helix chain 'G' and resid 538 through 571 removed outlier: 5.641A pdb=" N THR G 557 " --> pdb=" O PHE G 553 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU G 558 " --> pdb=" O GLY G 554 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL G 559 " --> pdb=" O SER G 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 612 through 614 No H-bonds generated for 'chain 'G' and resid 612 through 614' Processing helix chain 'G' and resid 638 through 656 Processing helix chain 'G' and resid 656 through 661 removed outlier: 3.679A pdb=" N GLY G 661 " --> pdb=" O GLU G 657 " (cutoff:3.500A) Processing helix chain 'G' and resid 692 through 711 Processing sheet with id=AA1, first strand: chain 'A' and resid 579 through 582 removed outlier: 6.746A pdb=" N GLY A 598 " --> pdb=" O GLU A 590 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N MET A 592 " --> pdb=" O SER A 596 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N SER A 596 " --> pdb=" O MET A 592 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY G 598 " --> pdb=" O GLU G 590 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N MET G 592 " --> pdb=" O SER G 596 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N SER G 596 " --> pdb=" O MET G 592 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE F 617 " --> pdb=" O ILE G 608 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY F 598 " --> pdb=" O GLU F 590 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N MET F 592 " --> pdb=" O SER F 596 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N SER F 596 " --> pdb=" O MET F 592 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY E 598 " --> pdb=" O GLU E 590 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N MET E 592 " --> pdb=" O SER E 596 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER E 596 " --> pdb=" O MET E 592 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE D 617 " --> pdb=" O ILE E 608 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY D 598 " --> pdb=" O GLU D 590 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N MET D 592 " --> pdb=" O SER D 596 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N SER D 596 " --> pdb=" O MET D 592 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 617 " --> pdb=" O ILE D 608 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY C 598 " --> pdb=" O GLU C 590 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N MET C 592 " --> pdb=" O SER C 596 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N SER C 596 " --> pdb=" O MET C 592 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 617 " --> pdb=" O ILE C 608 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY B 598 " --> pdb=" O GLU B 590 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N MET B 592 " --> pdb=" O SER B 596 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER B 596 " --> pdb=" O MET B 592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 625 through 634 removed outlier: 3.914A pdb=" N VAL A 627 " --> pdb=" O PHE A 686 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU A 675 " --> pdb=" O ALA A 679 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR A 681 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 683 " --> pdb=" O GLY A 671 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY A 671 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER A 685 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE A 669 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 625 through 634 removed outlier: 3.914A pdb=" N VAL B 627 " --> pdb=" O PHE B 686 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU B 675 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR B 681 " --> pdb=" O VAL B 673 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG B 683 " --> pdb=" O GLY B 671 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY B 671 " --> pdb=" O ARG B 683 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER B 685 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE B 669 " --> pdb=" O SER B 685 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 625 through 634 removed outlier: 3.914A pdb=" N VAL C 627 " --> pdb=" O PHE C 686 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU C 675 " --> pdb=" O ALA C 679 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR C 681 " --> pdb=" O VAL C 673 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C 683 " --> pdb=" O GLY C 671 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY C 671 " --> pdb=" O ARG C 683 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER C 685 " --> pdb=" O PHE C 669 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE C 669 " --> pdb=" O SER C 685 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 625 through 634 removed outlier: 3.914A pdb=" N VAL D 627 " --> pdb=" O PHE D 686 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU D 675 " --> pdb=" O ALA D 679 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR D 681 " --> pdb=" O VAL D 673 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG D 683 " --> pdb=" O GLY D 671 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY D 671 " --> pdb=" O ARG D 683 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER D 685 " --> pdb=" O PHE D 669 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE D 669 " --> pdb=" O SER D 685 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 625 through 634 removed outlier: 3.914A pdb=" N VAL E 627 " --> pdb=" O PHE E 686 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU E 675 " --> pdb=" O ALA E 679 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR E 681 " --> pdb=" O VAL E 673 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG E 683 " --> pdb=" O GLY E 671 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY E 671 " --> pdb=" O ARG E 683 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER E 685 " --> pdb=" O PHE E 669 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE E 669 " --> pdb=" O SER E 685 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 625 through 634 removed outlier: 3.914A pdb=" N VAL F 627 " --> pdb=" O PHE F 686 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA F 679 " --> pdb=" O LEU F 675 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU F 675 " --> pdb=" O ALA F 679 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR F 681 " --> pdb=" O VAL F 673 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG F 683 " --> pdb=" O GLY F 671 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY F 671 " --> pdb=" O ARG F 683 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N SER F 685 " --> pdb=" O PHE F 669 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE F 669 " --> pdb=" O SER F 685 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 625 through 634 removed outlier: 3.915A pdb=" N VAL G 627 " --> pdb=" O PHE G 686 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA G 679 " --> pdb=" O LEU G 675 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU G 675 " --> pdb=" O ALA G 679 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR G 681 " --> pdb=" O VAL G 673 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG G 683 " --> pdb=" O GLY G 671 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY G 671 " --> pdb=" O ARG G 683 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER G 685 " --> pdb=" O PHE G 669 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE G 669 " --> pdb=" O SER G 685 " (cutoff:3.500A) 760 hydrogen bonds defined for protein. 2208 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.42 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3838 1.34 - 1.45: 1524 1.45 - 1.57: 6251 1.57 - 1.68: 0 1.68 - 1.80: 56 Bond restraints: 11669 Sorted by residual: bond pdb=" N GLY E 625 " pdb=" CA GLY E 625 " ideal model delta sigma weight residual 1.454 1.442 0.013 9.90e-03 1.02e+04 1.60e+00 bond pdb=" N GLY D 625 " pdb=" CA GLY D 625 " ideal model delta sigma weight residual 1.454 1.442 0.012 9.90e-03 1.02e+04 1.47e+00 bond pdb=" N GLY B 625 " pdb=" CA GLY B 625 " ideal model delta sigma weight residual 1.454 1.442 0.012 9.90e-03 1.02e+04 1.44e+00 bond pdb=" N GLY C 625 " pdb=" CA GLY C 625 " ideal model delta sigma weight residual 1.454 1.442 0.012 9.90e-03 1.02e+04 1.43e+00 bond pdb=" N GLY G 625 " pdb=" CA GLY G 625 " ideal model delta sigma weight residual 1.454 1.443 0.012 9.90e-03 1.02e+04 1.42e+00 ... (remaining 11664 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.73: 245 106.73 - 113.54: 6916 113.54 - 120.35: 4066 120.35 - 127.17: 4572 127.17 - 133.98: 84 Bond angle restraints: 15883 Sorted by residual: angle pdb=" N GLY C 534 " pdb=" CA GLY C 534 " pdb=" C GLY C 534 " ideal model delta sigma weight residual 113.18 118.79 -5.61 2.37e+00 1.78e-01 5.60e+00 angle pdb=" N GLY D 534 " pdb=" CA GLY D 534 " pdb=" C GLY D 534 " ideal model delta sigma weight residual 113.18 118.78 -5.60 2.37e+00 1.78e-01 5.58e+00 angle pdb=" N GLY G 534 " pdb=" CA GLY G 534 " pdb=" C GLY G 534 " ideal model delta sigma weight residual 113.18 118.78 -5.60 2.37e+00 1.78e-01 5.57e+00 angle pdb=" N GLY B 534 " pdb=" CA GLY B 534 " pdb=" C GLY B 534 " ideal model delta sigma weight residual 113.18 118.77 -5.59 2.37e+00 1.78e-01 5.57e+00 angle pdb=" N GLY F 534 " pdb=" CA GLY F 534 " pdb=" C GLY F 534 " ideal model delta sigma weight residual 113.18 118.77 -5.59 2.37e+00 1.78e-01 5.57e+00 ... (remaining 15878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.70: 6167 11.70 - 23.39: 477 23.39 - 35.09: 125 35.09 - 46.78: 91 46.78 - 58.48: 35 Dihedral angle restraints: 6895 sinusoidal: 2471 harmonic: 4424 Sorted by residual: dihedral pdb=" CA ASP B 634 " pdb=" CB ASP B 634 " pdb=" CG ASP B 634 " pdb=" OD1 ASP B 634 " ideal model delta sinusoidal sigma weight residual -30.00 -88.48 58.48 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP A 634 " pdb=" CB ASP A 634 " pdb=" CG ASP A 634 " pdb=" OD1 ASP A 634 " ideal model delta sinusoidal sigma weight residual -30.00 -88.45 58.45 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP G 634 " pdb=" CB ASP G 634 " pdb=" CG ASP G 634 " pdb=" OD1 ASP G 634 " ideal model delta sinusoidal sigma weight residual -30.00 -88.44 58.44 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 6892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1079 0.026 - 0.052: 538 0.052 - 0.077: 180 0.077 - 0.103: 114 0.103 - 0.129: 56 Chirality restraints: 1967 Sorted by residual: chirality pdb=" CA VAL B 633 " pdb=" N VAL B 633 " pdb=" C VAL B 633 " pdb=" CB VAL B 633 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA VAL G 633 " pdb=" N VAL G 633 " pdb=" C VAL G 633 " pdb=" CB VAL G 633 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA VAL E 633 " pdb=" N VAL E 633 " pdb=" C VAL E 633 " pdb=" CB VAL E 633 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 1964 not shown) Planarity restraints: 2030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 560 " -0.004 2.00e-02 2.50e+03 7.09e-03 5.03e-01 pdb=" C LYS D 560 " 0.012 2.00e-02 2.50e+03 pdb=" O LYS D 560 " -0.005 2.00e-02 2.50e+03 pdb=" N ASP D 561 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 560 " 0.004 2.00e-02 2.50e+03 7.07e-03 5.00e-01 pdb=" C LYS C 560 " -0.012 2.00e-02 2.50e+03 pdb=" O LYS C 560 " 0.005 2.00e-02 2.50e+03 pdb=" N ASP C 561 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 560 " 0.003 2.00e-02 2.50e+03 6.98e-03 4.88e-01 pdb=" C LYS B 560 " -0.012 2.00e-02 2.50e+03 pdb=" O LYS B 560 " 0.005 2.00e-02 2.50e+03 pdb=" N ASP B 561 " 0.004 2.00e-02 2.50e+03 ... (remaining 2027 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2121 2.76 - 3.30: 11725 3.30 - 3.83: 18486 3.83 - 4.37: 20340 4.37 - 4.90: 37249 Nonbonded interactions: 89921 Sorted by model distance: nonbonded pdb=" OD1 ASP C 561 " pdb=" N SER C 612 " model vdw 2.225 2.520 nonbonded pdb=" OD1 ASP B 561 " pdb=" N SER B 612 " model vdw 2.226 2.520 nonbonded pdb=" OD1 ASP E 561 " pdb=" N SER E 612 " model vdw 2.226 2.520 nonbonded pdb=" OD1 ASP D 561 " pdb=" N SER D 612 " model vdw 2.226 2.520 nonbonded pdb=" OD1 ASP A 561 " pdb=" N SER A 612 " model vdw 2.227 2.520 ... (remaining 89916 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.830 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: 3.820 Check model and map are aligned: 0.160 Set scattering table: 0.080 Process input model: 33.560 Find NCS groups from input model: 0.790 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:11.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 11669 Z= 0.429 Angle : 0.610 5.606 15883 Z= 0.350 Chirality : 0.041 0.129 1967 Planarity : 0.002 0.017 2030 Dihedral : 12.011 58.478 4039 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.95 % Allowed : 5.36 % Favored : 88.69 % 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: -1.57 (0.21), residues: 1435 helix: -0.51 (0.19), residues: 616 sheet: -1.31 (0.31), residues: 273 loop : -1.30 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 694 HIS 0.004 0.001 HIS A 707 PHE 0.008 0.001 PHE G 680 TYR 0.009 0.001 TYR B 606 ARG 0.002 0.000 ARG A 714 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 496 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: A 572 ASN cc_start: 0.8870 (t0) cc_final: 0.8661 (t0) REVERT: A 612 SER cc_start: 0.9502 (p) cc_final: 0.9234 (m) REVERT: A 638 ASP cc_start: 0.8392 (t0) cc_final: 0.7982 (t0) REVERT: A 644 GLN cc_start: 0.7838 (tp-100) cc_final: 0.7632 (tp40) REVERT: A 652 GLU cc_start: 0.8865 (tt0) cc_final: 0.8557 (tt0) REVERT: A 656 ASN cc_start: 0.8701 (t0) cc_final: 0.8073 (t0) REVERT: A 659 ILE cc_start: 0.8992 (mm) cc_final: 0.8740 (mp) REVERT: A 660 ARG cc_start: 0.8871 (tpt90) cc_final: 0.8527 (tpt170) REVERT: A 676 SER cc_start: 0.8478 (m) cc_final: 0.8008 (p) REVERT: A 681 THR cc_start: 0.8567 (m) cc_final: 0.8281 (p) REVERT: A 685 SER cc_start: 0.8892 (m) cc_final: 0.8349 (p) REVERT: B 527 MET cc_start: 0.9311 (mtt) cc_final: 0.9107 (mtt) REVERT: B 572 ASN cc_start: 0.8939 (t0) cc_final: 0.8721 (t0) REVERT: B 590 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8221 (mt-10) REVERT: B 602 ASP cc_start: 0.8913 (p0) cc_final: 0.8658 (p0) REVERT: B 612 SER cc_start: 0.9526 (p) cc_final: 0.9316 (m) REVERT: B 637 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8231 (mm-30) REVERT: B 638 ASP cc_start: 0.8459 (t0) cc_final: 0.8078 (t0) REVERT: B 641 LYS cc_start: 0.8781 (tttt) cc_final: 0.8559 (tttm) REVERT: B 652 GLU cc_start: 0.8712 (tt0) cc_final: 0.8411 (tt0) REVERT: B 656 ASN cc_start: 0.8247 (t0) cc_final: 0.7922 (t0) REVERT: B 659 ILE cc_start: 0.8880 (mm) cc_final: 0.8551 (mp) REVERT: B 666 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8921 (mm-30) REVERT: B 668 ASN cc_start: 0.8528 (t0) cc_final: 0.8105 (t0) REVERT: B 676 SER cc_start: 0.8970 (m) cc_final: 0.8475 (p) REVERT: B 685 SER cc_start: 0.8779 (m) cc_final: 0.8358 (p) REVERT: C 638 ASP cc_start: 0.8413 (t0) cc_final: 0.7970 (t0) REVERT: C 668 ASN cc_start: 0.8471 (t0) cc_final: 0.8267 (t0) REVERT: C 676 SER cc_start: 0.9077 (m) cc_final: 0.8596 (p) REVERT: C 681 THR cc_start: 0.8801 (m) cc_final: 0.8584 (p) REVERT: C 685 SER cc_start: 0.9051 (m) cc_final: 0.8642 (p) REVERT: D 612 SER cc_start: 0.9499 (p) cc_final: 0.9145 (m) REVERT: D 637 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8401 (mm-30) REVERT: D 638 ASP cc_start: 0.8398 (t0) cc_final: 0.8059 (t0) REVERT: D 641 LYS cc_start: 0.8905 (tttt) cc_final: 0.8660 (ttpp) REVERT: D 648 ASP cc_start: 0.8831 (m-30) cc_final: 0.8583 (m-30) REVERT: D 668 ASN cc_start: 0.8763 (t0) cc_final: 0.8375 (t0) REVERT: D 676 SER cc_start: 0.9150 (m) cc_final: 0.8800 (p) REVERT: D 693 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8211 (mp10) REVERT: D 703 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8391 (mm110) REVERT: E 612 SER cc_start: 0.9594 (p) cc_final: 0.9229 (m) REVERT: E 613 SER cc_start: 0.9545 (m) cc_final: 0.9181 (p) REVERT: E 626 SER cc_start: 0.9289 (m) cc_final: 0.8967 (p) REVERT: E 638 ASP cc_start: 0.8456 (t0) cc_final: 0.7908 (t0) REVERT: E 648 ASP cc_start: 0.8834 (m-30) cc_final: 0.8505 (m-30) REVERT: E 660 ARG cc_start: 0.8838 (tpt90) cc_final: 0.8548 (tpt170) REVERT: E 664 ILE cc_start: 0.9546 (mm) cc_final: 0.9346 (OUTLIER) REVERT: E 666 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8889 (tp30) REVERT: E 668 ASN cc_start: 0.8689 (t0) cc_final: 0.8011 (t0) REVERT: E 676 SER cc_start: 0.8834 (m) cc_final: 0.8380 (p) REVERT: E 681 THR cc_start: 0.8621 (m) cc_final: 0.8385 (p) REVERT: E 685 SER cc_start: 0.9108 (m) cc_final: 0.8693 (p) REVERT: E 720 TYR cc_start: 0.7415 (m-10) cc_final: 0.7135 (m-10) REVERT: F 572 ASN cc_start: 0.9065 (t0) cc_final: 0.8855 (t0) REVERT: F 612 SER cc_start: 0.9550 (p) cc_final: 0.9286 (m) REVERT: F 638 ASP cc_start: 0.8478 (t0) cc_final: 0.8026 (t0) REVERT: F 656 ASN cc_start: 0.8112 (t0) cc_final: 0.7836 (t0) REVERT: F 659 ILE cc_start: 0.9010 (mm) cc_final: 0.8808 (mp) REVERT: F 668 ASN cc_start: 0.8595 (t0) cc_final: 0.8253 (t0) REVERT: F 676 SER cc_start: 0.8949 (m) cc_final: 0.8431 (p) REVERT: G 567 PHE cc_start: 0.9102 (m-10) cc_final: 0.8881 (m-10) REVERT: G 571 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8262 (mt-10) REVERT: G 572 ASN cc_start: 0.9086 (t0) cc_final: 0.8822 (t0) REVERT: G 660 ARG cc_start: 0.8835 (tpt90) cc_final: 0.8537 (tpt170) REVERT: G 668 ASN cc_start: 0.8855 (t0) cc_final: 0.8218 (t0) REVERT: G 676 SER cc_start: 0.8929 (m) cc_final: 0.8499 (p) REVERT: G 685 SER cc_start: 0.9093 (m) cc_final: 0.8632 (p) REVERT: G 693 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8604 (mp10) outliers start: 70 outliers final: 35 residues processed: 544 average time/residue: 0.9806 time to fit residues: 584.0153 Evaluate side-chains 434 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 398 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 570 PHE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain E residue 526 ILE Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 568 ILE Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 570 PHE Chi-restraints excluded: chain F residue 578 ASP Chi-restraints excluded: chain F residue 616 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain G residue 526 ILE Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 570 PHE Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 693 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 chunk 139 optimal weight: 0.9990 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 703 GLN B 569 GLN C 569 GLN D 569 GLN E 569 GLN ** E 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 630 ASN F 569 GLN F 643 ASN F 644 GLN G 601 GLN G 630 ASN ** G 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11669 Z= 0.197 Angle : 0.580 8.452 15883 Z= 0.292 Chirality : 0.042 0.198 1967 Planarity : 0.003 0.028 2030 Dihedral : 6.213 41.699 1686 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.36 % Allowed : 20.24 % Favored : 74.40 % 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: 0.63 (0.22), residues: 1435 helix: 1.56 (0.19), residues: 644 sheet: -0.55 (0.31), residues: 273 loop : -0.36 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 694 HIS 0.003 0.001 HIS C 607 PHE 0.008 0.001 PHE E 680 TYR 0.011 0.001 TYR E 606 ARG 0.005 0.001 ARG B 622 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 441 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 ASN cc_start: 0.9073 (t0) cc_final: 0.8549 (t0) REVERT: A 612 SER cc_start: 0.9515 (p) cc_final: 0.9226 (m) REVERT: A 622 ARG cc_start: 0.8508 (mmt-90) cc_final: 0.8185 (mmp80) REVERT: A 647 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8143 (mttm) REVERT: A 656 ASN cc_start: 0.8130 (t0) cc_final: 0.7883 (t0) REVERT: A 668 ASN cc_start: 0.8952 (t0) cc_final: 0.8303 (t0) REVERT: A 676 SER cc_start: 0.8492 (m) cc_final: 0.7987 (p) REVERT: A 681 THR cc_start: 0.8679 (m) cc_final: 0.8299 (p) REVERT: A 685 SER cc_start: 0.8989 (m) cc_final: 0.8483 (p) REVERT: B 572 ASN cc_start: 0.9210 (t0) cc_final: 0.8830 (t0) REVERT: B 590 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8254 (mt-10) REVERT: B 612 SER cc_start: 0.9554 (p) cc_final: 0.9346 (m) REVERT: B 613 SER cc_start: 0.9543 (m) cc_final: 0.9269 (p) REVERT: B 626 SER cc_start: 0.9379 (m) cc_final: 0.8943 (p) REVERT: B 654 MET cc_start: 0.9006 (mmm) cc_final: 0.8801 (mmm) REVERT: B 660 ARG cc_start: 0.8812 (tpp-160) cc_final: 0.8388 (tpm170) REVERT: B 668 ASN cc_start: 0.8682 (t0) cc_final: 0.8235 (t0) REVERT: B 676 SER cc_start: 0.8959 (m) cc_final: 0.8394 (p) REVERT: B 685 SER cc_start: 0.8850 (m) cc_final: 0.8526 (p) REVERT: C 572 ASN cc_start: 0.9213 (t0) cc_final: 0.8649 (t0) REVERT: C 596 SER cc_start: 0.9363 (p) cc_final: 0.8459 (p) REVERT: C 626 SER cc_start: 0.9306 (m) cc_final: 0.8732 (p) REVERT: C 655 GLU cc_start: 0.8910 (tp30) cc_final: 0.8601 (tp30) REVERT: C 676 SER cc_start: 0.8937 (m) cc_final: 0.8459 (p) REVERT: C 681 THR cc_start: 0.8675 (m) cc_final: 0.8430 (p) REVERT: C 685 SER cc_start: 0.9008 (m) cc_final: 0.8623 (p) REVERT: D 572 ASN cc_start: 0.9331 (t0) cc_final: 0.9081 (t0) REVERT: D 602 ASP cc_start: 0.8906 (p0) cc_final: 0.8619 (p0) REVERT: D 612 SER cc_start: 0.9499 (p) cc_final: 0.9179 (m) REVERT: D 626 SER cc_start: 0.9205 (m) cc_final: 0.8801 (p) REVERT: D 648 ASP cc_start: 0.8831 (m-30) cc_final: 0.8556 (m-30) REVERT: D 652 GLU cc_start: 0.9036 (tt0) cc_final: 0.8475 (tt0) REVERT: D 655 GLU cc_start: 0.9035 (tp30) cc_final: 0.8656 (tp30) REVERT: D 660 ARG cc_start: 0.9037 (tpp-160) cc_final: 0.8811 (tpm170) REVERT: D 666 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8934 (mm-30) REVERT: D 668 ASN cc_start: 0.8850 (t0) cc_final: 0.8448 (t0) REVERT: D 676 SER cc_start: 0.9092 (m) cc_final: 0.8628 (p) REVERT: E 574 MET cc_start: 0.9154 (ttm) cc_final: 0.8879 (mtt) REVERT: E 575 ASN cc_start: 0.8356 (m-40) cc_final: 0.7871 (m-40) REVERT: E 578 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7947 (m-30) REVERT: E 612 SER cc_start: 0.9569 (p) cc_final: 0.9280 (m) REVERT: E 613 SER cc_start: 0.9479 (m) cc_final: 0.9157 (p) REVERT: E 626 SER cc_start: 0.9229 (m) cc_final: 0.8694 (p) REVERT: E 648 ASP cc_start: 0.8795 (m-30) cc_final: 0.8411 (m-30) REVERT: E 652 GLU cc_start: 0.8879 (tt0) cc_final: 0.8475 (tt0) REVERT: E 655 GLU cc_start: 0.8993 (tp30) cc_final: 0.8651 (tp30) REVERT: E 660 ARG cc_start: 0.8935 (tpt90) cc_final: 0.8580 (tpt170) REVERT: E 666 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8894 (tp30) REVERT: E 668 ASN cc_start: 0.8763 (t0) cc_final: 0.8055 (t0) REVERT: E 676 SER cc_start: 0.8805 (m) cc_final: 0.8352 (p) REVERT: E 681 THR cc_start: 0.8625 (m) cc_final: 0.8351 (p) REVERT: E 685 SER cc_start: 0.9089 (m) cc_final: 0.8758 (p) REVERT: E 720 TYR cc_start: 0.7470 (m-10) cc_final: 0.7188 (m-10) REVERT: F 572 ASN cc_start: 0.9334 (t0) cc_final: 0.8869 (t0) REVERT: F 612 SER cc_start: 0.9556 (p) cc_final: 0.9299 (m) REVERT: F 624 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8784 (pp) REVERT: F 626 SER cc_start: 0.9199 (m) cc_final: 0.8748 (p) REVERT: F 655 GLU cc_start: 0.8916 (tp30) cc_final: 0.8581 (tp30) REVERT: F 660 ARG cc_start: 0.9017 (tpp-160) cc_final: 0.8780 (tpm170) REVERT: F 668 ASN cc_start: 0.8673 (t0) cc_final: 0.8088 (t0) REVERT: F 676 SER cc_start: 0.8916 (m) cc_final: 0.8406 (p) REVERT: F 685 SER cc_start: 0.8990 (m) cc_final: 0.8688 (p) REVERT: F 703 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8595 (tp40) REVERT: F 723 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7938 (tt) REVERT: G 572 ASN cc_start: 0.9233 (t0) cc_final: 0.8839 (t0) REVERT: G 578 ASP cc_start: 0.8303 (m-30) cc_final: 0.8069 (m-30) REVERT: G 612 SER cc_start: 0.9607 (p) cc_final: 0.9249 (m) REVERT: G 622 ARG cc_start: 0.8321 (mmp80) cc_final: 0.8046 (mmt-90) REVERT: G 626 SER cc_start: 0.9236 (m) cc_final: 0.8764 (p) REVERT: G 655 GLU cc_start: 0.8996 (tp30) cc_final: 0.8669 (tp30) REVERT: G 660 ARG cc_start: 0.8762 (tpt90) cc_final: 0.8474 (tpt170) REVERT: G 668 ASN cc_start: 0.8919 (t0) cc_final: 0.8312 (t0) REVERT: G 676 SER cc_start: 0.8882 (m) cc_final: 0.8455 (p) REVERT: G 685 SER cc_start: 0.9115 (m) cc_final: 0.8701 (p) REVERT: G 713 VAL cc_start: 0.9537 (t) cc_final: 0.9202 (p) outliers start: 63 outliers final: 37 residues processed: 468 average time/residue: 1.0733 time to fit residues: 549.9318 Evaluate side-chains 441 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 399 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 570 PHE Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 702 SER Chi-restraints excluded: chain E residue 704 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 570 PHE Chi-restraints excluded: chain F residue 614 ILE Chi-restraints excluded: chain F residue 624 ILE Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain F residue 704 VAL Chi-restraints excluded: chain F residue 723 LEU Chi-restraints excluded: chain G residue 537 ILE Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 586 THR Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 723 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 47 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 ASN A 693 GLN B 703 GLN C 668 ASN D 536 ASN D 575 ASN D 630 ASN E 536 ASN E 601 GLN E 630 ASN G 630 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11669 Z= 0.278 Angle : 0.582 8.766 15883 Z= 0.293 Chirality : 0.042 0.187 1967 Planarity : 0.003 0.026 2030 Dihedral : 4.864 37.136 1655 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.10 % Allowed : 23.21 % Favored : 71.68 % 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: 1.38 (0.22), residues: 1435 helix: 2.25 (0.19), residues: 644 sheet: -0.27 (0.30), residues: 273 loop : -0.05 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 694 HIS 0.003 0.001 HIS C 707 PHE 0.010 0.001 PHE G 680 TYR 0.013 0.001 TYR E 606 ARG 0.006 0.001 ARG D 591 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 420 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 ASN cc_start: 0.9108 (t0) cc_final: 0.8903 (t0) REVERT: A 612 SER cc_start: 0.9458 (p) cc_final: 0.9126 (m) REVERT: A 638 ASP cc_start: 0.8100 (t0) cc_final: 0.7646 (t0) REVERT: A 647 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8079 (mttm) REVERT: A 648 ASP cc_start: 0.8938 (m-30) cc_final: 0.8687 (m-30) REVERT: A 652 GLU cc_start: 0.8918 (tt0) cc_final: 0.8366 (tt0) REVERT: A 668 ASN cc_start: 0.8898 (t0) cc_final: 0.8237 (t0) REVERT: A 676 SER cc_start: 0.8495 (m) cc_final: 0.7985 (p) REVERT: A 681 THR cc_start: 0.8621 (m) cc_final: 0.8278 (p) REVERT: A 685 SER cc_start: 0.8994 (m) cc_final: 0.8469 (p) REVERT: B 572 ASN cc_start: 0.9192 (t0) cc_final: 0.8727 (t0) REVERT: B 590 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8226 (mt-10) REVERT: B 612 SER cc_start: 0.9564 (p) cc_final: 0.9316 (m) REVERT: B 613 SER cc_start: 0.9594 (m) cc_final: 0.9300 (p) REVERT: B 626 SER cc_start: 0.9334 (m) cc_final: 0.8896 (p) REVERT: B 638 ASP cc_start: 0.8132 (t0) cc_final: 0.7404 (t0) REVERT: B 641 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8440 (ttpp) REVERT: B 652 GLU cc_start: 0.8881 (tt0) cc_final: 0.8431 (tt0) REVERT: B 660 ARG cc_start: 0.8800 (tpp-160) cc_final: 0.8458 (tpm170) REVERT: B 668 ASN cc_start: 0.8755 (t0) cc_final: 0.8309 (t0) REVERT: B 676 SER cc_start: 0.8837 (m) cc_final: 0.8264 (p) REVERT: B 685 SER cc_start: 0.8867 (m) cc_final: 0.8524 (p) REVERT: C 572 ASN cc_start: 0.9138 (t0) cc_final: 0.8645 (t0) REVERT: C 626 SER cc_start: 0.9298 (m) cc_final: 0.8773 (p) REVERT: C 655 GLU cc_start: 0.8916 (tp30) cc_final: 0.8619 (tp30) REVERT: C 660 ARG cc_start: 0.8646 (tpt90) cc_final: 0.8353 (tpt170) REVERT: C 676 SER cc_start: 0.8847 (m) cc_final: 0.8405 (p) REVERT: C 681 THR cc_start: 0.8698 (m) cc_final: 0.8414 (p) REVERT: C 685 SER cc_start: 0.9091 (m) cc_final: 0.8653 (p) REVERT: D 560 LYS cc_start: 0.8598 (tttt) cc_final: 0.8310 (ptpt) REVERT: D 570 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8681 (m-80) REVERT: D 572 ASN cc_start: 0.9271 (t0) cc_final: 0.8970 (t0) REVERT: D 602 ASP cc_start: 0.8856 (p0) cc_final: 0.8597 (p0) REVERT: D 612 SER cc_start: 0.9477 (p) cc_final: 0.9150 (m) REVERT: D 626 SER cc_start: 0.9180 (m) cc_final: 0.8851 (p) REVERT: D 655 GLU cc_start: 0.9069 (tp30) cc_final: 0.8662 (tp30) REVERT: D 660 ARG cc_start: 0.8996 (tpp-160) cc_final: 0.8753 (tpm170) REVERT: D 666 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8958 (mm-30) REVERT: D 668 ASN cc_start: 0.8832 (t0) cc_final: 0.8431 (t0) REVERT: D 676 SER cc_start: 0.9034 (m) cc_final: 0.8568 (p) REVERT: D 693 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8227 (pm20) REVERT: D 723 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7435 (tt) REVERT: E 575 ASN cc_start: 0.8274 (m-40) cc_final: 0.7779 (m-40) REVERT: E 578 ASP cc_start: 0.8154 (m-30) cc_final: 0.7825 (m-30) REVERT: E 612 SER cc_start: 0.9569 (p) cc_final: 0.9257 (m) REVERT: E 613 SER cc_start: 0.9506 (m) cc_final: 0.9216 (p) REVERT: E 626 SER cc_start: 0.9261 (m) cc_final: 0.8647 (p) REVERT: E 648 ASP cc_start: 0.8875 (m-30) cc_final: 0.8543 (m-30) REVERT: E 652 GLU cc_start: 0.8868 (tt0) cc_final: 0.8476 (tt0) REVERT: E 655 GLU cc_start: 0.9002 (tp30) cc_final: 0.8622 (tp30) REVERT: E 660 ARG cc_start: 0.8946 (tpt90) cc_final: 0.8500 (tpt170) REVERT: E 666 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8952 (tp30) REVERT: E 668 ASN cc_start: 0.8783 (t0) cc_final: 0.8299 (t0) REVERT: E 676 SER cc_start: 0.8787 (m) cc_final: 0.8326 (p) REVERT: E 681 THR cc_start: 0.8706 (m) cc_final: 0.8382 (p) REVERT: E 685 SER cc_start: 0.9075 (m) cc_final: 0.8762 (p) REVERT: E 720 TYR cc_start: 0.7529 (m-10) cc_final: 0.7208 (m-10) REVERT: F 572 ASN cc_start: 0.9310 (t0) cc_final: 0.8869 (t0) REVERT: F 612 SER cc_start: 0.9549 (p) cc_final: 0.9262 (m) REVERT: F 626 SER cc_start: 0.9233 (m) cc_final: 0.8775 (p) REVERT: F 655 GLU cc_start: 0.8912 (tp30) cc_final: 0.8702 (tp30) REVERT: F 660 ARG cc_start: 0.8960 (tpp-160) cc_final: 0.8726 (tpm170) REVERT: F 668 ASN cc_start: 0.8709 (t0) cc_final: 0.8384 (t0) REVERT: F 676 SER cc_start: 0.8889 (m) cc_final: 0.8349 (p) REVERT: F 703 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8464 (mm-40) REVERT: G 572 ASN cc_start: 0.9150 (t0) cc_final: 0.8763 (t0) REVERT: G 612 SER cc_start: 0.9623 (p) cc_final: 0.9292 (m) REVERT: G 626 SER cc_start: 0.9266 (m) cc_final: 0.8809 (p) REVERT: G 652 GLU cc_start: 0.8880 (tt0) cc_final: 0.8611 (tt0) REVERT: G 655 GLU cc_start: 0.9011 (tp30) cc_final: 0.8686 (tp30) REVERT: G 660 ARG cc_start: 0.8771 (tpt90) cc_final: 0.8424 (tpt170) REVERT: G 668 ASN cc_start: 0.8897 (t0) cc_final: 0.8314 (t0) REVERT: G 676 SER cc_start: 0.8855 (m) cc_final: 0.8417 (p) REVERT: G 685 SER cc_start: 0.9089 (m) cc_final: 0.8664 (p) REVERT: G 693 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8443 (pm20) REVERT: G 713 VAL cc_start: 0.9607 (t) cc_final: 0.9238 (p) outliers start: 60 outliers final: 40 residues processed: 453 average time/residue: 1.0613 time to fit residues: 523.3527 Evaluate side-chains 458 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 412 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 570 PHE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 614 ILE Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 570 PHE Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 593 SER Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 570 PHE Chi-restraints excluded: chain F residue 593 SER Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 537 ILE Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 586 THR Chi-restraints excluded: chain G residue 593 SER Chi-restraints excluded: chain G residue 693 GLN Chi-restraints excluded: chain G residue 723 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 66 optimal weight: 30.0000 chunk 94 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 133 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 GLN B 703 GLN C 575 ASN D 536 ASN D 575 ASN E 536 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11669 Z= 0.209 Angle : 0.565 8.865 15883 Z= 0.280 Chirality : 0.041 0.173 1967 Planarity : 0.003 0.028 2030 Dihedral : 4.310 36.425 1644 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.59 % Allowed : 25.34 % Favored : 70.07 % 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: 1.79 (0.23), residues: 1435 helix: 2.57 (0.19), residues: 644 sheet: -0.04 (0.30), residues: 273 loop : 0.17 (0.30), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 694 HIS 0.003 0.001 HIS G 707 PHE 0.009 0.001 PHE G 680 TYR 0.011 0.001 TYR F 720 ARG 0.006 0.001 ARG D 591 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 432 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 ASN cc_start: 0.9149 (t0) cc_final: 0.8922 (t0) REVERT: A 612 SER cc_start: 0.9448 (p) cc_final: 0.9115 (m) REVERT: A 647 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8060 (mttm) REVERT: A 648 ASP cc_start: 0.8924 (m-30) cc_final: 0.8672 (m-30) REVERT: A 652 GLU cc_start: 0.8920 (tt0) cc_final: 0.8274 (tt0) REVERT: A 655 GLU cc_start: 0.8996 (tp30) cc_final: 0.8647 (tp30) REVERT: A 660 ARG cc_start: 0.8820 (tpt90) cc_final: 0.8438 (tpt170) REVERT: A 668 ASN cc_start: 0.8869 (t0) cc_final: 0.8190 (t0) REVERT: A 676 SER cc_start: 0.8485 (m) cc_final: 0.7969 (p) REVERT: A 681 THR cc_start: 0.8613 (m) cc_final: 0.8264 (p) REVERT: A 685 SER cc_start: 0.8967 (m) cc_final: 0.8455 (p) REVERT: A 703 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8380 (tp40) REVERT: B 572 ASN cc_start: 0.9065 (t0) cc_final: 0.8821 (t0) REVERT: B 590 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8180 (mt-10) REVERT: B 612 SER cc_start: 0.9569 (p) cc_final: 0.9316 (m) REVERT: B 613 SER cc_start: 0.9571 (m) cc_final: 0.9283 (p) REVERT: B 626 SER cc_start: 0.9316 (m) cc_final: 0.8908 (p) REVERT: B 652 GLU cc_start: 0.8836 (tt0) cc_final: 0.8398 (tt0) REVERT: B 654 MET cc_start: 0.9016 (mmm) cc_final: 0.8690 (mmm) REVERT: B 660 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8390 (tpp-160) REVERT: B 668 ASN cc_start: 0.8771 (t0) cc_final: 0.8332 (t0) REVERT: B 676 SER cc_start: 0.8897 (m) cc_final: 0.8362 (p) REVERT: B 685 SER cc_start: 0.8876 (m) cc_final: 0.8533 (p) REVERT: C 572 ASN cc_start: 0.9169 (t0) cc_final: 0.8625 (t0) REVERT: C 624 ILE cc_start: 0.8924 (pt) cc_final: 0.8695 (pp) REVERT: C 626 SER cc_start: 0.9228 (m) cc_final: 0.8637 (p) REVERT: C 655 GLU cc_start: 0.8908 (tp30) cc_final: 0.8628 (tp30) REVERT: C 676 SER cc_start: 0.8792 (m) cc_final: 0.8521 (t) REVERT: C 685 SER cc_start: 0.9078 (m) cc_final: 0.8612 (p) REVERT: D 560 LYS cc_start: 0.8548 (tttt) cc_final: 0.8236 (pttt) REVERT: D 570 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8602 (m-80) REVERT: D 572 ASN cc_start: 0.9260 (t0) cc_final: 0.8862 (t0) REVERT: D 612 SER cc_start: 0.9463 (p) cc_final: 0.9136 (m) REVERT: D 622 ARG cc_start: 0.8471 (mmp80) cc_final: 0.8138 (mmt-90) REVERT: D 626 SER cc_start: 0.9162 (m) cc_final: 0.8807 (p) REVERT: D 655 GLU cc_start: 0.9058 (tp30) cc_final: 0.8738 (tp30) REVERT: D 658 GLU cc_start: 0.9092 (tp30) cc_final: 0.8844 (tp30) REVERT: D 660 ARG cc_start: 0.8968 (tpp-160) cc_final: 0.8756 (tpm170) REVERT: D 666 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8926 (mm-30) REVERT: D 668 ASN cc_start: 0.8843 (t0) cc_final: 0.8461 (t0) REVERT: D 676 SER cc_start: 0.8989 (m) cc_final: 0.8525 (p) REVERT: D 693 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8205 (pm20) REVERT: D 723 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7417 (tt) REVERT: E 574 MET cc_start: 0.9213 (mtp) cc_final: 0.8985 (mtt) REVERT: E 575 ASN cc_start: 0.8179 (m-40) cc_final: 0.7683 (m-40) REVERT: E 578 ASP cc_start: 0.8087 (m-30) cc_final: 0.7767 (m-30) REVERT: E 612 SER cc_start: 0.9607 (p) cc_final: 0.9269 (m) REVERT: E 626 SER cc_start: 0.9198 (m) cc_final: 0.8504 (p) REVERT: E 648 ASP cc_start: 0.8897 (m-30) cc_final: 0.8581 (m-30) REVERT: E 652 GLU cc_start: 0.8845 (tt0) cc_final: 0.8474 (tt0) REVERT: E 655 GLU cc_start: 0.8968 (tp30) cc_final: 0.8569 (tp30) REVERT: E 660 ARG cc_start: 0.8938 (tpt90) cc_final: 0.8638 (tpp-160) REVERT: E 666 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8910 (tp30) REVERT: E 668 ASN cc_start: 0.8764 (t0) cc_final: 0.8238 (t0) REVERT: E 676 SER cc_start: 0.8759 (m) cc_final: 0.8305 (p) REVERT: E 681 THR cc_start: 0.8713 (m) cc_final: 0.8383 (p) REVERT: E 685 SER cc_start: 0.9077 (m) cc_final: 0.8748 (p) REVERT: E 703 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8407 (mm110) REVERT: E 720 TYR cc_start: 0.7537 (m-10) cc_final: 0.7183 (m-10) REVERT: F 572 ASN cc_start: 0.9292 (t0) cc_final: 0.8869 (t0) REVERT: F 612 SER cc_start: 0.9567 (p) cc_final: 0.9267 (m) REVERT: F 626 SER cc_start: 0.9188 (m) cc_final: 0.8725 (p) REVERT: F 655 GLU cc_start: 0.8936 (tp30) cc_final: 0.8716 (tp30) REVERT: F 658 GLU cc_start: 0.9167 (tp30) cc_final: 0.8936 (tp30) REVERT: F 668 ASN cc_start: 0.8713 (t0) cc_final: 0.8383 (t0) REVERT: F 676 SER cc_start: 0.8872 (m) cc_final: 0.8331 (p) REVERT: G 572 ASN cc_start: 0.9086 (t0) cc_final: 0.8802 (t0) REVERT: G 612 SER cc_start: 0.9533 (p) cc_final: 0.9037 (m) REVERT: G 626 SER cc_start: 0.9334 (m) cc_final: 0.8817 (p) REVERT: G 652 GLU cc_start: 0.8867 (tt0) cc_final: 0.8569 (tt0) REVERT: G 655 GLU cc_start: 0.8973 (tp30) cc_final: 0.8721 (tp30) REVERT: G 660 ARG cc_start: 0.8797 (tpt90) cc_final: 0.8369 (tpt170) REVERT: G 668 ASN cc_start: 0.8885 (t0) cc_final: 0.8309 (t0) REVERT: G 676 SER cc_start: 0.8782 (m) cc_final: 0.8326 (p) REVERT: G 685 SER cc_start: 0.9033 (m) cc_final: 0.8626 (p) REVERT: G 693 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8428 (pm20) REVERT: G 713 VAL cc_start: 0.9588 (t) cc_final: 0.9237 (p) outliers start: 54 outliers final: 32 residues processed: 453 average time/residue: 1.0941 time to fit residues: 538.1344 Evaluate side-chains 458 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 419 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 660 ARG Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain D residue 570 PHE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 614 ILE Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 570 PHE Chi-restraints excluded: chain E residue 593 SER Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 570 PHE Chi-restraints excluded: chain F residue 593 SER Chi-restraints excluded: chain G residue 586 THR Chi-restraints excluded: chain G residue 593 SER Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 693 GLN Chi-restraints excluded: chain G residue 723 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 30.0000 chunk 61 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 76 optimal weight: 0.9990 chunk 133 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 ASN B 703 GLN C 668 ASN C 693 GLN D 536 ASN D 575 ASN D 630 ASN E 536 ASN G 703 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11669 Z= 0.232 Angle : 0.579 8.670 15883 Z= 0.287 Chirality : 0.042 0.173 1967 Planarity : 0.003 0.030 2030 Dihedral : 4.021 36.630 1635 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.19 % Allowed : 25.94 % Favored : 68.88 % 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: 1.95 (0.23), residues: 1435 helix: 2.65 (0.19), residues: 644 sheet: 0.08 (0.30), residues: 273 loop : 0.31 (0.30), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 694 HIS 0.003 0.001 HIS B 607 PHE 0.012 0.001 PHE A 567 TYR 0.014 0.001 TYR F 720 ARG 0.007 0.001 ARG B 697 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 424 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 LYS cc_start: 0.8543 (tttt) cc_final: 0.8067 (pttt) REVERT: A 572 ASN cc_start: 0.9176 (t0) cc_final: 0.8875 (t0) REVERT: A 612 SER cc_start: 0.9428 (p) cc_final: 0.9121 (m) REVERT: A 622 ARG cc_start: 0.8651 (mmp80) cc_final: 0.8232 (mmp80) REVERT: A 648 ASP cc_start: 0.8889 (m-30) cc_final: 0.8660 (m-30) REVERT: A 652 GLU cc_start: 0.8893 (tt0) cc_final: 0.8236 (tt0) REVERT: A 655 GLU cc_start: 0.9005 (tp30) cc_final: 0.8661 (tp30) REVERT: A 660 ARG cc_start: 0.8810 (tpt90) cc_final: 0.8507 (tpt170) REVERT: A 664 ILE cc_start: 0.9310 (tp) cc_final: 0.9082 (pp) REVERT: A 668 ASN cc_start: 0.8798 (t0) cc_final: 0.8128 (t0) REVERT: A 676 SER cc_start: 0.8499 (m) cc_final: 0.7977 (p) REVERT: A 685 SER cc_start: 0.8970 (m) cc_final: 0.8443 (p) REVERT: A 703 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8420 (tp40) REVERT: B 572 ASN cc_start: 0.9093 (t0) cc_final: 0.8703 (t0) REVERT: B 590 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8137 (mt-10) REVERT: B 613 SER cc_start: 0.9575 (m) cc_final: 0.9337 (p) REVERT: B 626 SER cc_start: 0.9293 (m) cc_final: 0.8877 (p) REVERT: B 652 GLU cc_start: 0.8821 (tt0) cc_final: 0.8442 (tt0) REVERT: B 654 MET cc_start: 0.8940 (mmm) cc_final: 0.8607 (mmm) REVERT: B 660 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8392 (tpp-160) REVERT: B 668 ASN cc_start: 0.8802 (t0) cc_final: 0.8371 (t0) REVERT: B 676 SER cc_start: 0.8850 (m) cc_final: 0.8311 (p) REVERT: B 685 SER cc_start: 0.8902 (m) cc_final: 0.8528 (p) REVERT: C 572 ASN cc_start: 0.9170 (t0) cc_final: 0.8696 (t0) REVERT: C 626 SER cc_start: 0.9186 (m) cc_final: 0.8705 (p) REVERT: C 655 GLU cc_start: 0.8910 (tp30) cc_final: 0.8699 (tp30) REVERT: C 676 SER cc_start: 0.8763 (m) cc_final: 0.8485 (t) REVERT: C 685 SER cc_start: 0.9116 (m) cc_final: 0.8655 (p) REVERT: D 560 LYS cc_start: 0.8569 (tttt) cc_final: 0.8251 (pttt) REVERT: D 570 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8543 (m-80) REVERT: D 572 ASN cc_start: 0.9244 (t0) cc_final: 0.8947 (t0) REVERT: D 612 SER cc_start: 0.9390 (p) cc_final: 0.9065 (m) REVERT: D 626 SER cc_start: 0.9160 (m) cc_final: 0.8771 (p) REVERT: D 655 GLU cc_start: 0.9060 (tp30) cc_final: 0.8748 (tp30) REVERT: D 660 ARG cc_start: 0.8930 (tpp-160) cc_final: 0.8671 (tpm170) REVERT: D 668 ASN cc_start: 0.8840 (t0) cc_final: 0.8457 (t0) REVERT: D 676 SER cc_start: 0.8966 (m) cc_final: 0.8505 (p) REVERT: D 693 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8212 (pm20) REVERT: D 723 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7276 (tt) REVERT: E 560 LYS cc_start: 0.8489 (tttt) cc_final: 0.8128 (pttt) REVERT: E 575 ASN cc_start: 0.8164 (m-40) cc_final: 0.7674 (m-40) REVERT: E 578 ASP cc_start: 0.8078 (m-30) cc_final: 0.7757 (m-30) REVERT: E 612 SER cc_start: 0.9546 (p) cc_final: 0.9221 (m) REVERT: E 626 SER cc_start: 0.9187 (m) cc_final: 0.8482 (p) REVERT: E 648 ASP cc_start: 0.8915 (m-30) cc_final: 0.8613 (m-30) REVERT: E 652 GLU cc_start: 0.8832 (tt0) cc_final: 0.8477 (tt0) REVERT: E 655 GLU cc_start: 0.8969 (tp30) cc_final: 0.8575 (tp30) REVERT: E 658 GLU cc_start: 0.9160 (tp30) cc_final: 0.8949 (tp30) REVERT: E 660 ARG cc_start: 0.8995 (tpt90) cc_final: 0.8566 (tpt170) REVERT: E 666 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8894 (tp30) REVERT: E 668 ASN cc_start: 0.8769 (t0) cc_final: 0.8229 (t0) REVERT: E 676 SER cc_start: 0.8739 (m) cc_final: 0.8295 (p) REVERT: E 681 THR cc_start: 0.8707 (m) cc_final: 0.8371 (p) REVERT: E 685 SER cc_start: 0.9085 (m) cc_final: 0.8753 (p) REVERT: E 703 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8452 (mm110) REVERT: E 720 TYR cc_start: 0.7525 (m-10) cc_final: 0.7162 (m-10) REVERT: F 527 MET cc_start: 0.9244 (mtt) cc_final: 0.9033 (ptp) REVERT: F 572 ASN cc_start: 0.9286 (t0) cc_final: 0.8852 (t0) REVERT: F 578 ASP cc_start: 0.8298 (m-30) cc_final: 0.8033 (m-30) REVERT: F 612 SER cc_start: 0.9548 (p) cc_final: 0.9234 (m) REVERT: F 626 SER cc_start: 0.9194 (m) cc_final: 0.8728 (p) REVERT: F 658 GLU cc_start: 0.9225 (tp30) cc_final: 0.8993 (tp30) REVERT: F 668 ASN cc_start: 0.8743 (t0) cc_final: 0.8399 (t0) REVERT: F 676 SER cc_start: 0.8849 (m) cc_final: 0.8314 (p) REVERT: G 572 ASN cc_start: 0.9156 (t0) cc_final: 0.8906 (t0) REVERT: G 612 SER cc_start: 0.9543 (p) cc_final: 0.9017 (m) REVERT: G 626 SER cc_start: 0.9329 (m) cc_final: 0.8808 (p) REVERT: G 652 GLU cc_start: 0.8813 (tt0) cc_final: 0.8581 (tt0) REVERT: G 654 MET cc_start: 0.9073 (mmm) cc_final: 0.8862 (mmm) REVERT: G 655 GLU cc_start: 0.8941 (tp30) cc_final: 0.8597 (tp30) REVERT: G 660 ARG cc_start: 0.8763 (tpt90) cc_final: 0.8431 (tpt170) REVERT: G 668 ASN cc_start: 0.8888 (t0) cc_final: 0.8323 (t0) REVERT: G 676 SER cc_start: 0.8828 (m) cc_final: 0.8383 (p) REVERT: G 685 SER cc_start: 0.9034 (m) cc_final: 0.8636 (p) REVERT: G 693 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8427 (pm20) outliers start: 61 outliers final: 41 residues processed: 448 average time/residue: 1.0879 time to fit residues: 530.0593 Evaluate side-chains 451 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 404 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 660 ARG Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain D residue 570 PHE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 614 ILE Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 570 PHE Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 593 SER Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 593 SER Chi-restraints excluded: chain F residue 616 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain G residue 586 THR Chi-restraints excluded: chain G residue 593 SER Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 693 GLN Chi-restraints excluded: chain G residue 723 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 149 optimal weight: 0.4980 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 GLN B 556 GLN B 703 GLN C 575 ASN D 536 ASN D 575 ASN E 536 ASN ** F 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 ASN G 703 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11669 Z= 0.166 Angle : 0.579 8.855 15883 Z= 0.286 Chirality : 0.041 0.170 1967 Planarity : 0.003 0.034 2030 Dihedral : 3.782 36.186 1632 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.59 % Allowed : 27.38 % Favored : 68.03 % 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: 2.19 (0.23), residues: 1435 helix: 2.95 (0.19), residues: 637 sheet: 0.20 (0.30), residues: 273 loop : 0.32 (0.30), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 694 HIS 0.002 0.001 HIS B 607 PHE 0.011 0.001 PHE D 567 TYR 0.011 0.001 TYR F 720 ARG 0.007 0.001 ARG F 660 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 422 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 527 MET cc_start: 0.9332 (mtt) cc_final: 0.9122 (ptp) REVERT: A 560 LYS cc_start: 0.8516 (tttt) cc_final: 0.8083 (pttt) REVERT: A 572 ASN cc_start: 0.9139 (t0) cc_final: 0.8930 (t0) REVERT: A 612 SER cc_start: 0.9440 (p) cc_final: 0.9136 (m) REVERT: A 648 ASP cc_start: 0.8892 (m-30) cc_final: 0.8656 (m-30) REVERT: A 652 GLU cc_start: 0.8875 (tt0) cc_final: 0.8258 (tt0) REVERT: A 655 GLU cc_start: 0.8938 (tp30) cc_final: 0.8721 (tp30) REVERT: A 660 ARG cc_start: 0.8805 (tpt90) cc_final: 0.8464 (tpt170) REVERT: A 664 ILE cc_start: 0.9248 (tp) cc_final: 0.9041 (pp) REVERT: A 668 ASN cc_start: 0.8804 (t0) cc_final: 0.8157 (t0) REVERT: A 676 SER cc_start: 0.8485 (m) cc_final: 0.7926 (p) REVERT: A 685 SER cc_start: 0.8953 (m) cc_final: 0.8446 (p) REVERT: A 703 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8453 (tp40) REVERT: B 590 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8163 (mt-10) REVERT: B 613 SER cc_start: 0.9545 (m) cc_final: 0.9322 (p) REVERT: B 626 SER cc_start: 0.9209 (m) cc_final: 0.8811 (p) REVERT: B 652 GLU cc_start: 0.8804 (tt0) cc_final: 0.8451 (tt0) REVERT: B 654 MET cc_start: 0.8902 (mmm) cc_final: 0.8649 (mmm) REVERT: B 660 ARG cc_start: 0.8688 (tpp-160) cc_final: 0.8350 (tpp-160) REVERT: B 668 ASN cc_start: 0.8817 (t0) cc_final: 0.8397 (t0) REVERT: B 676 SER cc_start: 0.8854 (m) cc_final: 0.8325 (p) REVERT: B 685 SER cc_start: 0.8901 (m) cc_final: 0.8521 (p) REVERT: C 572 ASN cc_start: 0.9190 (t0) cc_final: 0.8692 (t0) REVERT: C 596 SER cc_start: 0.9268 (p) cc_final: 0.9063 (t) REVERT: C 626 SER cc_start: 0.9119 (m) cc_final: 0.8581 (p) REVERT: C 676 SER cc_start: 0.8730 (m) cc_final: 0.8468 (t) REVERT: D 558 LEU cc_start: 0.8383 (tp) cc_final: 0.8164 (tp) REVERT: D 572 ASN cc_start: 0.9259 (t0) cc_final: 0.8893 (t0) REVERT: D 612 SER cc_start: 0.9395 (p) cc_final: 0.9048 (m) REVERT: D 622 ARG cc_start: 0.8430 (mmp80) cc_final: 0.8080 (mmt-90) REVERT: D 626 SER cc_start: 0.9109 (m) cc_final: 0.8700 (p) REVERT: D 655 GLU cc_start: 0.9028 (tp30) cc_final: 0.8760 (tp30) REVERT: D 668 ASN cc_start: 0.8843 (t0) cc_final: 0.8492 (t0) REVERT: D 676 SER cc_start: 0.8892 (m) cc_final: 0.8413 (p) REVERT: D 693 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8179 (pm20) REVERT: D 723 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7584 (tt) REVERT: E 560 LYS cc_start: 0.8419 (tttt) cc_final: 0.8102 (pttt) REVERT: E 572 ASN cc_start: 0.9235 (t0) cc_final: 0.8978 (t0) REVERT: E 575 ASN cc_start: 0.8172 (m-40) cc_final: 0.7756 (m-40) REVERT: E 578 ASP cc_start: 0.8045 (m-30) cc_final: 0.7749 (m-30) REVERT: E 612 SER cc_start: 0.9551 (p) cc_final: 0.9188 (m) REVERT: E 626 SER cc_start: 0.9136 (m) cc_final: 0.8417 (p) REVERT: E 648 ASP cc_start: 0.8907 (m-30) cc_final: 0.8598 (m-30) REVERT: E 652 GLU cc_start: 0.8838 (tt0) cc_final: 0.8477 (tt0) REVERT: E 655 GLU cc_start: 0.8962 (tp30) cc_final: 0.8625 (tp30) REVERT: E 658 GLU cc_start: 0.9164 (tp30) cc_final: 0.8869 (tp30) REVERT: E 660 ARG cc_start: 0.8840 (tpt90) cc_final: 0.8435 (tpt170) REVERT: E 666 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8890 (tp30) REVERT: E 668 ASN cc_start: 0.8787 (t0) cc_final: 0.8276 (t0) REVERT: E 676 SER cc_start: 0.8739 (m) cc_final: 0.8265 (p) REVERT: E 685 SER cc_start: 0.9073 (m) cc_final: 0.8738 (p) REVERT: E 703 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8497 (mm110) REVERT: E 720 TYR cc_start: 0.7614 (m-10) cc_final: 0.7227 (m-10) REVERT: F 572 ASN cc_start: 0.9229 (t0) cc_final: 0.8913 (t0) REVERT: F 578 ASP cc_start: 0.8323 (m-30) cc_final: 0.8070 (m-30) REVERT: F 612 SER cc_start: 0.9563 (p) cc_final: 0.9260 (m) REVERT: F 626 SER cc_start: 0.9145 (m) cc_final: 0.8690 (p) REVERT: F 658 GLU cc_start: 0.9158 (tp30) cc_final: 0.8904 (tp30) REVERT: F 660 ARG cc_start: 0.8693 (tpt170) cc_final: 0.8466 (tpt170) REVERT: F 668 ASN cc_start: 0.8737 (t0) cc_final: 0.8477 (t0) REVERT: F 676 SER cc_start: 0.8825 (m) cc_final: 0.8286 (p) REVERT: G 572 ASN cc_start: 0.9158 (t0) cc_final: 0.8926 (t0) REVERT: G 612 SER cc_start: 0.9484 (p) cc_final: 0.8953 (m) REVERT: G 626 SER cc_start: 0.9289 (m) cc_final: 0.8646 (p) REVERT: G 652 GLU cc_start: 0.8805 (tt0) cc_final: 0.8574 (tt0) REVERT: G 655 GLU cc_start: 0.8949 (tp30) cc_final: 0.8667 (tp30) REVERT: G 660 ARG cc_start: 0.8742 (tpt90) cc_final: 0.8428 (tpt170) REVERT: G 668 ASN cc_start: 0.8900 (t0) cc_final: 0.8348 (t0) REVERT: G 676 SER cc_start: 0.8748 (m) cc_final: 0.8291 (p) REVERT: G 685 SER cc_start: 0.9036 (m) cc_final: 0.8644 (p) REVERT: G 693 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8342 (pm20) outliers start: 54 outliers final: 35 residues processed: 446 average time/residue: 1.0883 time to fit residues: 527.6046 Evaluate side-chains 440 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 401 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain D residue 570 PHE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 614 ILE Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 570 PHE Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 593 SER Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain G residue 586 THR Chi-restraints excluded: chain G residue 593 SER Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 693 GLN Chi-restraints excluded: chain G residue 723 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.8980 chunk 16 optimal weight: 0.0370 chunk 84 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 83 optimal weight: 0.0570 chunk 148 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 ASN B 703 GLN C 575 ASN ** C 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 ASN D 575 ASN ** F 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 ASN G 703 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11669 Z= 0.175 Angle : 0.599 8.568 15883 Z= 0.300 Chirality : 0.042 0.196 1967 Planarity : 0.003 0.029 2030 Dihedral : 3.731 36.225 1632 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.25 % Allowed : 28.23 % Favored : 67.52 % 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: 2.29 (0.23), residues: 1435 helix: 3.04 (0.19), residues: 637 sheet: 0.28 (0.30), residues: 273 loop : 0.36 (0.30), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 694 HIS 0.002 0.001 HIS B 607 PHE 0.013 0.001 PHE D 567 TYR 0.009 0.001 TYR F 720 ARG 0.007 0.001 ARG D 697 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 413 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 LYS cc_start: 0.8509 (tttt) cc_final: 0.8100 (pttt) REVERT: A 572 ASN cc_start: 0.9157 (t0) cc_final: 0.8906 (t0) REVERT: A 612 SER cc_start: 0.9415 (p) cc_final: 0.9103 (m) REVERT: A 622 ARG cc_start: 0.8563 (mmp80) cc_final: 0.8160 (mmp80) REVERT: A 648 ASP cc_start: 0.8908 (m-30) cc_final: 0.8671 (m-30) REVERT: A 652 GLU cc_start: 0.8870 (tt0) cc_final: 0.8281 (tt0) REVERT: A 655 GLU cc_start: 0.8955 (tp30) cc_final: 0.8749 (tp30) REVERT: A 660 ARG cc_start: 0.8908 (tpt90) cc_final: 0.8589 (tpt170) REVERT: A 668 ASN cc_start: 0.8826 (t0) cc_final: 0.8214 (t0) REVERT: A 676 SER cc_start: 0.8488 (m) cc_final: 0.7926 (p) REVERT: A 685 SER cc_start: 0.8967 (m) cc_final: 0.8454 (p) REVERT: A 703 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8385 (tp40) REVERT: B 590 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8173 (mt-10) REVERT: B 613 SER cc_start: 0.9526 (m) cc_final: 0.9311 (p) REVERT: B 626 SER cc_start: 0.9196 (m) cc_final: 0.8801 (p) REVERT: B 652 GLU cc_start: 0.8797 (tt0) cc_final: 0.8462 (tt0) REVERT: B 654 MET cc_start: 0.8895 (mmm) cc_final: 0.8635 (mmm) REVERT: B 660 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8341 (tpp-160) REVERT: B 668 ASN cc_start: 0.8835 (t0) cc_final: 0.8431 (t0) REVERT: B 676 SER cc_start: 0.8851 (m) cc_final: 0.8329 (p) REVERT: B 685 SER cc_start: 0.8902 (m) cc_final: 0.8536 (p) REVERT: C 572 ASN cc_start: 0.9157 (t0) cc_final: 0.8563 (t0) REVERT: C 626 SER cc_start: 0.9135 (m) cc_final: 0.8586 (p) REVERT: C 676 SER cc_start: 0.8676 (m) cc_final: 0.8428 (t) REVERT: C 685 SER cc_start: 0.9155 (m) cc_final: 0.8605 (p) REVERT: D 560 LYS cc_start: 0.8475 (tttt) cc_final: 0.8178 (pttt) REVERT: D 572 ASN cc_start: 0.9257 (t0) cc_final: 0.8993 (t0) REVERT: D 612 SER cc_start: 0.9407 (p) cc_final: 0.9073 (m) REVERT: D 626 SER cc_start: 0.9071 (m) cc_final: 0.8642 (p) REVERT: D 652 GLU cc_start: 0.8806 (tt0) cc_final: 0.8287 (tt0) REVERT: D 660 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8602 (tpm170) REVERT: D 668 ASN cc_start: 0.8820 (t0) cc_final: 0.8486 (t0) REVERT: D 676 SER cc_start: 0.8868 (m) cc_final: 0.8376 (p) REVERT: D 693 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8163 (pm20) REVERT: E 560 LYS cc_start: 0.8427 (tttt) cc_final: 0.8127 (pttt) REVERT: E 572 ASN cc_start: 0.9255 (t0) cc_final: 0.9019 (t0) REVERT: E 575 ASN cc_start: 0.8154 (m-40) cc_final: 0.7770 (m-40) REVERT: E 578 ASP cc_start: 0.8048 (m-30) cc_final: 0.7719 (m-30) REVERT: E 612 SER cc_start: 0.9547 (p) cc_final: 0.9181 (m) REVERT: E 626 SER cc_start: 0.9132 (m) cc_final: 0.8409 (p) REVERT: E 648 ASP cc_start: 0.8910 (m-30) cc_final: 0.8600 (m-30) REVERT: E 652 GLU cc_start: 0.8834 (tt0) cc_final: 0.8456 (tt0) REVERT: E 655 GLU cc_start: 0.8950 (tp30) cc_final: 0.8702 (tp30) REVERT: E 658 GLU cc_start: 0.9172 (tp30) cc_final: 0.8873 (tp30) REVERT: E 660 ARG cc_start: 0.8763 (tpt90) cc_final: 0.8295 (tpt170) REVERT: E 666 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8890 (tp30) REVERT: E 668 ASN cc_start: 0.8792 (t0) cc_final: 0.8096 (t0) REVERT: E 676 SER cc_start: 0.8726 (m) cc_final: 0.8263 (p) REVERT: E 685 SER cc_start: 0.9073 (m) cc_final: 0.8722 (p) REVERT: E 703 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8399 (mm110) REVERT: E 720 TYR cc_start: 0.7591 (m-10) cc_final: 0.7304 (m-10) REVERT: F 527 MET cc_start: 0.9257 (mtt) cc_final: 0.9034 (ptp) REVERT: F 572 ASN cc_start: 0.9232 (t0) cc_final: 0.8903 (t0) REVERT: F 612 SER cc_start: 0.9555 (p) cc_final: 0.9240 (m) REVERT: F 626 SER cc_start: 0.9137 (m) cc_final: 0.8690 (p) REVERT: F 658 GLU cc_start: 0.9147 (tp30) cc_final: 0.8847 (tp30) REVERT: F 668 ASN cc_start: 0.8786 (t0) cc_final: 0.8476 (t0) REVERT: F 676 SER cc_start: 0.8823 (m) cc_final: 0.8283 (p) REVERT: G 572 ASN cc_start: 0.9119 (t0) cc_final: 0.8919 (t0) REVERT: G 578 ASP cc_start: 0.8247 (m-30) cc_final: 0.7961 (m-30) REVERT: G 612 SER cc_start: 0.9429 (p) cc_final: 0.8860 (m) REVERT: G 622 ARG cc_start: 0.8443 (mmp80) cc_final: 0.8199 (tpp-160) REVERT: G 626 SER cc_start: 0.9213 (m) cc_final: 0.8586 (p) REVERT: G 652 GLU cc_start: 0.8791 (tt0) cc_final: 0.8568 (tt0) REVERT: G 655 GLU cc_start: 0.8917 (tp30) cc_final: 0.8700 (tp30) REVERT: G 660 ARG cc_start: 0.8744 (tpt90) cc_final: 0.8374 (tpm170) REVERT: G 668 ASN cc_start: 0.8909 (t0) cc_final: 0.8337 (t0) REVERT: G 676 SER cc_start: 0.8743 (m) cc_final: 0.8287 (p) REVERT: G 685 SER cc_start: 0.9026 (m) cc_final: 0.8609 (p) REVERT: G 693 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8324 (pm20) REVERT: G 714 ARG cc_start: 0.8624 (mtp85) cc_final: 0.8367 (mtm-85) outliers start: 50 outliers final: 31 residues processed: 431 average time/residue: 1.1007 time to fit residues: 516.0594 Evaluate side-chains 445 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 409 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 660 ARG Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain D residue 570 PHE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 614 ILE Chi-restraints excluded: chain D residue 660 ARG Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 593 SER Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 593 SER Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain G residue 570 PHE Chi-restraints excluded: chain G residue 586 THR Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 693 GLN Chi-restraints excluded: chain G residue 723 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 30.0000 chunk 44 optimal weight: 30.0000 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 94 optimal weight: 0.3980 chunk 101 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 0.0570 chunk 116 optimal weight: 0.6980 chunk 135 optimal weight: 0.0370 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 703 GLN C 575 ASN C 644 GLN ** C 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 ASN D 575 ASN E 556 GLN ** F 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 556 GLN G 630 ASN G 703 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11669 Z= 0.163 Angle : 0.617 8.533 15883 Z= 0.311 Chirality : 0.043 0.184 1967 Planarity : 0.003 0.034 2030 Dihedral : 3.701 35.322 1632 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.06 % Allowed : 29.68 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.23), residues: 1435 helix: 3.10 (0.19), residues: 637 sheet: 0.33 (0.31), residues: 273 loop : 0.33 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 694 HIS 0.002 0.001 HIS B 607 PHE 0.016 0.001 PHE C 567 TYR 0.008 0.001 TYR F 720 ARG 0.009 0.001 ARG F 660 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 420 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 LYS cc_start: 0.8490 (tttt) cc_final: 0.8129 (pttt) REVERT: A 612 SER cc_start: 0.9421 (p) cc_final: 0.9100 (m) REVERT: A 622 ARG cc_start: 0.8498 (mmp80) cc_final: 0.8070 (mmp80) REVERT: A 648 ASP cc_start: 0.8904 (m-30) cc_final: 0.8670 (m-30) REVERT: A 652 GLU cc_start: 0.8880 (tt0) cc_final: 0.8431 (tt0) REVERT: A 660 ARG cc_start: 0.8863 (tpt90) cc_final: 0.8591 (tpt170) REVERT: A 668 ASN cc_start: 0.8798 (t0) cc_final: 0.8238 (t0) REVERT: A 676 SER cc_start: 0.8480 (m) cc_final: 0.7920 (p) REVERT: A 685 SER cc_start: 0.8910 (m) cc_final: 0.8401 (p) REVERT: B 613 SER cc_start: 0.9514 (m) cc_final: 0.9300 (p) REVERT: B 626 SER cc_start: 0.9133 (m) cc_final: 0.8703 (p) REVERT: B 652 GLU cc_start: 0.8776 (tt0) cc_final: 0.8463 (tt0) REVERT: B 654 MET cc_start: 0.8905 (mmm) cc_final: 0.8669 (mmm) REVERT: B 660 ARG cc_start: 0.8649 (tpp-160) cc_final: 0.8325 (tpp-160) REVERT: B 668 ASN cc_start: 0.8817 (t0) cc_final: 0.8359 (t0) REVERT: B 676 SER cc_start: 0.8828 (m) cc_final: 0.8288 (p) REVERT: B 685 SER cc_start: 0.8899 (m) cc_final: 0.8494 (p) REVERT: C 572 ASN cc_start: 0.9011 (t0) cc_final: 0.8456 (t0) REVERT: C 626 SER cc_start: 0.9138 (m) cc_final: 0.8578 (p) REVERT: C 668 ASN cc_start: 0.8625 (t0) cc_final: 0.7881 (t0) REVERT: C 676 SER cc_start: 0.8637 (m) cc_final: 0.8397 (t) REVERT: C 685 SER cc_start: 0.9155 (m) cc_final: 0.8578 (p) REVERT: D 572 ASN cc_start: 0.9252 (t0) cc_final: 0.8940 (t0) REVERT: D 612 SER cc_start: 0.9417 (p) cc_final: 0.9083 (m) REVERT: D 626 SER cc_start: 0.9073 (m) cc_final: 0.8628 (p) REVERT: D 652 GLU cc_start: 0.8777 (tt0) cc_final: 0.8272 (tt0) REVERT: D 668 ASN cc_start: 0.8838 (t0) cc_final: 0.8510 (t0) REVERT: D 676 SER cc_start: 0.8847 (m) cc_final: 0.8352 (p) REVERT: D 693 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8138 (pm20) REVERT: E 560 LYS cc_start: 0.8409 (tttt) cc_final: 0.8132 (pttt) REVERT: E 612 SER cc_start: 0.9548 (p) cc_final: 0.9200 (m) REVERT: E 626 SER cc_start: 0.9084 (m) cc_final: 0.8324 (p) REVERT: E 648 ASP cc_start: 0.8903 (m-30) cc_final: 0.8591 (m-30) REVERT: E 652 GLU cc_start: 0.8821 (tt0) cc_final: 0.8335 (tt0) REVERT: E 655 GLU cc_start: 0.8971 (tp30) cc_final: 0.8742 (tp30) REVERT: E 658 GLU cc_start: 0.9184 (tp30) cc_final: 0.8928 (tp30) REVERT: E 660 ARG cc_start: 0.8759 (tpt90) cc_final: 0.8285 (tpt170) REVERT: E 666 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8906 (tp30) REVERT: E 668 ASN cc_start: 0.8818 (t0) cc_final: 0.8134 (t0) REVERT: E 676 SER cc_start: 0.8753 (m) cc_final: 0.8256 (p) REVERT: E 685 SER cc_start: 0.9066 (m) cc_final: 0.8709 (p) REVERT: E 703 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8354 (mm110) REVERT: E 706 LYS cc_start: 0.8429 (ttpp) cc_final: 0.8063 (tmmt) REVERT: E 720 TYR cc_start: 0.7597 (m-10) cc_final: 0.7322 (m-10) REVERT: F 527 MET cc_start: 0.9249 (mtt) cc_final: 0.8969 (ptp) REVERT: F 560 LYS cc_start: 0.8391 (tttt) cc_final: 0.7974 (pttt) REVERT: F 612 SER cc_start: 0.9544 (p) cc_final: 0.9265 (m) REVERT: F 626 SER cc_start: 0.9092 (m) cc_final: 0.8636 (p) REVERT: F 668 ASN cc_start: 0.8755 (t0) cc_final: 0.8460 (t0) REVERT: F 676 SER cc_start: 0.8807 (m) cc_final: 0.8272 (p) REVERT: G 572 ASN cc_start: 0.9101 (t0) cc_final: 0.8880 (t0) REVERT: G 578 ASP cc_start: 0.8279 (m-30) cc_final: 0.8031 (m-30) REVERT: G 612 SER cc_start: 0.9425 (p) cc_final: 0.8857 (m) REVERT: G 622 ARG cc_start: 0.8441 (mmp80) cc_final: 0.8177 (mmp80) REVERT: G 626 SER cc_start: 0.9174 (m) cc_final: 0.8515 (p) REVERT: G 652 GLU cc_start: 0.8797 (tt0) cc_final: 0.8555 (tt0) REVERT: G 658 GLU cc_start: 0.9198 (tp30) cc_final: 0.8976 (tp30) REVERT: G 660 ARG cc_start: 0.8783 (tpt90) cc_final: 0.8450 (tpm170) REVERT: G 668 ASN cc_start: 0.8899 (t0) cc_final: 0.8343 (t0) REVERT: G 676 SER cc_start: 0.8731 (m) cc_final: 0.8277 (p) REVERT: G 685 SER cc_start: 0.8974 (m) cc_final: 0.8541 (p) REVERT: G 693 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8342 (pm20) REVERT: G 714 ARG cc_start: 0.8673 (mtp85) cc_final: 0.8394 (mtm-85) outliers start: 36 outliers final: 30 residues processed: 435 average time/residue: 1.1013 time to fit residues: 521.0000 Evaluate side-chains 434 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 402 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain D residue 570 PHE Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 614 ILE Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain G residue 570 PHE Chi-restraints excluded: chain G residue 586 THR Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 693 GLN Chi-restraints excluded: chain G residue 723 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 0.0270 chunk 108 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 ASN B 703 GLN C 575 ASN ** C 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 ASN E 575 ASN ** F 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 ASN G 703 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11669 Z= 0.199 Angle : 0.664 8.249 15883 Z= 0.338 Chirality : 0.043 0.187 1967 Planarity : 0.003 0.046 2030 Dihedral : 3.712 34.847 1632 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.49 % Allowed : 29.51 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.23), residues: 1435 helix: 3.12 (0.19), residues: 637 sheet: 0.33 (0.31), residues: 273 loop : 0.30 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 694 HIS 0.002 0.001 HIS B 607 PHE 0.015 0.001 PHE D 567 TYR 0.009 0.001 TYR F 720 ARG 0.009 0.001 ARG F 660 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 419 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 612 SER cc_start: 0.9390 (p) cc_final: 0.9024 (m) REVERT: A 622 ARG cc_start: 0.8522 (mmp80) cc_final: 0.8321 (tpp80) REVERT: A 648 ASP cc_start: 0.8920 (m-30) cc_final: 0.8687 (m-30) REVERT: A 652 GLU cc_start: 0.8868 (tt0) cc_final: 0.8405 (tt0) REVERT: A 660 ARG cc_start: 0.8851 (tpt90) cc_final: 0.8581 (tpt170) REVERT: A 668 ASN cc_start: 0.8803 (t0) cc_final: 0.8205 (t0) REVERT: A 676 SER cc_start: 0.8497 (m) cc_final: 0.7945 (p) REVERT: A 685 SER cc_start: 0.8925 (m) cc_final: 0.8417 (p) REVERT: B 613 SER cc_start: 0.9533 (m) cc_final: 0.9333 (p) REVERT: B 626 SER cc_start: 0.9037 (m) cc_final: 0.8650 (p) REVERT: B 652 GLU cc_start: 0.8802 (tt0) cc_final: 0.8495 (tt0) REVERT: B 654 MET cc_start: 0.8899 (mmm) cc_final: 0.8637 (mmm) REVERT: B 655 GLU cc_start: 0.8961 (tp30) cc_final: 0.8694 (tp30) REVERT: B 660 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8468 (tpp-160) REVERT: B 668 ASN cc_start: 0.8875 (t0) cc_final: 0.8483 (t0) REVERT: B 676 SER cc_start: 0.8825 (m) cc_final: 0.8288 (p) REVERT: B 685 SER cc_start: 0.8952 (m) cc_final: 0.8677 (p) REVERT: C 572 ASN cc_start: 0.8995 (t0) cc_final: 0.8441 (t0) REVERT: C 626 SER cc_start: 0.9178 (m) cc_final: 0.8623 (p) REVERT: C 668 ASN cc_start: 0.8615 (t0) cc_final: 0.7878 (t0) REVERT: C 676 SER cc_start: 0.8627 (m) cc_final: 0.8393 (t) REVERT: C 685 SER cc_start: 0.9162 (m) cc_final: 0.8581 (p) REVERT: C 703 GLN cc_start: 0.8659 (tp40) cc_final: 0.8354 (tp-100) REVERT: D 572 ASN cc_start: 0.9199 (t0) cc_final: 0.8795 (t0) REVERT: D 612 SER cc_start: 0.9414 (p) cc_final: 0.9063 (m) REVERT: D 626 SER cc_start: 0.9110 (m) cc_final: 0.8651 (p) REVERT: D 652 GLU cc_start: 0.8713 (tt0) cc_final: 0.8258 (tt0) REVERT: D 654 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8668 (mmm) REVERT: D 668 ASN cc_start: 0.8831 (t0) cc_final: 0.8511 (t0) REVERT: D 676 SER cc_start: 0.8825 (m) cc_final: 0.8341 (p) REVERT: D 693 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8145 (pm20) REVERT: E 560 LYS cc_start: 0.8477 (tttt) cc_final: 0.8200 (pttt) REVERT: E 575 ASN cc_start: 0.8216 (m-40) cc_final: 0.7862 (m-40) REVERT: E 612 SER cc_start: 0.9548 (p) cc_final: 0.9178 (m) REVERT: E 626 SER cc_start: 0.9089 (m) cc_final: 0.8364 (p) REVERT: E 652 GLU cc_start: 0.8814 (tt0) cc_final: 0.8453 (tt0) REVERT: E 655 GLU cc_start: 0.8990 (tp30) cc_final: 0.8740 (tp30) REVERT: E 658 GLU cc_start: 0.9204 (tp30) cc_final: 0.8924 (tp30) REVERT: E 660 ARG cc_start: 0.8779 (tpt90) cc_final: 0.8316 (tpt170) REVERT: E 666 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8912 (tp30) REVERT: E 668 ASN cc_start: 0.8824 (t0) cc_final: 0.8150 (t0) REVERT: E 676 SER cc_start: 0.8730 (m) cc_final: 0.8270 (p) REVERT: E 685 SER cc_start: 0.9074 (m) cc_final: 0.8719 (p) REVERT: E 703 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8401 (mm110) REVERT: E 720 TYR cc_start: 0.7561 (m-10) cc_final: 0.7282 (m-10) REVERT: F 612 SER cc_start: 0.9560 (p) cc_final: 0.9223 (m) REVERT: F 626 SER cc_start: 0.9120 (m) cc_final: 0.8672 (p) REVERT: F 668 ASN cc_start: 0.8811 (t0) cc_final: 0.8516 (t0) REVERT: F 676 SER cc_start: 0.8798 (m) cc_final: 0.8271 (p) REVERT: G 572 ASN cc_start: 0.9095 (t0) cc_final: 0.8823 (t0) REVERT: G 578 ASP cc_start: 0.8274 (m-30) cc_final: 0.8021 (m-30) REVERT: G 612 SER cc_start: 0.9426 (p) cc_final: 0.8835 (m) REVERT: G 622 ARG cc_start: 0.8437 (mmp80) cc_final: 0.8160 (mmp80) REVERT: G 626 SER cc_start: 0.9213 (m) cc_final: 0.8558 (p) REVERT: G 652 GLU cc_start: 0.8824 (tt0) cc_final: 0.8596 (tt0) REVERT: G 658 GLU cc_start: 0.9227 (tp30) cc_final: 0.8940 (tp30) REVERT: G 660 ARG cc_start: 0.8761 (tpt90) cc_final: 0.8452 (tpm170) REVERT: G 668 ASN cc_start: 0.8894 (t0) cc_final: 0.8333 (t0) REVERT: G 676 SER cc_start: 0.8746 (m) cc_final: 0.8291 (p) REVERT: G 685 SER cc_start: 0.8990 (m) cc_final: 0.8558 (p) REVERT: G 693 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8365 (pm20) REVERT: G 714 ARG cc_start: 0.8677 (mtp85) cc_final: 0.8396 (mtm-85) outliers start: 41 outliers final: 33 residues processed: 434 average time/residue: 1.0728 time to fit residues: 506.1692 Evaluate side-chains 445 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 408 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 660 ARG Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 614 ILE Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain G residue 570 PHE Chi-restraints excluded: chain G residue 586 THR Chi-restraints excluded: chain G residue 593 SER Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 693 GLN Chi-restraints excluded: chain G residue 703 GLN Chi-restraints excluded: chain G residue 723 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.9980 chunk 89 optimal weight: 20.0000 chunk 69 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 94 optimal weight: 0.1980 chunk 74 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 703 GLN C 575 ASN ** C 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 ASN E 572 ASN ** F 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 ASN ** G 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 : 0.003 0.033 11669 Z= 0.195 Angle : 0.680 10.643 15883 Z= 0.347 Chirality : 0.044 0.207 1967 Planarity : 0.004 0.064 2030 Dihedral : 3.750 34.438 1632 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.72 % Allowed : 31.29 % Favored : 65.99 % 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: 2.37 (0.23), residues: 1435 helix: 3.13 (0.19), residues: 637 sheet: 0.37 (0.31), residues: 273 loop : 0.32 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 694 HIS 0.002 0.001 HIS B 607 PHE 0.010 0.001 PHE C 567 TYR 0.009 0.001 TYR F 720 ARG 0.014 0.001 ARG F 660 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 413 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 612 SER cc_start: 0.9380 (p) cc_final: 0.9022 (m) REVERT: A 622 ARG cc_start: 0.8544 (mmp80) cc_final: 0.8184 (mmp80) REVERT: A 648 ASP cc_start: 0.8919 (m-30) cc_final: 0.8687 (m-30) REVERT: A 652 GLU cc_start: 0.8858 (tt0) cc_final: 0.8399 (tt0) REVERT: A 660 ARG cc_start: 0.8842 (tpt90) cc_final: 0.8594 (tpt170) REVERT: A 668 ASN cc_start: 0.8797 (t0) cc_final: 0.8196 (t0) REVERT: A 676 SER cc_start: 0.8495 (m) cc_final: 0.7936 (p) REVERT: A 685 SER cc_start: 0.8950 (m) cc_final: 0.8443 (p) REVERT: B 626 SER cc_start: 0.9063 (m) cc_final: 0.8649 (p) REVERT: B 652 GLU cc_start: 0.8794 (tt0) cc_final: 0.8513 (tt0) REVERT: B 654 MET cc_start: 0.8894 (mmm) cc_final: 0.8643 (mmm) REVERT: B 660 ARG cc_start: 0.8615 (tpp-160) cc_final: 0.8299 (tpp-160) REVERT: B 668 ASN cc_start: 0.8888 (t0) cc_final: 0.8507 (t0) REVERT: B 676 SER cc_start: 0.8823 (m) cc_final: 0.8286 (p) REVERT: B 685 SER cc_start: 0.8975 (m) cc_final: 0.8747 (p) REVERT: C 560 LYS cc_start: 0.8482 (tppp) cc_final: 0.8164 (pttt) REVERT: C 572 ASN cc_start: 0.8984 (t0) cc_final: 0.8431 (t0) REVERT: C 626 SER cc_start: 0.9178 (m) cc_final: 0.8622 (p) REVERT: C 668 ASN cc_start: 0.8611 (t0) cc_final: 0.7876 (t0) REVERT: C 676 SER cc_start: 0.8613 (m) cc_final: 0.8385 (t) REVERT: C 685 SER cc_start: 0.9162 (m) cc_final: 0.8576 (p) REVERT: C 703 GLN cc_start: 0.8663 (tp40) cc_final: 0.8358 (tp-100) REVERT: D 572 ASN cc_start: 0.9124 (t0) cc_final: 0.8799 (t0) REVERT: D 612 SER cc_start: 0.9413 (p) cc_final: 0.9061 (m) REVERT: D 626 SER cc_start: 0.9085 (m) cc_final: 0.8638 (p) REVERT: D 652 GLU cc_start: 0.8693 (tt0) cc_final: 0.8244 (tt0) REVERT: D 668 ASN cc_start: 0.8819 (t0) cc_final: 0.8501 (t0) REVERT: D 676 SER cc_start: 0.8798 (m) cc_final: 0.8533 (t) REVERT: D 693 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8141 (pm20) REVERT: E 560 LYS cc_start: 0.8479 (tttt) cc_final: 0.8223 (pttt) REVERT: E 596 SER cc_start: 0.9233 (t) cc_final: 0.8973 (p) REVERT: E 612 SER cc_start: 0.9549 (p) cc_final: 0.9177 (m) REVERT: E 626 SER cc_start: 0.9082 (m) cc_final: 0.8403 (p) REVERT: E 648 ASP cc_start: 0.8967 (m-30) cc_final: 0.8596 (m-30) REVERT: E 652 GLU cc_start: 0.8809 (tt0) cc_final: 0.8470 (tt0) REVERT: E 655 GLU cc_start: 0.8982 (tp30) cc_final: 0.8740 (tp30) REVERT: E 658 GLU cc_start: 0.9222 (tp30) cc_final: 0.8943 (tp30) REVERT: E 660 ARG cc_start: 0.8775 (tpt90) cc_final: 0.8377 (tpt170) REVERT: E 666 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8920 (tp30) REVERT: E 668 ASN cc_start: 0.8824 (t0) cc_final: 0.8151 (t0) REVERT: E 676 SER cc_start: 0.8720 (m) cc_final: 0.8263 (p) REVERT: E 685 SER cc_start: 0.9072 (m) cc_final: 0.8717 (p) REVERT: E 703 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8407 (mm110) REVERT: E 720 TYR cc_start: 0.7430 (m-10) cc_final: 0.7166 (m-10) REVERT: F 527 MET cc_start: 0.9235 (mtt) cc_final: 0.9013 (ptp) REVERT: F 612 SER cc_start: 0.9562 (p) cc_final: 0.9220 (m) REVERT: F 626 SER cc_start: 0.9122 (m) cc_final: 0.8668 (p) REVERT: F 652 GLU cc_start: 0.9014 (tt0) cc_final: 0.8278 (tm-30) REVERT: F 668 ASN cc_start: 0.8810 (t0) cc_final: 0.8517 (t0) REVERT: F 676 SER cc_start: 0.8799 (m) cc_final: 0.8271 (p) REVERT: G 578 ASP cc_start: 0.8264 (m-30) cc_final: 0.8017 (m-30) REVERT: G 612 SER cc_start: 0.9423 (p) cc_final: 0.8840 (m) REVERT: G 622 ARG cc_start: 0.8477 (mmp80) cc_final: 0.8162 (mmp80) REVERT: G 626 SER cc_start: 0.9142 (m) cc_final: 0.8510 (p) REVERT: G 658 GLU cc_start: 0.9236 (tp30) cc_final: 0.8951 (tp30) REVERT: G 660 ARG cc_start: 0.8732 (tpt90) cc_final: 0.8493 (tpm170) REVERT: G 668 ASN cc_start: 0.8914 (t0) cc_final: 0.8354 (t0) REVERT: G 676 SER cc_start: 0.8750 (m) cc_final: 0.8293 (p) REVERT: G 685 SER cc_start: 0.8993 (m) cc_final: 0.8559 (p) REVERT: G 693 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8361 (pm20) REVERT: G 714 ARG cc_start: 0.8676 (mtp85) cc_final: 0.8397 (mtm-85) outliers start: 32 outliers final: 30 residues processed: 425 average time/residue: 1.0782 time to fit residues: 497.9231 Evaluate side-chains 441 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 409 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 614 ILE Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain G residue 570 PHE Chi-restraints excluded: chain G residue 586 THR Chi-restraints excluded: chain G residue 593 SER Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 693 GLN Chi-restraints excluded: chain G residue 723 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 0.0030 chunk 51 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 30.0000 chunk 107 optimal weight: 0.6980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 703 GLN C 575 ASN ** C 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 ASN E 572 ASN E 575 ASN ** F 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 ASN ** G 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.127571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.088662 restraints weight = 17512.385| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.75 r_work: 0.2815 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11669 Z= 0.199 Angle : 0.705 13.508 15883 Z= 0.358 Chirality : 0.044 0.204 1967 Planarity : 0.004 0.055 2030 Dihedral : 3.742 34.037 1632 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.98 % Allowed : 31.04 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.23), residues: 1435 helix: 3.15 (0.19), residues: 637 sheet: 0.42 (0.31), residues: 273 loop : 0.34 (0.30), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 694 HIS 0.002 0.001 HIS B 607 PHE 0.009 0.001 PHE D 567 TYR 0.008 0.001 TYR F 720 ARG 0.012 0.001 ARG F 660 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7020.61 seconds wall clock time: 122 minutes 48.59 seconds (7368.59 seconds total)