Starting phenix.real_space_refine on Tue Nov 19 05:48:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3s_17393/11_2024/8p3s_17393.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3s_17393/11_2024/8p3s_17393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3s_17393/11_2024/8p3s_17393.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3s_17393/11_2024/8p3s_17393.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3s_17393/11_2024/8p3s_17393.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3s_17393/11_2024/8p3s_17393.cif" } resolution = 2.95 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= 0.049 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 127 5.16 5 C 11954 2.51 5 N 2866 2.21 5 O 3243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18195 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3103 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3081 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 15} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Conformer: "B" Number of residues, atoms: 404, 3081 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 15} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 bond proxies already assigned to first conformer: 3125 Chain: "B" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3077 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3015 Classifications: {'peptide': 395} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 383} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 3100 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3078 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Conformer: "B" Number of residues, atoms: 404, 3078 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 bond proxies already assigned to first conformer: 3122 Chain: "E" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1368 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1373 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 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: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1359 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: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'OLC': 1, 'PLM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'PLM': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 4 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 A 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 623 " occ=0.50 residue: pdb=" N APHE D 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 574 " occ=0.50 residue: pdb=" N APHE D 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.50 Time building chain proxies: 13.85, per 1000 atoms: 0.76 Number of scatterers: 18195 At special positions: 0 Unit cell: (118.531, 127.204, 137.323, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 127 16.00 P 5 15.00 O 3243 8.00 N 2866 7.00 C 11954 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=2.02 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=2.05 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.06 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=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.06 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.02 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 - 3.00 Amino acid : True - 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: 5.27 Conformation dependent library (CDL) restraints added in 3.3 seconds 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4208 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 26 sheets defined 60.5% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.727A 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 629 Processing helix chain 'A' and resid 635 through 641 Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 677 removed outlier: 3.678A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.531A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 820 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 416 through 419 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.665A 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 629 removed outlier: 3.735A pdb=" N ARG B 628 " --> pdb=" O LEU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 677 removed outlier: 3.675A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.542A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 792 through 823 removed outlier: 3.590A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS B 823 " --> pdb=" O ARG B 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 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: 3.686A pdb=" N GLU C 550 " --> pdb=" O SER C 547 " (cutoff:3.500A) removed outlier: 3.784A 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 626 Processing helix chain 'C' and resid 635 through 641 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 677 removed outlier: 3.732A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.539A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 792 through 821 removed outlier: 3.765A 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 416 through 419 Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.743A 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: 3.619A pdb=" N TRP D 578 " --> pdb=" O BPHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 677 removed outlier: 3.678A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.545A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 823 removed outlier: 3.539A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (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 125 Processing helix chain 'E' and resid 133 through 161 removed outlier: 3.728A pdb=" N SER E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA E 161 " --> pdb=" O ILE E 157 " (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: 3.506A pdb=" N LEU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 127 removed outlier: 3.900A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 3.876A 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: 3.740A 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: 4.091A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 162 Processing helix chain 'G' and resid 177 through 210 Processing helix chain 'H' and resid 6 through 30 removed outlier: 3.944A pdb=" N MET H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) removed outlier: 3.981A 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 Processing helix chain 'H' and resid 177 through 210 removed outlier: 4.030A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 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 496 through 498 removed outlier: 3.847A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.338A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 440 through 444 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 489 through 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.823A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.316A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 440 through 444 Processing sheet with id=AB3, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB5, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.847A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.352A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 440 through 444 Processing sheet with id=AB8, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC1, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.833A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.327A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 34 through 38 Processing sheet with id=AC4, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AC5, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.794A pdb=" N LYS F 78 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 34 through 38 Processing sheet with id=AC7, first strand: chain 'H' and resid 36 through 38 Processing sheet with id=AC8, first strand: chain 'H' and resid 65 through 67 1131 hydrogen bonds defined for protein. 3272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.51 Time building geometry restraints manager: 5.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2816 1.31 - 1.44: 5174 1.44 - 1.57: 10374 1.57 - 1.71: 10 1.71 - 1.84: 206 Bond restraints: 18580 Sorted by residual: bond pdb=" C PRO B 512 " pdb=" O PRO B 512 " ideal model delta sigma weight residual 1.233 1.178 0.055 1.13e-02 7.83e+03 2.34e+01 bond pdb=" N VAL D 488 " pdb=" CA VAL D 488 " ideal model delta sigma weight residual 1.456 1.498 -0.042 9.50e-03 1.11e+04 1.94e+01 bond pdb=" N VAL C 488 " pdb=" CA VAL C 488 " ideal model delta sigma weight residual 1.456 1.497 -0.041 9.50e-03 1.11e+04 1.86e+01 bond pdb=" C LYS A 506 " pdb=" O LYS A 506 " ideal model delta sigma weight residual 1.238 1.183 0.055 1.28e-02 6.10e+03 1.84e+01 bond pdb=" N VAL B 488 " pdb=" CA VAL B 488 " ideal model delta sigma weight residual 1.456 1.497 -0.041 9.50e-03 1.11e+04 1.83e+01 ... (remaining 18575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 22193 2.24 - 4.48: 2617 4.48 - 6.71: 193 6.71 - 8.95: 27 8.95 - 11.19: 8 Bond angle restraints: 25038 Sorted by residual: angle pdb=" O LYS A 506 " pdb=" C LYS A 506 " pdb=" N PRO A 507 " ideal model delta sigma weight residual 121.32 110.49 10.83 1.15e+00 7.56e-01 8.88e+01 angle pdb=" N ASP C 590 " pdb=" CA ASP C 590 " pdb=" C ASP C 590 " ideal model delta sigma weight residual 113.88 104.62 9.26 1.23e+00 6.61e-01 5.67e+01 angle pdb=" N PRO B 512 " pdb=" CA PRO B 512 " pdb=" C PRO B 512 " ideal model delta sigma weight residual 110.80 100.86 9.94 1.51e+00 4.39e-01 4.33e+01 angle pdb=" C LYS A 506 " pdb=" N PRO A 507 " pdb=" CA PRO A 507 " ideal model delta sigma weight residual 119.84 111.94 7.90 1.25e+00 6.40e-01 4.00e+01 angle pdb=" N PRO B 632 " pdb=" CA PRO B 632 " pdb=" CB PRO B 632 " ideal model delta sigma weight residual 103.25 96.64 6.61 1.05e+00 9.07e-01 3.97e+01 ... (remaining 25033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.03: 10376 29.03 - 58.07: 435 58.07 - 87.10: 52 87.10 - 116.14: 8 116.14 - 145.17: 2 Dihedral angle restraints: 10873 sinusoidal: 4263 harmonic: 6610 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 23.57 69.43 1 1.00e+01 1.00e-02 6.23e+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 35.60 57.40 1 1.00e+01 1.00e-02 4.43e+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 43.29 49.71 1 1.00e+01 1.00e-02 3.39e+01 ... (remaining 10870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 2587 0.173 - 0.347: 197 0.347 - 0.520: 8 0.520 - 0.693: 0 0.693 - 0.866: 1 Chirality restraints: 2793 Sorted by residual: chirality pdb=" CB VAL A 626 " pdb=" CA VAL A 626 " pdb=" CG1 VAL A 626 " pdb=" CG2 VAL A 626 " both_signs ideal model delta sigma weight residual False -2.63 -1.76 -0.87 2.00e-01 2.50e+01 1.88e+01 chirality pdb=" CG LEU A 483 " pdb=" CB LEU A 483 " pdb=" CD1 LEU A 483 " pdb=" CD2 LEU A 483 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 6.04e+00 chirality pdb=" CG LEU D 483 " pdb=" CB LEU D 483 " pdb=" CD1 LEU D 483 " pdb=" CD2 LEU D 483 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.64e+00 ... (remaining 2790 not shown) Planarity restraints: 3050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 628 " 0.693 9.50e-02 1.11e+02 3.11e-01 5.88e+01 pdb=" NE ARG B 628 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG B 628 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 628 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 628 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BPHE D 574 " 0.033 2.00e-02 2.50e+03 6.76e-02 4.56e+01 pdb=" C BPHE D 574 " -0.117 2.00e-02 2.50e+03 pdb=" O BPHE D 574 " 0.044 2.00e-02 2.50e+03 pdb=" N ASN D 575 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 675 " -0.601 9.50e-02 1.11e+02 2.70e-01 4.44e+01 pdb=" NE ARG D 675 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG D 675 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 675 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 675 " -0.021 2.00e-02 2.50e+03 ... (remaining 3047 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2409 2.75 - 3.29: 18613 3.29 - 3.83: 29986 3.83 - 4.36: 37700 4.36 - 4.90: 62814 Nonbonded interactions: 151522 Sorted by model distance: nonbonded pdb=" O LYS E 129 " pdb=" OG1 THR E 130 " model vdw 2.216 3.040 nonbonded pdb=" O GLU B 627 " pdb=" N MET B 629 " model vdw 2.254 3.120 nonbonded pdb=" O SER E 104 " pdb=" N ILE E 106 " model vdw 2.271 3.120 nonbonded pdb=" O GLU H 70 " pdb=" OE1 GLU H 70 " model vdw 2.279 3.040 nonbonded pdb=" OG SER A 592 " pdb=" OD2 ASP B 590 " model vdw 2.287 3.040 ... (remaining 151517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 506 or resid 510 through 573 or resid 575 thro \ ugh 593 or (resid 594 and (name N or name CA or name C or name O or name CB )) o \ r resid 595 through 622 or resid 624 through 626 or (resid 633 through 634 and ( \ name N or name CA or name C or name O or name CB )) or resid 635 through 812 or \ (resid 813 and (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 510 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 622 or resid 624 through 626 or (res \ id 633 through 634 and (name N or name CA or name C or name O or name CB )) or r \ esid 635 through 773 or (resid 784 and (name N or name CA or name C or name O or \ name CB )) or resid 785 through 823)) selection = (chain 'C' and (resid 393 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 622 or resid 624 \ through 626 or (resid 633 through 634 and (name N or name CA or name C or name O \ or name CB )) or resid 635 through 812 or (resid 813 and (name N or name CA or \ name C or name O or name CB )) or resid 814 through 818 or (resid 819 through 82 \ 3 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 393 through 506 or resid 510 through 551 or (resid 569 and \ (name N or name CA or name C or name O or name CB )) or resid 570 through 573 o \ r 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 or na \ me O or name CB )) or resid 595 through 622 or resid 624 through 626 or resid 63 \ 3 through 773 or (resid 784 and (name N or name CA or name C or name O or name C \ B )) or resid 785 through 823)) } ncs_group { reference = (chain 'E' and (resid 5 through 84 or resid 93 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB )) or resid 96 through 203 or (resi \ d 204 and (name N or name CA or name C or name O or name CB )) or resid 205 thro \ ugh 206 or (resid 207 and (name N or name CA or name C or name O or name CB )) o \ r resid 208 through 210)) selection = (chain 'F' and (resid 5 through 42 or resid 55 through 84 or resid 93 through 20 \ 3 or (resid 204 and (name N or name CA or name C or name O or name CB )) or resi \ d 205 through 206 or (resid 207 and (name N or name CA or name C or name O or na \ me CB )) or resid 208 through 210)) selection = (chain 'G' and (resid 5 through 84 or resid 93 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB )) or resid 96 through 203 or (resi \ d 204 and (name N or name CA or name C or name O or name CB )) or resid 205 or ( \ resid 206 through 207 and (name N or name CA or name C or name O or name CB )) o \ r resid 208 through 210)) selection = (chain 'H' and (resid 5 through 42 or resid 55 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB )) or resid 96 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 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: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 47.170 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4965 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 : 0.012 0.064 18580 Z= 0.802 Angle : 1.458 11.189 25038 Z= 1.036 Chirality : 0.107 0.866 2793 Planarity : 0.015 0.311 3050 Dihedral : 15.799 145.169 6629 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.26 % Favored : 95.21 % Rotamer: Outliers : 1.80 % Allowed : 3.66 % Favored : 94.54 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 20.69 % 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: -0.32 (0.17), residues: 2268 helix: 0.97 (0.14), residues: 1332 sheet: -1.68 (0.37), residues: 107 loop : -1.98 (0.19), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.006 TRP B 578 HIS 0.011 0.003 HIS E 60 PHE 0.021 0.005 PHE A 517 TYR 0.034 0.005 TYR B 469 ARG 0.016 0.002 ARG A 628 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 365 time to evaluate : 2.195 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: A 591 ILE cc_start: 0.8820 (tp) cc_final: 0.8549 (pt) REVERT: B 585 MET cc_start: 0.8907 (mmt) cc_final: 0.8300 (mmt) REVERT: E 81 ASP cc_start: 0.8323 (t0) cc_final: 0.7968 (p0) REVERT: E 92 ASP cc_start: 0.7509 (t0) cc_final: 0.7065 (p0) REVERT: E 207 GLN cc_start: 0.8904 (mm110) cc_final: 0.8653 (tm-30) REVERT: F 24 MET cc_start: 0.9162 (tpt) cc_final: 0.8905 (tpt) REVERT: F 61 SER cc_start: 0.9389 (t) cc_final: 0.9060 (p) REVERT: F 65 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.7997 (mtm110) REVERT: F 81 ASP cc_start: 0.8811 (t0) cc_final: 0.8584 (t70) REVERT: F 98 LEU cc_start: 0.8486 (tt) cc_final: 0.8235 (mm) REVERT: F 126 GLU cc_start: 0.9529 (mt-10) cc_final: 0.9191 (tm-30) REVERT: G 13 THR cc_start: 0.9374 (t) cc_final: 0.9027 (p) REVERT: G 81 ASP cc_start: 0.9230 (p0) cc_final: 0.8832 (t0) REVERT: G 84 PRO cc_start: 0.5605 (Cg_exo) cc_final: 0.5203 (Cg_endo) REVERT: G 99 ARG cc_start: 0.9299 (mtt-85) cc_final: 0.8961 (mtm180) REVERT: H 6 ARG cc_start: 0.8404 (tmt-80) cc_final: 0.8176 (tmm160) REVERT: H 10 MET cc_start: 0.9034 (tpp) cc_final: 0.8704 (tpp) REVERT: H 13 THR cc_start: 0.9102 (m) cc_final: 0.8697 (t) REVERT: H 35 TYR cc_start: 0.8828 (m-80) cc_final: 0.8553 (m-80) REVERT: H 61 SER cc_start: 0.9502 (t) cc_final: 0.8932 (p) REVERT: H 70 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8495 (pp20) REVERT: H 74 LYS cc_start: 0.9234 (ttpp) cc_final: 0.8999 (ttmm) outliers start: 33 outliers final: 8 residues processed: 392 average time/residue: 1.5401 time to fit residues: 666.7272 Evaluate side-chains 203 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 195 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 743 ARG Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain E residue 12 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 191 optimal weight: 0.6980 chunk 172 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 177 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 206 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN E 160 ASN F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN H 133 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4984 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 18580 Z= 0.211 Angle : 0.660 17.640 25038 Z= 0.343 Chirality : 0.043 0.230 2793 Planarity : 0.004 0.040 3050 Dihedral : 11.468 104.557 2841 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.99 % Favored : 97.83 % Rotamer: Outliers : 2.24 % Allowed : 13.44 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.17 (0.18), residues: 2268 helix: 2.21 (0.14), residues: 1341 sheet: -1.46 (0.36), residues: 154 loop : -1.38 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 460 HIS 0.006 0.001 HIS B 412 PHE 0.032 0.002 PHE A 658 TYR 0.016 0.001 TYR D 711 ARG 0.009 0.001 ARG D 594 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 239 time to evaluate : 2.271 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: B 408 MET cc_start: 0.2873 (mmm) cc_final: 0.2657 (mmm) REVERT: C 496 MET cc_start: -0.0261 (mtp) cc_final: -0.0897 (mtp) REVERT: C 674 MET cc_start: 0.0013 (ptm) cc_final: -0.0280 (ptp) REVERT: D 414 MET cc_start: 0.4126 (mpt) cc_final: 0.3604 (tmt) REVERT: E 160 ASN cc_start: 0.8855 (m-40) cc_final: 0.8612 (m110) REVERT: F 24 MET cc_start: 0.9107 (tpt) cc_final: 0.8888 (tpt) REVERT: F 61 SER cc_start: 0.9345 (t) cc_final: 0.8978 (p) REVERT: F 65 ARG cc_start: 0.8184 (mtm-85) cc_final: 0.7808 (mtm110) REVERT: F 67 CYS cc_start: 0.8298 (m) cc_final: 0.8091 (m) REVERT: F 81 ASP cc_start: 0.8885 (t0) cc_final: 0.8658 (t70) REVERT: F 126 GLU cc_start: 0.9544 (mt-10) cc_final: 0.9223 (tm-30) REVERT: G 13 THR cc_start: 0.9359 (t) cc_final: 0.9154 (p) REVERT: G 81 ASP cc_start: 0.9191 (p0) cc_final: 0.8758 (t0) REVERT: G 203 ASP cc_start: 0.9088 (m-30) cc_final: 0.8676 (m-30) REVERT: H 6 ARG cc_start: 0.8491 (tmt-80) cc_final: 0.8168 (tmm160) REVERT: H 34 LEU cc_start: 0.9033 (tp) cc_final: 0.8703 (tp) REVERT: H 61 SER cc_start: 0.9211 (t) cc_final: 0.8290 (p) REVERT: H 70 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8781 (pp20) REVERT: H 115 LEU cc_start: 0.9098 (mt) cc_final: 0.8837 (mt) outliers start: 41 outliers final: 7 residues processed: 262 average time/residue: 1.6001 time to fit residues: 465.1923 Evaluate side-chains 187 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 180 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 120 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 114 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 171 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 206 optimal weight: 0.8980 chunk 223 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS F 60 HIS ** 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: 0.5046 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 18580 Z= 0.262 Angle : 0.627 16.026 25038 Z= 0.326 Chirality : 0.043 0.237 2793 Planarity : 0.004 0.042 3050 Dihedral : 10.572 85.446 2828 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.57 % Favored : 97.25 % Rotamer: Outliers : 2.84 % Allowed : 14.91 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.49 (0.18), residues: 2268 helix: 2.36 (0.14), residues: 1347 sheet: -1.09 (0.37), residues: 156 loop : -1.12 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 460 HIS 0.004 0.001 HIS B 412 PHE 0.022 0.002 PHE A 658 TYR 0.030 0.002 TYR A 405 ARG 0.010 0.001 ARG D 660 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 196 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.5756 (mpt) cc_final: 0.5059 (mmt) REVERT: C 674 MET cc_start: -0.0158 (ptm) cc_final: -0.0569 (ptp) REVERT: D 503 MET cc_start: 0.5764 (OUTLIER) cc_final: 0.5268 (tpt) REVERT: E 135 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8497 (pt) REVERT: F 24 MET cc_start: 0.9095 (tpt) cc_final: 0.8866 (tpt) REVERT: F 61 SER cc_start: 0.9171 (t) cc_final: 0.8794 (p) REVERT: F 65 ARG cc_start: 0.8321 (mtm-85) cc_final: 0.7901 (mtm110) REVERT: F 67 CYS cc_start: 0.8278 (m) cc_final: 0.7787 (m) REVERT: F 81 ASP cc_start: 0.8864 (t0) cc_final: 0.8652 (t70) REVERT: G 81 ASP cc_start: 0.9321 (p0) cc_final: 0.8888 (t0) REVERT: H 6 ARG cc_start: 0.8583 (tmt-80) cc_final: 0.8022 (tmm160) REVERT: H 34 LEU cc_start: 0.9183 (tp) cc_final: 0.8727 (tp) REVERT: H 61 SER cc_start: 0.9391 (t) cc_final: 0.8686 (p) REVERT: H 74 LYS cc_start: 0.9161 (ttpp) cc_final: 0.8853 (ttmt) outliers start: 52 outliers final: 13 residues processed: 226 average time/residue: 1.4303 time to fit residues: 361.3469 Evaluate side-chains 188 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 125 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 204 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 587 GLN E 205 HIS F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5045 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 18580 Z= 0.230 Angle : 0.606 13.581 25038 Z= 0.313 Chirality : 0.042 0.307 2793 Planarity : 0.004 0.040 3050 Dihedral : 10.132 88.546 2828 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.26 % Favored : 97.56 % Rotamer: Outliers : 2.95 % Allowed : 15.73 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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 (0.18), residues: 2268 helix: 2.53 (0.14), residues: 1342 sheet: -0.81 (0.39), residues: 147 loop : -1.09 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 671 HIS 0.006 0.001 HIS G 60 PHE 0.019 0.001 PHE H 73 TYR 0.018 0.001 TYR A 424 ARG 0.009 0.001 ARG C 586 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.5606 (mpt) cc_final: 0.5174 (mmt) REVERT: B 721 MET cc_start: 0.5941 (ptm) cc_final: 0.5704 (ptm) REVERT: C 585 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.7806 (mpt) REVERT: C 674 MET cc_start: -0.0186 (ptm) cc_final: -0.0544 (ptp) REVERT: D 503 MET cc_start: 0.5838 (OUTLIER) cc_final: 0.5503 (tpt) REVERT: E 69 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7655 (pp) REVERT: F 61 SER cc_start: 0.9155 (t) cc_final: 0.8761 (p) REVERT: F 65 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.7876 (mtm110) REVERT: F 67 CYS cc_start: 0.8447 (m) cc_final: 0.7991 (m) REVERT: F 76 LEU cc_start: 0.8549 (mm) cc_final: 0.8343 (tt) REVERT: F 81 ASP cc_start: 0.8804 (t0) cc_final: 0.8575 (t70) REVERT: G 81 ASP cc_start: 0.9283 (p0) cc_final: 0.8929 (t0) REVERT: G 99 ARG cc_start: 0.9610 (tpp80) cc_final: 0.9290 (tpp80) REVERT: G 176 TYR cc_start: 0.9324 (m-80) cc_final: 0.9092 (m-80) REVERT: G 200 MET cc_start: 0.9177 (ptp) cc_final: 0.8916 (ptp) REVERT: H 6 ARG cc_start: 0.8610 (tmt-80) cc_final: 0.8121 (tmm160) REVERT: H 34 LEU cc_start: 0.9121 (tp) cc_final: 0.8606 (tp) REVERT: H 35 TYR cc_start: 0.8785 (m-80) cc_final: 0.8533 (m-80) REVERT: H 61 SER cc_start: 0.9466 (t) cc_final: 0.8749 (p) outliers start: 54 outliers final: 16 residues processed: 232 average time/residue: 1.3332 time to fit residues: 348.9244 Evaluate side-chains 196 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 182 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 112 optimal weight: 6.9990 chunk 196 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 HIS G 149 ASN ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5143 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 18580 Z= 0.489 Angle : 0.727 13.509 25038 Z= 0.375 Chirality : 0.048 0.288 2793 Planarity : 0.004 0.043 3050 Dihedral : 10.784 89.594 2828 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.19 % Favored : 96.63 % Rotamer: Outliers : 3.06 % Allowed : 17.48 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.31 (0.18), residues: 2268 helix: 2.13 (0.14), residues: 1349 sheet: -1.08 (0.40), residues: 130 loop : -1.07 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 460 HIS 0.007 0.002 HIS E 60 PHE 0.023 0.002 PHE B 659 TYR 0.024 0.002 TYR A 768 ARG 0.011 0.001 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.4816 (mpt) cc_final: 0.4530 (mmt) REVERT: C 674 MET cc_start: 0.0198 (ptm) cc_final: -0.0249 (ptp) REVERT: D 463 MET cc_start: 0.3698 (mmm) cc_final: 0.3318 (mmp) REVERT: E 80 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8493 (mp) REVERT: F 61 SER cc_start: 0.9365 (t) cc_final: 0.8979 (p) REVERT: F 65 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.7826 (mtm110) REVERT: F 81 ASP cc_start: 0.8839 (t0) cc_final: 0.8637 (t70) REVERT: G 81 ASP cc_start: 0.9234 (p0) cc_final: 0.8858 (t0) REVERT: G 99 ARG cc_start: 0.9610 (tpp80) cc_final: 0.9307 (tpp80) REVERT: H 6 ARG cc_start: 0.8440 (tmt-80) cc_final: 0.7829 (tmm160) outliers start: 56 outliers final: 23 residues processed: 217 average time/residue: 1.1227 time to fit residues: 274.9661 Evaluate side-chains 188 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 73 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 219 optimal weight: 0.8980 chunk 182 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 chunk 72 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN E 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5085 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18580 Z= 0.239 Angle : 0.645 14.112 25038 Z= 0.327 Chirality : 0.043 0.197 2793 Planarity : 0.004 0.042 3050 Dihedral : 10.044 87.069 2828 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.17 % Favored : 97.65 % Rotamer: Outliers : 2.95 % Allowed : 17.80 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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 (0.18), residues: 2268 helix: 2.48 (0.14), residues: 1346 sheet: -0.75 (0.43), residues: 131 loop : -1.00 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 460 HIS 0.006 0.001 HIS G 60 PHE 0.013 0.001 PHE G 73 TYR 0.019 0.001 TYR B 647 ARG 0.007 0.001 ARG C 586 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 187 time to evaluate : 2.320 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 408 MET cc_start: 0.4747 (mpt) cc_final: 0.4453 (mmt) REVERT: B 463 MET cc_start: 0.0751 (mmp) cc_final: 0.0330 (mmm) REVERT: B 721 MET cc_start: 0.6169 (ptm) cc_final: 0.5927 (ptm) REVERT: C 674 MET cc_start: -0.0080 (ptm) cc_final: -0.0347 (ptp) REVERT: F 65 ARG cc_start: 0.8333 (mtm-85) cc_final: 0.7871 (mtm180) REVERT: F 81 ASP cc_start: 0.8813 (t0) cc_final: 0.8594 (t70) REVERT: G 81 ASP cc_start: 0.9161 (p0) cc_final: 0.8815 (t0) REVERT: G 99 ARG cc_start: 0.9594 (tpp80) cc_final: 0.9297 (tpp80) REVERT: G 126 GLU cc_start: 0.9014 (tt0) cc_final: 0.8805 (tp30) REVERT: G 176 TYR cc_start: 0.9446 (m-80) cc_final: 0.9226 (m-80) REVERT: G 205 HIS cc_start: 0.8779 (OUTLIER) cc_final: 0.8450 (t-90) REVERT: H 6 ARG cc_start: 0.8499 (tmt-80) cc_final: 0.8018 (tmm160) REVERT: H 35 TYR cc_start: 0.8843 (m-80) cc_final: 0.8558 (m-80) REVERT: H 61 SER cc_start: 0.9519 (t) cc_final: 0.8830 (p) outliers start: 54 outliers final: 23 residues processed: 226 average time/residue: 1.3411 time to fit residues: 342.0982 Evaluate side-chains 194 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 40 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 211 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 184 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 218 optimal weight: 0.5980 chunk 136 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5091 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18580 Z= 0.252 Angle : 0.665 13.834 25038 Z= 0.333 Chirality : 0.043 0.215 2793 Planarity : 0.004 0.040 3050 Dihedral : 9.820 88.547 2828 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.66 % Favored : 97.16 % Rotamer: Outliers : 2.84 % Allowed : 18.30 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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 (0.18), residues: 2268 helix: 2.48 (0.14), residues: 1345 sheet: -0.67 (0.43), residues: 131 loop : -0.95 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 460 HIS 0.004 0.001 HIS G 60 PHE 0.028 0.001 PHE H 127 TYR 0.019 0.001 TYR B 768 ARG 0.007 0.001 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.4903 (mpt) cc_final: 0.4612 (mmt) REVERT: C 674 MET cc_start: -0.0070 (ptm) cc_final: -0.0289 (ptp) REVERT: F 65 ARG cc_start: 0.8279 (mtm-85) cc_final: 0.7823 (mtm180) REVERT: F 81 ASP cc_start: 0.8814 (t0) cc_final: 0.8585 (t70) REVERT: G 81 ASP cc_start: 0.9142 (p0) cc_final: 0.8820 (t0) REVERT: G 99 ARG cc_start: 0.9600 (tpp80) cc_final: 0.9310 (tpp80) REVERT: G 126 GLU cc_start: 0.9034 (tt0) cc_final: 0.8814 (tp30) REVERT: G 205 HIS cc_start: 0.8764 (OUTLIER) cc_final: 0.8464 (t-90) REVERT: H 6 ARG cc_start: 0.8515 (tmt-80) cc_final: 0.7822 (tmm160) REVERT: H 35 TYR cc_start: 0.8859 (m-80) cc_final: 0.8631 (m-80) REVERT: H 61 SER cc_start: 0.9477 (t) cc_final: 0.8768 (p) REVERT: H 205 HIS cc_start: 0.8731 (OUTLIER) cc_final: 0.7855 (m-70) outliers start: 52 outliers final: 31 residues processed: 222 average time/residue: 1.2973 time to fit residues: 324.4733 Evaluate side-chains 202 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 135 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 20 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 412 HIS ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5119 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18580 Z= 0.344 Angle : 0.707 13.844 25038 Z= 0.354 Chirality : 0.044 0.247 2793 Planarity : 0.004 0.043 3050 Dihedral : 9.887 88.575 2828 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.88 % Favored : 96.94 % Rotamer: Outliers : 2.73 % Allowed : 18.73 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.58 (0.18), residues: 2268 helix: 2.37 (0.14), residues: 1345 sheet: -1.04 (0.44), residues: 123 loop : -0.96 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 460 HIS 0.005 0.001 HIS G 60 PHE 0.016 0.002 PHE F 73 TYR 0.020 0.002 TYR C 647 ARG 0.007 0.001 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ARG cc_start: 0.9297 (mmm-85) cc_final: 0.8608 (tmm160) REVERT: C 674 MET cc_start: 0.0454 (ptm) cc_final: 0.0245 (ptp) REVERT: F 65 ARG cc_start: 0.8260 (mtm-85) cc_final: 0.7823 (mtm180) REVERT: F 81 ASP cc_start: 0.8842 (t0) cc_final: 0.8618 (t70) REVERT: G 81 ASP cc_start: 0.9143 (p0) cc_final: 0.8814 (t0) REVERT: G 99 ARG cc_start: 0.9602 (tpp80) cc_final: 0.9317 (tpp80) REVERT: G 205 HIS cc_start: 0.8737 (OUTLIER) cc_final: 0.8364 (t-90) REVERT: H 6 ARG cc_start: 0.8443 (tmt-80) cc_final: 0.7917 (tmm160) REVERT: H 61 SER cc_start: 0.9584 (t) cc_final: 0.9023 (p) REVERT: H 205 HIS cc_start: 0.8690 (OUTLIER) cc_final: 0.7854 (m-70) outliers start: 50 outliers final: 35 residues processed: 214 average time/residue: 1.2890 time to fit residues: 311.0270 Evaluate side-chains 202 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 76 LEU 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: 227 random chunks: chunk 209 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 chunk 203 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 160 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5078 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18580 Z= 0.213 Angle : 0.708 22.372 25038 Z= 0.346 Chirality : 0.042 0.243 2793 Planarity : 0.004 0.041 3050 Dihedral : 9.364 85.414 2828 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.17 % Favored : 97.65 % Rotamer: Outliers : 2.08 % Allowed : 19.77 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.78 (0.18), residues: 2268 helix: 2.55 (0.14), residues: 1347 sheet: -0.67 (0.44), residues: 127 loop : -0.97 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 460 HIS 0.005 0.001 HIS E 132 PHE 0.036 0.001 PHE A 658 TYR 0.022 0.001 TYR B 647 ARG 0.008 0.001 ARG C 586 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 2.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 65 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7767 (mtm110) REVERT: F 81 ASP cc_start: 0.8825 (t0) cc_final: 0.8610 (t70) REVERT: G 81 ASP cc_start: 0.9160 (p0) cc_final: 0.8878 (t0) REVERT: G 99 ARG cc_start: 0.9598 (tpp80) cc_final: 0.9314 (tpp80) REVERT: G 205 HIS cc_start: 0.8716 (OUTLIER) cc_final: 0.8419 (t-90) REVERT: H 6 ARG cc_start: 0.8442 (tmt-80) cc_final: 0.7914 (tmm160) REVERT: H 61 SER cc_start: 0.9412 (t) cc_final: 0.8684 (p) REVERT: H 205 HIS cc_start: 0.8628 (OUTLIER) cc_final: 0.7708 (m-70) outliers start: 38 outliers final: 22 residues processed: 211 average time/residue: 1.3919 time to fit residues: 330.5212 Evaluate side-chains 194 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 131 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 149 optimal weight: 0.7980 chunk 226 optimal weight: 0.8980 chunk 208 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 143 optimal weight: 20.0000 chunk 191 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS H 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5071 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18580 Z= 0.201 Angle : 0.706 14.070 25038 Z= 0.349 Chirality : 0.042 0.237 2793 Planarity : 0.004 0.041 3050 Dihedral : 9.164 84.359 2828 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.30 % Favored : 97.52 % Rotamer: Outliers : 1.80 % Allowed : 20.43 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.81 (0.18), residues: 2268 helix: 2.58 (0.14), residues: 1350 sheet: -0.50 (0.46), residues: 122 loop : -1.04 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 460 HIS 0.006 0.001 HIS B 412 PHE 0.037 0.001 PHE A 658 TYR 0.017 0.001 TYR B 647 ARG 0.011 0.001 ARG E 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 174 TYR cc_start: 0.8704 (p90) cc_final: 0.8463 (p90) REVERT: F 65 ARG cc_start: 0.8138 (mtm-85) cc_final: 0.7744 (mtm110) REVERT: G 81 ASP cc_start: 0.9147 (p0) cc_final: 0.8870 (t0) REVERT: G 99 ARG cc_start: 0.9580 (tpp80) cc_final: 0.9312 (tpp80) REVERT: H 6 ARG cc_start: 0.8338 (tmt-80) cc_final: 0.7774 (tmm160) REVERT: H 61 SER cc_start: 0.9367 (t) cc_final: 0.8643 (p) REVERT: H 205 HIS cc_start: 0.8673 (OUTLIER) cc_final: 0.7723 (m-70) outliers start: 33 outliers final: 19 residues processed: 202 average time/residue: 1.3071 time to fit residues: 297.7895 Evaluate side-chains 191 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 55 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 180 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 185 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.150468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.078966 restraints weight = 75124.832| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 4.36 r_work: 0.2920 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18580 Z= 0.274 Angle : 0.726 14.157 25038 Z= 0.359 Chirality : 0.043 0.232 2793 Planarity : 0.004 0.044 3050 Dihedral : 9.280 84.266 2828 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.53 % Favored : 97.30 % Rotamer: Outliers : 1.58 % Allowed : 20.48 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.71 (0.18), residues: 2268 helix: 2.53 (0.14), residues: 1348 sheet: -0.80 (0.45), residues: 118 loop : -1.06 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 460 HIS 0.004 0.001 HIS B 412 PHE 0.035 0.002 PHE A 658 TYR 0.016 0.001 TYR C 647 ARG 0.011 0.001 ARG E 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6697.18 seconds wall clock time: 131 minutes 43.88 seconds (7903.88 seconds total)