Starting phenix.real_space_refine on Sun Mar 17 07:26:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3y_17399/03_2024/8p3y_17399_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3y_17399/03_2024/8p3y_17399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3y_17399/03_2024/8p3y_17399.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3y_17399/03_2024/8p3y_17399.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3y_17399/03_2024/8p3y_17399_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3y_17399/03_2024/8p3y_17399_neut.pdb" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.048 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 120 5.16 5 C 11128 2.51 5 N 2746 2.21 5 O 3018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 453": "NH1" <-> "NH2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A GLU 813": "OE1" <-> "OE2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B GLU 550": "OE1" <-> "OE2" Residue "B PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C GLU 486": "OE1" <-> "OE2" Residue "C PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 705": "OE1" <-> "OE2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "D GLU 486": "OE1" <-> "OE2" Residue "D GLU 570": "OE1" <-> "OE2" Residue "D GLU 634": "OE1" <-> "OE2" Residue "D GLU 705": "OE1" <-> "OE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E GLU 191": "OE1" <-> "OE2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "H GLU 56": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17012 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2865 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 391, 2854 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 379} Chain breaks: 4 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 110 Conformer: "B" Number of residues, atoms: 391, 2854 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 379} Chain breaks: 4 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 110 bond proxies already assigned to first conformer: 2905 Chain: "B" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2878 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 383} Chain breaks: 3 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 124 Chain: "C" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2859 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 381} Chain breaks: 4 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 119 Chain: "D" Number of atoms: 2935 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 403, 2924 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 389} Chain breaks: 2 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 125 Conformer: "B" Number of residues, atoms: 403, 2924 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 389} Chain breaks: 2 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 125 bond proxies already assigned to first conformer: 2979 Chain: "E" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1372 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1358 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1372 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1373 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N APHE A 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 574 " occ=0.50 residue: pdb=" N APHE D 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 574 " occ=0.50 Time building chain proxies: 12.05, per 1000 atoms: 0.71 Number of scatterers: 17012 At special positions: 0 Unit cell: (118.531, 137.323, 145.996, 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 120 16.00 O 3018 8.00 N 2746 7.00 C 11128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.00 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.02 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.04 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.04 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.04 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.04 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.05 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.09 Conformation dependent library (CDL) restraints added in 4.3 seconds 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4186 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 29 sheets defined 60.5% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.882A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.657A pdb=" N ASP A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 488 removed outlier: 3.815A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.781A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 624 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 757 removed outlier: 3.646A pdb=" N LEU A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 788 through 820 removed outlier: 3.574A pdb=" N VAL A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLY A 794 " --> pdb=" O SER A 790 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 795 " --> pdb=" O ASN A 791 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.722A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 482 through 488 removed outlier: 3.811A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.620A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 624 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 677 Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 757 removed outlier: 3.523A pdb=" N ASN B 747 " --> pdb=" O GLY B 743 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 769 through 771 No H-bonds generated for 'chain 'B' and resid 769 through 771' Processing helix chain 'B' and resid 792 through 823 removed outlier: 3.547A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 822 " --> pdb=" O SER B 818 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS B 823 " --> pdb=" O ARG B 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 removed outlier: 3.626A pdb=" N MET C 414 " --> pdb=" O ASN C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.529A pdb=" N ASP C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 489 removed outlier: 3.836A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 removed outlier: 3.626A pdb=" N GLU C 550 " --> pdb=" O SER C 547 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP C 551 " --> pdb=" O PRO C 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 547 through 551' Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 620 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 664 through 677 Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 757 removed outlier: 3.684A pdb=" N ASN C 747 " --> pdb=" O GLY C 743 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 removed outlier: 3.632A pdb=" N LYS C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 821 removed outlier: 3.662A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.627A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 488 removed outlier: 3.761A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.820A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 545 Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.669A pdb=" N TRP D 578 " --> pdb=" O BPHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 624 removed outlier: 3.598A pdb=" N LEU D 624 " --> pdb=" O LEU D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 629 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 677 Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 757 removed outlier: 3.685A pdb=" N LEU D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 823 removed outlier: 3.791A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 823 " --> pdb=" O ARG D 819 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 30 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 105 through 124 Processing helix chain 'E' and resid 133 through 160 removed outlier: 3.824A pdb=" N SER E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 210 Processing helix chain 'F' and resid 6 through 28 Processing helix chain 'F' and resid 93 through 104 removed outlier: 3.513A pdb=" N LEU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 127 removed outlier: 4.037A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 160 Processing helix chain 'F' and resid 177 through 209 Processing helix chain 'G' and resid 7 through 30 removed outlier: 3.581A pdb=" N LEU G 11 " --> pdb=" O GLY G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 104 Processing helix chain 'G' and resid 105 through 127 removed outlier: 4.166A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 161 removed outlier: 3.868A pdb=" N SER G 137 " --> pdb=" O ASN G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 210 Processing helix chain 'H' and resid 6 through 30 removed outlier: 3.963A pdb=" N MET H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU H 11 " --> pdb=" O GLY H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 105 through 124 Processing helix chain 'H' and resid 133 through 161 removed outlier: 3.562A pdb=" N ALA H 161 " --> pdb=" O ILE H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 209 removed outlier: 3.938A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 394 through 399 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.464A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.464A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 394 through 399 Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 451 through 453 removed outlier: 3.611A pdb=" N ALA B 452 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.509A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.509A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 394 through 399 removed outlier: 6.432A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'C' and resid 453 through 454 removed outlier: 3.613A pdb=" N ILE C 459 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 480 through 481 removed outlier: 4.490A pdb=" N GLY C 731 " --> pdb=" O ILE C 481 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 480 through 481 removed outlier: 4.490A pdb=" N GLY C 731 " --> pdb=" O ILE C 481 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AB9, first strand: chain 'D' and resid 394 through 399 Processing sheet with id=AC1, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC2, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC3, first strand: chain 'D' and resid 646 through 649 removed outlier: 6.666A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 646 through 649 removed outlier: 6.666A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 34 through 38 Processing sheet with id=AC6, first strand: chain 'F' and resid 34 through 35 Processing sheet with id=AC7, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AC8, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.753A pdb=" N LYS F 78 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AD1, first strand: chain 'H' and resid 36 through 38 Processing sheet with id=AD2, first strand: chain 'H' and resid 65 through 67 1115 hydrogen bonds defined for protein. 3258 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.94 Time building geometry restraints manager: 7.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2625 1.30 - 1.43: 4982 1.43 - 1.56: 9603 1.56 - 1.69: 0 1.69 - 1.82: 192 Bond restraints: 17402 Sorted by residual: bond pdb=" C LEU D 624 " pdb=" O LEU D 624 " ideal model delta sigma weight residual 1.235 1.306 -0.070 1.26e-02 6.30e+03 3.11e+01 bond pdb=" C PHE D 584 " pdb=" O PHE D 584 " ideal model delta sigma weight residual 1.237 1.172 0.065 1.19e-02 7.06e+03 2.99e+01 bond pdb=" CA SER A 592 " pdb=" CB SER A 592 " ideal model delta sigma weight residual 1.535 1.470 0.065 1.21e-02 6.83e+03 2.88e+01 bond pdb=" CA SER C 592 " pdb=" CB SER C 592 " ideal model delta sigma weight residual 1.536 1.460 0.076 1.48e-02 4.57e+03 2.64e+01 bond pdb=" C PHE A 584 " pdb=" O PHE A 584 " ideal model delta sigma weight residual 1.237 1.179 0.058 1.19e-02 7.06e+03 2.38e+01 ... (remaining 17397 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.55: 309 105.55 - 112.84: 9171 112.84 - 120.13: 9242 120.13 - 127.42: 4765 127.42 - 134.71: 149 Bond angle restraints: 23636 Sorted by residual: angle pdb=" N LEU C 620 " pdb=" CA LEU C 620 " pdb=" C LEU C 620 " ideal model delta sigma weight residual 113.37 102.49 10.88 1.38e+00 5.25e-01 6.22e+01 angle pdb=" N GLU A 772 " pdb=" CA GLU A 772 " pdb=" C GLU A 772 " ideal model delta sigma weight residual 113.61 102.23 11.38 1.50e+00 4.44e-01 5.75e+01 angle pdb=" O PHE D 623 " pdb=" C PHE D 623 " pdb=" N LEU D 624 " ideal model delta sigma weight residual 122.59 113.24 9.35 1.33e+00 5.65e-01 4.94e+01 angle pdb=" N ASP C 590 " pdb=" CA ASP C 590 " pdb=" C ASP C 590 " ideal model delta sigma weight residual 113.88 105.67 8.21 1.23e+00 6.61e-01 4.45e+01 angle pdb=" N LEU B 803 " pdb=" CA LEU B 803 " pdb=" C LEU B 803 " ideal model delta sigma weight residual 111.28 104.46 6.82 1.09e+00 8.42e-01 3.91e+01 ... (remaining 23631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8935 17.90 - 35.80: 866 35.80 - 53.70: 145 53.70 - 71.60: 24 71.60 - 89.49: 11 Dihedral angle restraints: 9981 sinusoidal: 3429 harmonic: 6552 Sorted by residual: dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual 93.00 22.51 70.49 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" CB CYS G 40 " pdb=" SG CYS G 40 " pdb=" SG CYS G 68 " pdb=" CB CYS G 68 " ideal model delta sinusoidal sigma weight residual 93.00 39.50 53.50 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 68 " pdb=" CB CYS E 68 " ideal model delta sinusoidal sigma weight residual 93.00 41.10 51.90 1 1.00e+01 1.00e-02 3.68e+01 ... (remaining 9978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 916 0.066 - 0.132: 1035 0.132 - 0.198: 614 0.198 - 0.264: 163 0.264 - 0.329: 11 Chirality restraints: 2739 Sorted by residual: chirality pdb=" CA CYS C 589 " pdb=" N CYS C 589 " pdb=" C CYS C 589 " pdb=" CB CYS C 589 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB VAL D 795 " pdb=" CA VAL D 795 " pdb=" CG1 VAL D 795 " pdb=" CG2 VAL D 795 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ILE C 734 " pdb=" N ILE C 734 " pdb=" C ILE C 734 " pdb=" CB ILE C 734 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 2736 not shown) Planarity restraints: 2905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 623 " 0.072 2.00e-02 2.50e+03 1.37e-01 1.88e+02 pdb=" C PHE D 623 " -0.237 2.00e-02 2.50e+03 pdb=" O PHE D 623 " 0.092 2.00e-02 2.50e+03 pdb=" N LEU D 624 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BPHE D 574 " -0.032 2.00e-02 2.50e+03 6.58e-02 4.33e+01 pdb=" C BPHE D 574 " 0.114 2.00e-02 2.50e+03 pdb=" O BPHE D 574 " -0.042 2.00e-02 2.50e+03 pdb=" N ASN D 575 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 420 " 0.521 9.50e-02 1.11e+02 2.33e-01 3.34e+01 pdb=" NE ARG B 420 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG B 420 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 420 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 420 " 0.019 2.00e-02 2.50e+03 ... (remaining 2902 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1656 2.71 - 3.26: 18508 3.26 - 3.81: 26906 3.81 - 4.35: 35539 4.35 - 4.90: 56841 Nonbonded interactions: 139450 Sorted by model distance: nonbonded pdb=" O PHE D 623 " pdb=" N THR D 625 " model vdw 2.163 2.520 nonbonded pdb=" O LYS E 129 " pdb=" OG1 THR E 130 " model vdw 2.232 2.440 nonbonded pdb=" O SER E 104 " pdb=" N ILE E 106 " model vdw 2.248 2.520 nonbonded pdb=" O ASP A 427 " pdb=" OE1 GLU A 431 " model vdw 2.293 3.040 nonbonded pdb=" O ASP B 427 " pdb=" OE1 GLU B 431 " model vdw 2.293 3.040 ... (remaining 139445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 549 or (resid 550 and (name N or name CA or na \ me C or name O or name CB )) or resid 551 through 573 or resid 575 through 593 o \ r (resid 594 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 95 through 624 or resid 633 through 773 or resid 785 through 812 or (resid 813 a \ nd (name N or name CA or name C or name O or name CB )) or resid 814 through 818 \ or (resid 819 through 823 and (name N or name CA or name C or name O or name CB \ )))) selection = (chain 'B' and (resid 393 through 506 or resid 513 through 549 or (resid 550 and \ (name N or name CA or name C or name O or name CB )) or resid 551 or (resid 569 \ and (name N or name CA or name C or name O or name CB )) or resid 570 through 5 \ 73 or resid 575 or (resid 576 and (name N or name CA or name C or name O or name \ CB )) or resid 577 through 593 or (resid 594 and (name N or name CA or name C o \ r name O or name CB )) or resid 595 through 773 or resid 785 through 823)) selection = (chain 'C' and (resid 393 through 506 or resid 513 through 573 or resid 575 or ( \ resid 576 and (name N or name CA or name C or name O or name CB )) or resid 577 \ through 624 or resid 633 through 812 or (resid 813 and (name N or name CA or nam \ e C or name O or name CB )) or resid 814 through 818 or (resid 819 through 823 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 393 through 506 or resid 513 through 549 or (resid 550 and \ (name N or name CA or name C or name O or name CB )) or resid 551 or (resid 569 \ and (name N or name CA or name C or name O or name CB )) or resid 570 through 5 \ 73 or resid 575 or (resid 576 and (name N or name CA or name C or name O or name \ CB )) or resid 577 through 593 or (resid 594 and (name N or name CA or name C o \ r name O or name CB )) or resid 595 through 624 or resid 633 or (resid 634 and ( \ name N or name CA or name C or name O or name CB )) or resid 635 through 823)) } ncs_group { reference = (chain 'E' and (resid 5 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 42 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 69 or (resid 70 and (n \ ame N or name CA or name C or name O or name CB )) or resid 71 through 84 or res \ id 93 through 210)) selection = (chain 'F' and (resid 5 through 42 or resid 56 through 84 or resid 93 through 21 \ 0)) selection = (chain 'G' and (resid 5 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 42 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 69 or (resid 70 and (n \ ame N or name CA or name C or name O or name CB )) or resid 71 through 84 or res \ id 93 through 210)) selection = (chain 'H' and (resid 5 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 42 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 69 or (resid 70 and (n \ ame N or name CA or name C or name O or name CB )) or resid 71 through 210)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 4.540 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 52.540 Find NCS groups from input model: 1.300 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 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 : 0.013 0.081 17402 Z= 0.840 Angle : 1.692 11.379 23636 Z= 1.280 Chirality : 0.115 0.329 2739 Planarity : 0.014 0.233 2905 Dihedral : 14.446 89.494 5759 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.45 % Favored : 95.01 % Rotamer: Outliers : 2.22 % Allowed : 7.02 % Favored : 90.76 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 22.22 % 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: -1.70 (0.15), residues: 2231 helix: -0.32 (0.12), residues: 1292 sheet: -2.10 (0.38), residues: 146 loop : -2.18 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.006 TRP C 767 HIS 0.010 0.002 HIS H 205 PHE 0.055 0.004 PHE C 667 TYR 0.046 0.004 TYR C 700 ARG 0.018 0.001 ARG C 694 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 426 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 ASP cc_start: 0.8831 (p0) cc_final: 0.8330 (p0) REVERT: A 591 ILE cc_start: 0.9193 (tp) cc_final: 0.8993 (pt) REVERT: A 594 ARG cc_start: 0.9623 (mtm-85) cc_final: 0.9402 (ttm110) REVERT: C 422 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5857 (pm20) REVERT: C 730 LYS cc_start: -0.2508 (OUTLIER) cc_final: -0.3624 (ttmt) REVERT: D 493 LYS cc_start: 0.5694 (OUTLIER) cc_final: 0.5035 (mmmt) REVERT: D 506 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6454 (tptp) REVERT: D 533 TYR cc_start: 0.9090 (t80) cc_final: 0.8755 (t80) REVERT: D 545 ARG cc_start: 0.9144 (mtm180) cc_final: 0.8701 (mmm-85) REVERT: D 576 SER cc_start: 0.9592 (m) cc_final: 0.9357 (p) REVERT: E 24 MET cc_start: 0.8910 (tpt) cc_final: 0.8663 (tpt) REVERT: E 200 MET cc_start: 0.9331 (mtm) cc_final: 0.9060 (mtt) REVERT: F 76 LEU cc_start: 0.8270 (mm) cc_final: 0.7952 (tt) REVERT: F 174 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.8187 (p90) REVERT: F 206 LYS cc_start: 0.9246 (mtpt) cc_final: 0.8959 (mmmt) REVERT: G 126 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8909 (pt0) REVERT: H 13 THR cc_start: 0.9466 (m) cc_final: 0.9015 (t) REVERT: H 24 MET cc_start: 0.9574 (tpt) cc_final: 0.9355 (tpp) REVERT: H 83 PHE cc_start: 0.8196 (m-80) cc_final: 0.7900 (m-80) REVERT: H 192 MET cc_start: 0.8704 (mtt) cc_final: 0.8460 (mtp) outliers start: 37 outliers final: 10 residues processed: 451 average time/residue: 0.3352 time to fit residues: 213.7768 Evaluate side-chains 256 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 241 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 747 ASN Chi-restraints excluded: chain D residue 493 LYS Chi-restraints excluded: chain D residue 506 LYS Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain F residue 174 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 0.6980 chunk 170 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 176 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 131 optimal weight: 0.7980 chunk 204 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN B 412 HIS B 619 ASN C 726 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN H 133 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 17402 Z= 0.187 Angle : 0.609 11.844 23636 Z= 0.323 Chirality : 0.042 0.291 2739 Planarity : 0.004 0.054 2905 Dihedral : 5.125 58.905 2470 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.80 % Favored : 98.07 % Rotamer: Outliers : 2.10 % Allowed : 16.50 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.64 (0.18), residues: 2231 helix: 1.88 (0.14), residues: 1316 sheet: -1.88 (0.33), residues: 177 loop : -1.72 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 766 HIS 0.007 0.001 HIS H 60 PHE 0.020 0.001 PHE F 97 TYR 0.017 0.001 TYR A 673 ARG 0.007 0.001 ARG D 586 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 286 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 ASP cc_start: 0.8842 (p0) cc_final: 0.8352 (p0) REVERT: A 594 ARG cc_start: 0.9612 (mtm-85) cc_final: 0.9364 (ttm110) REVERT: A 817 LYS cc_start: 0.9297 (mtpt) cc_final: 0.9033 (mtpp) REVERT: C 463 MET cc_start: 0.2934 (mtp) cc_final: 0.2537 (mtm) REVERT: C 496 MET cc_start: 0.1362 (ptm) cc_final: 0.0999 (mtp) REVERT: C 670 MET cc_start: 0.6697 (mmp) cc_final: 0.5730 (mmm) REVERT: C 730 LYS cc_start: -0.2576 (OUTLIER) cc_final: -0.3669 (ttmt) REVERT: C 791 ASN cc_start: 0.8864 (m110) cc_final: 0.8583 (m110) REVERT: D 493 LYS cc_start: 0.5597 (OUTLIER) cc_final: 0.4888 (mmmt) REVERT: D 545 ARG cc_start: 0.8907 (mtm180) cc_final: 0.8620 (mtp180) REVERT: D 670 MET cc_start: 0.6893 (mmm) cc_final: 0.6653 (mmm) REVERT: E 203 ASP cc_start: 0.9413 (t0) cc_final: 0.9175 (t0) REVERT: E 206 LYS cc_start: 0.9036 (mmmt) cc_final: 0.8707 (mttp) REVERT: F 76 LEU cc_start: 0.8233 (mm) cc_final: 0.7943 (tp) REVERT: F 140 ILE cc_start: 0.9534 (mm) cc_final: 0.9306 (tp) REVERT: F 174 TYR cc_start: 0.8510 (p90) cc_final: 0.8146 (p90) REVERT: F 206 LYS cc_start: 0.9212 (mtpt) cc_final: 0.8854 (mmmt) REVERT: G 56 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8825 (mm-30) REVERT: G 78 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8901 (pttt) REVERT: G 95 GLU cc_start: 0.9400 (tp30) cc_final: 0.9103 (tm-30) REVERT: H 13 THR cc_start: 0.9463 (m) cc_final: 0.9036 (t) REVERT: H 24 MET cc_start: 0.9495 (tpt) cc_final: 0.8819 (tpp) REVERT: H 70 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8711 (pp20) REVERT: H 83 PHE cc_start: 0.8140 (m-80) cc_final: 0.7854 (m-80) REVERT: H 99 ARG cc_start: 0.9166 (tpp-160) cc_final: 0.8948 (tpp80) outliers start: 35 outliers final: 11 residues processed: 311 average time/residue: 0.3226 time to fit residues: 144.0168 Evaluate side-chains 246 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 232 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 493 LYS Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 170 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 202 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 756 GLN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS F 149 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN G 205 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17402 Z= 0.176 Angle : 0.569 12.431 23636 Z= 0.297 Chirality : 0.040 0.254 2739 Planarity : 0.004 0.044 2905 Dihedral : 4.197 52.760 2444 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.98 % Favored : 97.89 % Rotamer: Outliers : 3.18 % Allowed : 16.74 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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 (0.18), residues: 2231 helix: 2.46 (0.14), residues: 1324 sheet: -1.86 (0.36), residues: 164 loop : -1.37 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 766 HIS 0.006 0.001 HIS A 435 PHE 0.014 0.001 PHE F 97 TYR 0.012 0.001 TYR A 673 ARG 0.007 0.001 ARG D 684 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 246 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ARG cc_start: 0.9614 (mtm-85) cc_final: 0.9377 (ttm110) REVERT: A 817 LYS cc_start: 0.9332 (mtpt) cc_final: 0.9071 (mtpp) REVERT: B 787 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9075 (tp) REVERT: C 463 MET cc_start: 0.2850 (mtp) cc_final: 0.2416 (mtm) REVERT: C 670 MET cc_start: 0.5328 (mmp) cc_final: 0.5098 (mmm) REVERT: C 730 LYS cc_start: -0.2869 (OUTLIER) cc_final: -0.3436 (ttmt) REVERT: C 791 ASN cc_start: 0.8827 (m110) cc_final: 0.8572 (m110) REVERT: D 519 ASP cc_start: 0.9269 (m-30) cc_final: 0.9064 (t70) REVERT: D 545 ARG cc_start: 0.8935 (mtm180) cc_final: 0.8370 (mtp180) REVERT: D 550 GLU cc_start: 0.7502 (tm-30) cc_final: 0.6993 (pp20) REVERT: E 206 LYS cc_start: 0.9031 (mmmt) cc_final: 0.8669 (mttp) REVERT: F 76 LEU cc_start: 0.8202 (mm) cc_final: 0.7893 (tp) REVERT: F 206 LYS cc_start: 0.9207 (mtpt) cc_final: 0.8856 (mmmt) REVERT: G 95 GLU cc_start: 0.9420 (tp30) cc_final: 0.9125 (tm-30) REVERT: H 13 THR cc_start: 0.9457 (m) cc_final: 0.9039 (t) REVERT: H 24 MET cc_start: 0.9480 (tpt) cc_final: 0.8785 (tpp) REVERT: H 69 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8146 (pp) REVERT: H 83 PHE cc_start: 0.8143 (m-80) cc_final: 0.7820 (m-80) outliers start: 53 outliers final: 31 residues processed: 285 average time/residue: 0.3025 time to fit residues: 126.8422 Evaluate side-chains 263 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 229 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 787 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 493 LYS Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 202 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 217 optimal weight: 1.9990 chunk 107 optimal weight: 40.0000 chunk 194 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 756 GLN B 461 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17402 Z= 0.306 Angle : 0.609 9.845 23636 Z= 0.318 Chirality : 0.041 0.190 2739 Planarity : 0.004 0.050 2905 Dihedral : 4.139 54.132 2442 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.43 % Favored : 97.44 % Rotamer: Outliers : 3.84 % Allowed : 16.98 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 1.51 (0.18), residues: 2231 helix: 2.55 (0.14), residues: 1324 sheet: -1.68 (0.35), residues: 182 loop : -1.30 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 605 HIS 0.029 0.002 HIS E 205 PHE 0.020 0.001 PHE C 658 TYR 0.016 0.001 TYR D 700 ARG 0.007 0.001 ARG C 586 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 226 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ARG cc_start: 0.9614 (mtm-85) cc_final: 0.9385 (ttm110) REVERT: A 817 LYS cc_start: 0.9379 (mtpt) cc_final: 0.9082 (mtpp) REVERT: C 463 MET cc_start: 0.2978 (mtp) cc_final: 0.2453 (mtm) REVERT: C 670 MET cc_start: 0.5388 (mmp) cc_final: 0.5162 (mmm) REVERT: C 791 ASN cc_start: 0.9063 (m110) cc_final: 0.8854 (m110) REVERT: D 545 ARG cc_start: 0.8929 (mtm180) cc_final: 0.8497 (mtp180) REVERT: D 674 MET cc_start: 0.6531 (mpp) cc_final: 0.6028 (mpp) REVERT: E 191 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8916 (mm-30) REVERT: E 205 HIS cc_start: 0.8915 (OUTLIER) cc_final: 0.8529 (t-90) REVERT: E 206 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8673 (mttp) REVERT: F 76 LEU cc_start: 0.8202 (mm) cc_final: 0.7843 (tp) REVERT: F 206 LYS cc_start: 0.9268 (mtpt) cc_final: 0.8889 (mmmt) REVERT: G 95 GLU cc_start: 0.9392 (tp30) cc_final: 0.9112 (tm-30) REVERT: H 13 THR cc_start: 0.9463 (m) cc_final: 0.9042 (t) REVERT: H 69 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8010 (pp) REVERT: H 70 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8593 (pp20) outliers start: 64 outliers final: 42 residues processed: 277 average time/residue: 0.3038 time to fit residues: 124.2485 Evaluate side-chains 253 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 209 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 493 LYS Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 181 optimal weight: 9.9990 chunk 123 optimal weight: 0.0470 chunk 3 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 150 optimal weight: 0.0000 chunk 0 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 chunk 195 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN D 461 ASN ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN E 205 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17402 Z= 0.214 Angle : 0.594 11.725 23636 Z= 0.308 Chirality : 0.040 0.177 2739 Planarity : 0.004 0.043 2905 Dihedral : 4.021 51.932 2438 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.38 % Favored : 97.53 % Rotamer: Outliers : 3.18 % Allowed : 18.36 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 1.66 (0.19), residues: 2231 helix: 2.62 (0.14), residues: 1330 sheet: -1.47 (0.38), residues: 169 loop : -1.22 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 766 HIS 0.006 0.001 HIS B 412 PHE 0.022 0.001 PHE H 73 TYR 0.013 0.001 TYR D 700 ARG 0.007 0.001 ARG D 586 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 235 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ARG cc_start: 0.9602 (mtm-85) cc_final: 0.9379 (ttm110) REVERT: A 817 LYS cc_start: 0.9394 (mtpt) cc_final: 0.9149 (mtpp) REVERT: C 463 MET cc_start: 0.2822 (mtp) cc_final: 0.2471 (mtm) REVERT: C 586 ARG cc_start: 0.9550 (mmm-85) cc_final: 0.9316 (tpp80) REVERT: C 791 ASN cc_start: 0.9060 (m110) cc_final: 0.8812 (m110) REVERT: D 545 ARG cc_start: 0.8896 (mtm180) cc_final: 0.8400 (mtp180) REVERT: D 623 PHE cc_start: 0.6794 (OUTLIER) cc_final: 0.6474 (m-10) REVERT: E 160 ASN cc_start: 0.9063 (OUTLIER) cc_final: 0.8722 (t0) REVERT: E 206 LYS cc_start: 0.9043 (mmmt) cc_final: 0.8630 (mttp) REVERT: F 206 LYS cc_start: 0.9217 (mtpt) cc_final: 0.8871 (mmmt) REVERT: G 95 GLU cc_start: 0.9419 (tp30) cc_final: 0.9145 (tm-30) REVERT: H 13 THR cc_start: 0.9456 (m) cc_final: 0.9023 (t) REVERT: H 41 LYS cc_start: 0.8698 (tmmt) cc_final: 0.8287 (mmtt) REVERT: H 69 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7979 (pp) REVERT: H 70 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8673 (pp20) outliers start: 53 outliers final: 33 residues processed: 274 average time/residue: 0.3030 time to fit residues: 121.3154 Evaluate side-chains 243 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 207 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 493 LYS Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 73 optimal weight: 10.0000 chunk 195 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 180 optimal weight: 20.0000 chunk 100 optimal weight: 30.0000 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN C 412 HIS ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** E 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 17402 Z= 0.418 Angle : 0.701 9.039 23636 Z= 0.363 Chirality : 0.043 0.194 2739 Planarity : 0.004 0.046 2905 Dihedral : 4.335 55.640 2438 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.24 % Favored : 96.67 % Rotamer: Outliers : 3.84 % Allowed : 18.30 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.46 (0.18), residues: 2231 helix: 2.42 (0.14), residues: 1322 sheet: -1.53 (0.39), residues: 162 loop : -1.17 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 33 HIS 0.004 0.001 HIS H 205 PHE 0.020 0.002 PHE H 73 TYR 0.020 0.002 TYR D 700 ARG 0.007 0.001 ARG D 684 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 212 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 ASP cc_start: 0.9402 (p0) cc_final: 0.9183 (p0) REVERT: A 594 ARG cc_start: 0.9586 (mtm-85) cc_final: 0.9355 (ttm110) REVERT: B 674 MET cc_start: 0.1308 (ptt) cc_final: -0.0523 (ttt) REVERT: C 463 MET cc_start: 0.2957 (mtp) cc_final: 0.2409 (mtm) REVERT: C 620 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8852 (tp) REVERT: C 791 ASN cc_start: 0.9119 (m110) cc_final: 0.8696 (m110) REVERT: D 503 MET cc_start: 0.5917 (mmp) cc_final: 0.5515 (mmp) REVERT: D 623 PHE cc_start: 0.6860 (OUTLIER) cc_final: 0.6193 (m-80) REVERT: E 206 LYS cc_start: 0.9001 (mmmt) cc_final: 0.8664 (mttp) REVERT: F 206 LYS cc_start: 0.9325 (mtpt) cc_final: 0.8912 (mmmt) REVERT: G 60 HIS cc_start: 0.8980 (OUTLIER) cc_final: 0.8714 (p90) REVERT: G 95 GLU cc_start: 0.9409 (tp30) cc_final: 0.9148 (tm-30) REVERT: H 13 THR cc_start: 0.9464 (m) cc_final: 0.9035 (t) REVERT: H 69 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7934 (pp) REVERT: H 70 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8630 (pp20) outliers start: 64 outliers final: 48 residues processed: 259 average time/residue: 0.2957 time to fit residues: 114.5363 Evaluate side-chains 246 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 194 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 688 GLU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 493 LYS Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 60 HIS Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 209 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 124 optimal weight: 0.5980 chunk 158 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 183 optimal weight: 0.6980 chunk 121 optimal weight: 8.9990 chunk 216 optimal weight: 0.2980 chunk 135 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 100 optimal weight: 30.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN D 569 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17402 Z= 0.176 Angle : 0.608 9.511 23636 Z= 0.310 Chirality : 0.040 0.179 2739 Planarity : 0.004 0.050 2905 Dihedral : 4.065 51.396 2438 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.43 % Favored : 97.48 % Rotamer: Outliers : 2.28 % Allowed : 20.88 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 1.69 (0.19), residues: 2231 helix: 2.64 (0.14), residues: 1327 sheet: -1.56 (0.39), residues: 167 loop : -1.15 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 178 HIS 0.004 0.001 HIS B 412 PHE 0.016 0.001 PHE H 73 TYR 0.016 0.001 TYR F 174 ARG 0.008 0.001 ARG D 684 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 211 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.5422 (mmt) cc_final: 0.4781 (mmp) REVERT: A 590 ASP cc_start: 0.9368 (p0) cc_final: 0.9143 (p0) REVERT: A 594 ARG cc_start: 0.9595 (mtm-85) cc_final: 0.9371 (ttm110) REVERT: B 674 MET cc_start: 0.1938 (ptt) cc_final: -0.0035 (ttt) REVERT: C 463 MET cc_start: 0.2845 (mtp) cc_final: 0.2423 (mtm) REVERT: C 791 ASN cc_start: 0.9055 (m110) cc_final: 0.8841 (m110) REVERT: D 503 MET cc_start: 0.5935 (mmp) cc_final: 0.5681 (mmp) REVERT: D 623 PHE cc_start: 0.6362 (OUTLIER) cc_final: 0.5960 (m-10) REVERT: D 674 MET cc_start: 0.6521 (mpp) cc_final: 0.5949 (mpp) REVERT: E 205 HIS cc_start: 0.8650 (OUTLIER) cc_final: 0.7967 (t-90) REVERT: F 206 LYS cc_start: 0.9277 (mtpt) cc_final: 0.8875 (mmmt) REVERT: G 60 HIS cc_start: 0.8875 (OUTLIER) cc_final: 0.8636 (p90) REVERT: G 95 GLU cc_start: 0.9393 (tp30) cc_final: 0.9110 (tm-30) REVERT: H 13 THR cc_start: 0.9455 (m) cc_final: 0.9006 (t) REVERT: H 69 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7952 (pp) REVERT: H 70 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8727 (pp20) outliers start: 38 outliers final: 27 residues processed: 242 average time/residue: 0.2984 time to fit residues: 107.2610 Evaluate side-chains 227 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 196 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 493 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 703 LEU Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 60 HIS Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 160 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 134 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 137 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 197 optimal weight: 0.2980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN C 587 GLN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17402 Z= 0.260 Angle : 0.622 9.901 23636 Z= 0.321 Chirality : 0.040 0.174 2739 Planarity : 0.004 0.047 2905 Dihedral : 4.087 52.945 2438 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.79 % Favored : 97.12 % Rotamer: Outliers : 2.64 % Allowed : 20.94 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 1.68 (0.19), residues: 2231 helix: 2.60 (0.14), residues: 1333 sheet: -1.42 (0.40), residues: 162 loop : -1.17 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 766 HIS 0.004 0.001 HIS B 412 PHE 0.027 0.001 PHE H 73 TYR 0.015 0.001 TYR D 732 ARG 0.008 0.001 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 208 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 ASP cc_start: 0.9395 (p0) cc_final: 0.9180 (p0) REVERT: A 594 ARG cc_start: 0.9601 (mtm-85) cc_final: 0.9376 (ttm110) REVERT: B 407 MET cc_start: 0.3644 (mmm) cc_final: 0.3438 (mmm) REVERT: B 708 MET cc_start: 0.2975 (ptp) cc_final: 0.2620 (ptm) REVERT: C 463 MET cc_start: 0.2852 (mtp) cc_final: 0.2407 (mtm) REVERT: C 791 ASN cc_start: 0.8998 (m110) cc_final: 0.8681 (m-40) REVERT: D 623 PHE cc_start: 0.6638 (OUTLIER) cc_final: 0.6269 (m-10) REVERT: D 674 MET cc_start: 0.6470 (mpp) cc_final: 0.5923 (mpp) REVERT: E 128 TYR cc_start: 0.7835 (t80) cc_final: 0.7621 (t80) REVERT: E 205 HIS cc_start: 0.8706 (OUTLIER) cc_final: 0.7974 (t-90) REVERT: F 206 LYS cc_start: 0.9312 (mtpt) cc_final: 0.8895 (mmmt) REVERT: G 60 HIS cc_start: 0.8910 (OUTLIER) cc_final: 0.8588 (p90) REVERT: G 70 GLU cc_start: 0.8432 (pp20) cc_final: 0.7939 (pp20) REVERT: G 95 GLU cc_start: 0.9382 (tp30) cc_final: 0.9118 (tm-30) REVERT: H 69 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8167 (pp) REVERT: H 70 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8640 (pp20) outliers start: 44 outliers final: 37 residues processed: 244 average time/residue: 0.3056 time to fit residues: 110.7027 Evaluate side-chains 237 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 196 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 493 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 703 LEU Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 60 HIS Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 207 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 chunk 88 optimal weight: 30.0000 chunk 158 optimal weight: 7.9990 chunk 62 optimal weight: 50.0000 chunk 182 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 201 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17402 Z= 0.328 Angle : 0.667 11.113 23636 Z= 0.344 Chirality : 0.041 0.181 2739 Planarity : 0.004 0.051 2905 Dihedral : 4.239 52.728 2438 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.01 % Favored : 96.90 % Rotamer: Outliers : 2.94 % Allowed : 21.00 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 1.60 (0.19), residues: 2231 helix: 2.53 (0.14), residues: 1328 sheet: -1.39 (0.40), residues: 161 loop : -1.16 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 766 HIS 0.004 0.001 HIS E 205 PHE 0.027 0.001 PHE H 73 TYR 0.015 0.001 TYR D 700 ARG 0.008 0.001 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 200 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 ASP cc_start: 0.9409 (p0) cc_final: 0.9199 (p0) REVERT: A 594 ARG cc_start: 0.9609 (mtm-85) cc_final: 0.9392 (ttm110) REVERT: B 708 MET cc_start: 0.2967 (ptp) cc_final: 0.2692 (ptm) REVERT: C 463 MET cc_start: 0.3034 (mtp) cc_final: 0.2679 (mtm) REVERT: C 496 MET cc_start: 0.1127 (mtt) cc_final: 0.0770 (mtm) REVERT: C 587 GLN cc_start: 0.9053 (tp-100) cc_final: 0.8790 (tp40) REVERT: C 791 ASN cc_start: 0.9106 (m110) cc_final: 0.8759 (m110) REVERT: D 623 PHE cc_start: 0.6696 (OUTLIER) cc_final: 0.6362 (m-10) REVERT: D 674 MET cc_start: 0.6343 (mpp) cc_final: 0.5896 (mpp) REVERT: E 205 HIS cc_start: 0.8665 (OUTLIER) cc_final: 0.8088 (t-90) REVERT: F 13 THR cc_start: 0.9167 (m) cc_final: 0.8845 (t) REVERT: F 206 LYS cc_start: 0.9333 (mtpt) cc_final: 0.8910 (mmmt) REVERT: G 60 HIS cc_start: 0.8908 (OUTLIER) cc_final: 0.8549 (p90) REVERT: G 70 GLU cc_start: 0.8460 (pp20) cc_final: 0.7985 (pp20) REVERT: G 95 GLU cc_start: 0.9381 (tp30) cc_final: 0.9114 (tm-30) REVERT: H 13 THR cc_start: 0.9463 (m) cc_final: 0.9016 (t) REVERT: H 69 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8398 (pp) outliers start: 49 outliers final: 42 residues processed: 239 average time/residue: 0.2946 time to fit residues: 106.6117 Evaluate side-chains 241 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 195 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 493 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 703 LEU Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain D residue 760 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 60 HIS Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 101 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 224 optimal weight: 0.7980 chunk 206 optimal weight: 0.8980 chunk 178 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 109 optimal weight: 30.0000 chunk 141 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17402 Z= 0.175 Angle : 0.638 12.117 23636 Z= 0.324 Chirality : 0.040 0.192 2739 Planarity : 0.004 0.047 2905 Dihedral : 4.135 49.394 2438 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.43 % Favored : 97.48 % Rotamer: Outliers : 2.04 % Allowed : 21.72 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 1.73 (0.19), residues: 2231 helix: 2.64 (0.14), residues: 1334 sheet: -1.30 (0.41), residues: 157 loop : -1.18 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 178 HIS 0.003 0.001 HIS E 132 PHE 0.024 0.001 PHE H 73 TYR 0.016 0.001 TYR D 732 ARG 0.008 0.001 ARG B 594 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 216 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ARG cc_start: 0.9306 (mtp85) cc_final: 0.9097 (mtp85) REVERT: A 590 ASP cc_start: 0.9388 (p0) cc_final: 0.9161 (p0) REVERT: A 594 ARG cc_start: 0.9603 (mtm-85) cc_final: 0.9384 (ttm110) REVERT: B 674 MET cc_start: 0.2008 (ptt) cc_final: 0.0253 (ttm) REVERT: C 463 MET cc_start: 0.3703 (mtp) cc_final: 0.3278 (mtm) REVERT: C 496 MET cc_start: 0.1011 (mtt) cc_final: 0.0675 (mtm) REVERT: C 791 ASN cc_start: 0.9120 (m110) cc_final: 0.8798 (m110) REVERT: D 623 PHE cc_start: 0.6157 (OUTLIER) cc_final: 0.5771 (m-10) REVERT: D 674 MET cc_start: 0.6228 (mpp) cc_final: 0.5809 (mpp) REVERT: E 205 HIS cc_start: 0.8696 (OUTLIER) cc_final: 0.8392 (t-90) REVERT: F 10 MET cc_start: 0.8432 (tmm) cc_final: 0.8207 (tmm) REVERT: F 206 LYS cc_start: 0.9292 (mtpt) cc_final: 0.8876 (mmmt) REVERT: G 70 GLU cc_start: 0.8467 (pp20) cc_final: 0.8019 (pp20) REVERT: G 95 GLU cc_start: 0.9387 (tp30) cc_final: 0.9101 (tm-30) REVERT: H 64 TRP cc_start: 0.8915 (m100) cc_final: 0.8225 (m-10) REVERT: H 69 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8193 (pp) REVERT: H 70 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8592 (pp20) outliers start: 34 outliers final: 27 residues processed: 243 average time/residue: 0.2907 time to fit residues: 105.8981 Evaluate side-chains 239 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 209 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 703 LEU Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 190 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 178 optimal weight: 0.0570 chunk 74 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.133290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.074721 restraints weight = 81019.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.077837 restraints weight = 25729.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.079831 restraints weight = 13748.923| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17402 Z= 0.253 Angle : 0.641 11.664 23636 Z= 0.332 Chirality : 0.040 0.174 2739 Planarity : 0.004 0.049 2905 Dihedral : 3.967 26.497 2434 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.88 % Favored : 97.03 % Rotamer: Outliers : 2.34 % Allowed : 21.54 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 1.65 (0.19), residues: 2231 helix: 2.56 (0.14), residues: 1336 sheet: -1.36 (0.40), residues: 162 loop : -1.17 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 766 HIS 0.004 0.001 HIS G 60 PHE 0.025 0.001 PHE H 73 TYR 0.022 0.001 TYR D 732 ARG 0.008 0.001 ARG B 594 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3668.83 seconds wall clock time: 66 minutes 39.85 seconds (3999.85 seconds total)