Starting phenix.real_space_refine on Tue Feb 20 09:11:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgj_23325/02_2024/7lgj_23325_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgj_23325/02_2024/7lgj_23325.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgj_23325/02_2024/7lgj_23325_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgj_23325/02_2024/7lgj_23325_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgj_23325/02_2024/7lgj_23325_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgj_23325/02_2024/7lgj_23325.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgj_23325/02_2024/7lgj_23325.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgj_23325/02_2024/7lgj_23325_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgj_23325/02_2024/7lgj_23325_neut_trim_updated.pdb" } resolution = 2.6 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= 0.005 sd= 0.134 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: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 12 5.21 5 S 96 5.16 5 C 16948 2.51 5 N 4756 2.21 5 O 5256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 558": "OE1" <-> "OE2" Residue "A GLU 677": "OE1" <-> "OE2" Residue "B GLU 558": "OE1" <-> "OE2" Residue "B GLU 677": "OE1" <-> "OE2" Residue "C GLU 558": "OE1" <-> "OE2" Residue "C GLU 677": "OE1" <-> "OE2" Residue "D GLU 558": "OE1" <-> "OE2" Residue "D GLU 677": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27092 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6645 Classifications: {'peptide': 869} Link IDs: {'PTRANS': 40, 'TRANS': 828} Chain breaks: 1 Chain: "B" Number of atoms: 6645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6645 Classifications: {'peptide': 869} Link IDs: {'PTRANS': 40, 'TRANS': 828} Chain breaks: 1 Chain: "C" Number of atoms: 6645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6645 Classifications: {'peptide': 869} Link IDs: {'PTRANS': 40, 'TRANS': 828} Chain breaks: 1 Chain: "D" Number of atoms: 6645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6645 Classifications: {'peptide': 869} Link IDs: {'PTRANS': 40, 'TRANS': 828} Chain breaks: 1 Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 63 Unusual residues: {'NH2': 1} Classifications: {'peptide': 4, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="7ID E 8 " pdbres="NH2 E 9 " Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-1': 1, '7ID:plan-4': 4} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 63 Unusual residues: {'NH2': 1} Classifications: {'peptide': 4, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="7ID F 8 " pdbres="NH2 F 9 " Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-1': 1, '7ID:plan-4': 4} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 63 Unusual residues: {'NH2': 1} Classifications: {'peptide': 4, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="7ID G 8 " pdbres="NH2 G 9 " Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-1': 1, '7ID:plan-4': 4} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 63 Unusual residues: {'NH2': 1} Classifications: {'peptide': 4, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="7ID H 8 " pdbres="NH2 H 9 " Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-1': 1, '7ID:plan-4': 4} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'ACP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'ACP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'ACP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'ACP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 13.97, per 1000 atoms: 0.52 Number of scatterers: 27092 At special positions: 0 Unit cell: (135.945, 141.075, 147.915, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 24 15.00 Mg 12 11.99 O 5256 8.00 N 4756 7.00 C 16948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.28 Conformation dependent library (CDL) restraints added in 5.0 seconds 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 24 sheets defined 33.9% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.80 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 80 through 92 removed outlier: 3.953A pdb=" N VAL A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 137 removed outlier: 3.557A pdb=" N VAL A 137 " --> pdb=" O CYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 3.780A pdb=" N GLU A 148 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYS A 149 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 158 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 176 removed outlier: 3.522A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.590A pdb=" N ALA A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 253 removed outlier: 5.082A pdb=" N ASN A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 290 removed outlier: 4.122A pdb=" N GLU A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 364 through 373 removed outlier: 3.735A pdb=" N GLN A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 410 through 422 Processing helix chain 'A' and resid 441 through 444 No H-bonds generated for 'chain 'A' and resid 441 through 444' Processing helix chain 'A' and resid 458 through 461 No H-bonds generated for 'chain 'A' and resid 458 through 461' Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.695A pdb=" N MET A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 513 removed outlier: 3.615A pdb=" N GLN A 512 " --> pdb=" O HIS A 508 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.894A pdb=" N VAL A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 595 through 608 removed outlier: 3.593A pdb=" N LYS A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 629 removed outlier: 3.872A pdb=" N ALA A 626 " --> pdb=" O PRO A 622 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA A 628 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASP A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 622 through 629' Processing helix chain 'A' and resid 645 through 653 removed outlier: 3.694A pdb=" N ARG A 653 " --> pdb=" O ALA A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 681 No H-bonds generated for 'chain 'A' and resid 679 through 681' Processing helix chain 'A' and resid 691 through 706 Processing helix chain 'A' and resid 711 through 720 Processing helix chain 'A' and resid 750 through 761 removed outlier: 3.842A pdb=" N ALA A 755 " --> pdb=" O GLY A 752 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 756 " --> pdb=" O TYR A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 791 removed outlier: 3.994A pdb=" N GLN A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 823 removed outlier: 3.809A pdb=" N GLU A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 867 removed outlier: 4.200A pdb=" N LYS A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 Processing helix chain 'B' and resid 80 through 92 removed outlier: 3.953A pdb=" N VAL B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 137 removed outlier: 3.557A pdb=" N VAL B 137 " --> pdb=" O CYS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 160 removed outlier: 3.780A pdb=" N GLU B 148 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYS B 149 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 158 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN B 160 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 176 removed outlier: 3.522A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 211 through 218 Processing helix chain 'B' and resid 220 through 230 removed outlier: 3.590A pdb=" N ALA B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 253 removed outlier: 5.083A pdb=" N ASN B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP B 252 " --> pdb=" O GLU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 290 removed outlier: 4.122A pdb=" N GLU B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 364 through 373 removed outlier: 3.735A pdb=" N GLN B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 397 No H-bonds generated for 'chain 'B' and resid 395 through 397' Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 410 through 422 Processing helix chain 'B' and resid 441 through 444 No H-bonds generated for 'chain 'B' and resid 441 through 444' Processing helix chain 'B' and resid 458 through 461 No H-bonds generated for 'chain 'B' and resid 458 through 461' Processing helix chain 'B' and resid 473 through 479 removed outlier: 3.695A pdb=" N MET B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 513 removed outlier: 3.615A pdb=" N GLN B 512 " --> pdb=" O HIS B 508 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR B 513 " --> pdb=" O ILE B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.894A pdb=" N VAL B 545 " --> pdb=" O GLN B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 595 through 608 removed outlier: 3.593A pdb=" N LYS B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 629 removed outlier: 3.871A pdb=" N ALA B 626 " --> pdb=" O PRO B 622 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET B 627 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA B 628 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 622 through 629' Processing helix chain 'B' and resid 645 through 653 removed outlier: 3.693A pdb=" N ARG B 653 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 681 No H-bonds generated for 'chain 'B' and resid 679 through 681' Processing helix chain 'B' and resid 691 through 706 Processing helix chain 'B' and resid 711 through 720 Processing helix chain 'B' and resid 750 through 761 removed outlier: 3.842A pdb=" N ALA B 755 " --> pdb=" O GLY B 752 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 756 " --> pdb=" O TYR B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 791 removed outlier: 3.993A pdb=" N GLN B 791 " --> pdb=" O GLN B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 823 removed outlier: 3.809A pdb=" N GLU B 823 " --> pdb=" O GLY B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 867 removed outlier: 4.200A pdb=" N LYS B 867 " --> pdb=" O ILE B 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 50 Processing helix chain 'C' and resid 80 through 92 removed outlier: 3.954A pdb=" N VAL C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 137 removed outlier: 3.557A pdb=" N VAL C 137 " --> pdb=" O CYS C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 160 removed outlier: 3.780A pdb=" N GLU C 148 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYS C 149 " --> pdb=" O GLU C 146 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 158 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN C 160 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 176 removed outlier: 3.522A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 220 through 230 removed outlier: 3.590A pdb=" N ALA C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 253 removed outlier: 5.082A pdb=" N ASN C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 290 removed outlier: 4.122A pdb=" N GLU C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 364 through 373 removed outlier: 3.735A pdb=" N GLN C 373 " --> pdb=" O VAL C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 397 No H-bonds generated for 'chain 'C' and resid 395 through 397' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 410 through 422 Processing helix chain 'C' and resid 441 through 444 No H-bonds generated for 'chain 'C' and resid 441 through 444' Processing helix chain 'C' and resid 458 through 461 No H-bonds generated for 'chain 'C' and resid 458 through 461' Processing helix chain 'C' and resid 473 through 479 removed outlier: 3.695A pdb=" N MET C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 513 removed outlier: 3.615A pdb=" N GLN C 512 " --> pdb=" O HIS C 508 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR C 513 " --> pdb=" O ILE C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 547 removed outlier: 3.894A pdb=" N VAL C 545 " --> pdb=" O GLN C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 567 Processing helix chain 'C' and resid 595 through 608 removed outlier: 3.593A pdb=" N LYS C 600 " --> pdb=" O GLU C 596 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA C 606 " --> pdb=" O LYS C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 629 removed outlier: 3.871A pdb=" N ALA C 626 " --> pdb=" O PRO C 622 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET C 627 " --> pdb=" O LEU C 623 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA C 628 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASP C 629 " --> pdb=" O ALA C 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 622 through 629' Processing helix chain 'C' and resid 645 through 653 removed outlier: 3.694A pdb=" N ARG C 653 " --> pdb=" O ALA C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 681 No H-bonds generated for 'chain 'C' and resid 679 through 681' Processing helix chain 'C' and resid 691 through 706 Processing helix chain 'C' and resid 711 through 720 Processing helix chain 'C' and resid 750 through 761 removed outlier: 3.842A pdb=" N ALA C 755 " --> pdb=" O GLY C 752 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 756 " --> pdb=" O TYR C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 791 removed outlier: 3.994A pdb=" N GLN C 791 " --> pdb=" O GLN C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 823 removed outlier: 3.809A pdb=" N GLU C 823 " --> pdb=" O GLY C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 867 removed outlier: 4.200A pdb=" N LYS C 867 " --> pdb=" O ILE C 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 50 Processing helix chain 'D' and resid 80 through 92 removed outlier: 3.953A pdb=" N VAL D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 137 removed outlier: 3.557A pdb=" N VAL D 137 " --> pdb=" O CYS D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 160 removed outlier: 3.780A pdb=" N GLU D 148 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LYS D 149 " --> pdb=" O GLU D 146 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY D 158 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN D 160 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 176 removed outlier: 3.522A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 220 through 230 removed outlier: 3.589A pdb=" N ALA D 230 " --> pdb=" O ILE D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 253 removed outlier: 5.082A pdb=" N ASN D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP D 252 " --> pdb=" O GLU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 290 removed outlier: 4.122A pdb=" N GLU D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 364 through 373 removed outlier: 3.734A pdb=" N GLN D 373 " --> pdb=" O VAL D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 397 No H-bonds generated for 'chain 'D' and resid 395 through 397' Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 410 through 422 Processing helix chain 'D' and resid 441 through 444 No H-bonds generated for 'chain 'D' and resid 441 through 444' Processing helix chain 'D' and resid 458 through 461 No H-bonds generated for 'chain 'D' and resid 458 through 461' Processing helix chain 'D' and resid 473 through 479 removed outlier: 3.696A pdb=" N MET D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 513 removed outlier: 3.615A pdb=" N GLN D 512 " --> pdb=" O HIS D 508 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR D 513 " --> pdb=" O ILE D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 547 removed outlier: 3.894A pdb=" N VAL D 545 " --> pdb=" O GLN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 567 Processing helix chain 'D' and resid 595 through 608 removed outlier: 3.593A pdb=" N LYS D 600 " --> pdb=" O GLU D 596 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL D 604 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA D 606 " --> pdb=" O LYS D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 629 removed outlier: 3.871A pdb=" N ALA D 626 " --> pdb=" O PRO D 622 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET D 627 " --> pdb=" O LEU D 623 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA D 628 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASP D 629 " --> pdb=" O ALA D 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 622 through 629' Processing helix chain 'D' and resid 645 through 653 removed outlier: 3.694A pdb=" N ARG D 653 " --> pdb=" O ALA D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 681 No H-bonds generated for 'chain 'D' and resid 679 through 681' Processing helix chain 'D' and resid 691 through 706 Processing helix chain 'D' and resid 711 through 720 Processing helix chain 'D' and resid 750 through 761 removed outlier: 3.842A pdb=" N ALA D 755 " --> pdb=" O GLY D 752 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 756 " --> pdb=" O TYR D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 782 through 791 removed outlier: 3.994A pdb=" N GLN D 791 " --> pdb=" O GLN D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 823 removed outlier: 3.810A pdb=" N GLU D 823 " --> pdb=" O GLY D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 859 through 867 removed outlier: 4.200A pdb=" N LYS D 867 " --> pdb=" O ILE D 863 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 99 through 104 removed outlier: 4.286A pdb=" N VAL A 109 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 5 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP A 28 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ILE A 3 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= C, first strand: chain 'A' and resid 400 through 403 removed outlier: 6.746A pdb=" N LEU A 311 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL A 320 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG A 309 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU A 322 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP A 307 " --> pdb=" O GLU A 322 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 433 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE A 448 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 327 through 329 Processing sheet with id= E, first strand: chain 'A' and resid 672 through 678 removed outlier: 6.833A pdb=" N LEU A 665 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL A 635 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N ALA A 658 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR A 637 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N TYR A 660 " --> pdb=" O TYR A 637 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N SER A 639 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN A 618 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE A 527 " --> pdb=" O CYS A 531 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N CYS A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 733 through 736 Processing sheet with id= G, first strand: chain 'B' and resid 99 through 104 removed outlier: 4.286A pdb=" N VAL B 109 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 5 " --> pdb=" O ARG B 26 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP B 28 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ILE B 3 " --> pdb=" O ASP B 28 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= I, first strand: chain 'B' and resid 400 through 403 removed outlier: 6.746A pdb=" N LEU B 311 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL B 320 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG B 309 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU B 322 " --> pdb=" O ASP B 307 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ASP B 307 " --> pdb=" O GLU B 322 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 433 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE B 448 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 327 through 329 Processing sheet with id= K, first strand: chain 'B' and resid 672 through 678 removed outlier: 6.832A pdb=" N LEU B 665 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL B 635 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N ALA B 658 " --> pdb=" O VAL B 635 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR B 637 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N TYR B 660 " --> pdb=" O TYR B 637 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N SER B 639 " --> pdb=" O TYR B 660 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN B 618 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 527 " --> pdb=" O CYS B 531 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N CYS B 531 " --> pdb=" O ILE B 527 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 733 through 736 Processing sheet with id= M, first strand: chain 'C' and resid 99 through 104 removed outlier: 4.286A pdb=" N VAL C 109 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS C 5 " --> pdb=" O ARG C 26 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP C 28 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ILE C 3 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= O, first strand: chain 'C' and resid 400 through 403 removed outlier: 6.746A pdb=" N LEU C 311 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL C 320 " --> pdb=" O ARG C 309 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG C 309 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU C 322 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP C 307 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 433 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE C 448 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 327 through 329 Processing sheet with id= Q, first strand: chain 'C' and resid 672 through 678 removed outlier: 6.833A pdb=" N LEU C 665 " --> pdb=" O VAL C 676 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL C 635 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N ALA C 658 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR C 637 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N TYR C 660 " --> pdb=" O TYR C 637 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N SER C 639 " --> pdb=" O TYR C 660 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN C 618 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE C 527 " --> pdb=" O CYS C 531 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N CYS C 531 " --> pdb=" O ILE C 527 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 733 through 736 Processing sheet with id= S, first strand: chain 'D' and resid 99 through 104 removed outlier: 4.287A pdb=" N VAL D 109 " --> pdb=" O THR D 104 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS D 5 " --> pdb=" O ARG D 26 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP D 28 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ILE D 3 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= U, first strand: chain 'D' and resid 400 through 403 removed outlier: 6.746A pdb=" N LEU D 311 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL D 320 " --> pdb=" O ARG D 309 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG D 309 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU D 322 " --> pdb=" O ASP D 307 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP D 307 " --> pdb=" O GLU D 322 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL D 433 " --> pdb=" O ILE D 448 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ILE D 448 " --> pdb=" O VAL D 433 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 327 through 329 Processing sheet with id= W, first strand: chain 'D' and resid 672 through 678 removed outlier: 6.833A pdb=" N LEU D 665 " --> pdb=" O VAL D 676 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL D 635 " --> pdb=" O ILE D 656 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N ALA D 658 " --> pdb=" O VAL D 635 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR D 637 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N TYR D 660 " --> pdb=" O TYR D 637 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N SER D 639 " --> pdb=" O TYR D 660 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN D 618 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE D 527 " --> pdb=" O CYS D 531 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N CYS D 531 " --> pdb=" O ILE D 527 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 733 through 736 932 hydrogen bonds defined for protein. 2484 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: 9.85 Time building geometry restraints manager: 10.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 4712 1.29 - 1.43: 6524 1.43 - 1.57: 15933 1.57 - 1.70: 187 1.70 - 1.84: 184 Bond restraints: 27540 Sorted by residual: bond pdb=" C 7ID E 5 " pdb=" N 7ID E 6 " ideal model delta sigma weight residual 1.329 1.518 -0.189 1.40e-02 5.10e+03 1.82e+02 bond pdb=" C 7ID F 5 " pdb=" N 7ID F 6 " ideal model delta sigma weight residual 1.329 1.518 -0.189 1.40e-02 5.10e+03 1.82e+02 bond pdb=" C 7ID G 5 " pdb=" N 7ID G 6 " ideal model delta sigma weight residual 1.329 1.518 -0.189 1.40e-02 5.10e+03 1.82e+02 bond pdb=" C 7ID H 5 " pdb=" N 7ID H 6 " ideal model delta sigma weight residual 1.329 1.518 -0.189 1.40e-02 5.10e+03 1.82e+02 bond pdb=" C 7ID G 6 " pdb=" N 7ID G 7 " ideal model delta sigma weight residual 1.329 1.479 -0.150 1.40e-02 5.10e+03 1.15e+02 ... (remaining 27535 not shown) Histogram of bond angle deviations from ideal: 96.23 - 105.36: 810 105.36 - 114.48: 15672 114.48 - 123.61: 19345 123.61 - 132.73: 1593 132.73 - 141.86: 40 Bond angle restraints: 37460 Sorted by residual: angle pdb=" N HIS B 353 " pdb=" CA HIS B 353 " pdb=" CB HIS B 353 " ideal model delta sigma weight residual 113.15 133.73 -20.58 1.63e+00 3.76e-01 1.59e+02 angle pdb=" N HIS D 353 " pdb=" CA HIS D 353 " pdb=" CB HIS D 353 " ideal model delta sigma weight residual 113.15 133.73 -20.58 1.63e+00 3.76e-01 1.59e+02 angle pdb=" N HIS A 353 " pdb=" CA HIS A 353 " pdb=" CB HIS A 353 " ideal model delta sigma weight residual 113.15 133.69 -20.54 1.63e+00 3.76e-01 1.59e+02 angle pdb=" N HIS C 353 " pdb=" CA HIS C 353 " pdb=" CB HIS C 353 " ideal model delta sigma weight residual 113.15 133.68 -20.53 1.63e+00 3.76e-01 1.59e+02 angle pdb=" N GLY D 424 " pdb=" CA GLY D 424 " pdb=" C GLY D 424 " ideal model delta sigma weight residual 113.48 128.98 -15.50 1.46e+00 4.69e-01 1.13e+02 ... (remaining 37455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.41: 16440 32.41 - 64.81: 231 64.81 - 97.22: 61 97.22 - 129.63: 4 129.63 - 162.03: 8 Dihedral angle restraints: 16744 sinusoidal: 6804 harmonic: 9940 Sorted by residual: dihedral pdb=" N HIS B 353 " pdb=" C HIS B 353 " pdb=" CA HIS B 353 " pdb=" CB HIS B 353 " ideal model delta harmonic sigma weight residual 122.80 159.29 -36.49 0 2.50e+00 1.60e-01 2.13e+02 dihedral pdb=" N HIS C 353 " pdb=" C HIS C 353 " pdb=" CA HIS C 353 " pdb=" CB HIS C 353 " ideal model delta harmonic sigma weight residual 122.80 159.27 -36.47 0 2.50e+00 1.60e-01 2.13e+02 dihedral pdb=" N HIS A 353 " pdb=" C HIS A 353 " pdb=" CA HIS A 353 " pdb=" CB HIS A 353 " ideal model delta harmonic sigma weight residual 122.80 159.26 -36.46 0 2.50e+00 1.60e-01 2.13e+02 ... (remaining 16741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.288: 4280 0.288 - 0.576: 32 0.576 - 0.864: 0 0.864 - 1.152: 0 1.152 - 1.440: 12 Chirality restraints: 4324 Sorted by residual: chirality pdb=" CA HIS B 353 " pdb=" N HIS B 353 " pdb=" C HIS B 353 " pdb=" CB HIS B 353 " both_signs ideal model delta sigma weight residual False 2.51 1.07 1.44 2.00e-01 2.50e+01 5.19e+01 chirality pdb=" CA HIS C 353 " pdb=" N HIS C 353 " pdb=" C HIS C 353 " pdb=" CB HIS C 353 " both_signs ideal model delta sigma weight residual False 2.51 1.07 1.44 2.00e-01 2.50e+01 5.19e+01 chirality pdb=" CA HIS A 353 " pdb=" N HIS A 353 " pdb=" C HIS A 353 " pdb=" CB HIS A 353 " both_signs ideal model delta sigma weight residual False 2.51 1.07 1.44 2.00e-01 2.50e+01 5.18e+01 ... (remaining 4321 not shown) Planarity restraints: 4872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 353 " 0.048 2.00e-02 2.50e+03 3.88e-02 2.26e+01 pdb=" CG HIS A 353 " -0.077 2.00e-02 2.50e+03 pdb=" ND1 HIS A 353 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS A 353 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS A 353 " 0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS A 353 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 353 " -0.048 2.00e-02 2.50e+03 3.88e-02 2.26e+01 pdb=" CG HIS C 353 " 0.077 2.00e-02 2.50e+03 pdb=" ND1 HIS C 353 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS C 353 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS C 353 " -0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS C 353 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 353 " 0.048 2.00e-02 2.50e+03 3.88e-02 2.26e+01 pdb=" CG HIS B 353 " -0.077 2.00e-02 2.50e+03 pdb=" ND1 HIS B 353 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 353 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS B 353 " 0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS B 353 " 0.019 2.00e-02 2.50e+03 ... (remaining 4869 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 556 2.65 - 3.21: 24531 3.21 - 3.77: 39596 3.77 - 4.34: 59092 4.34 - 4.90: 92485 Nonbonded interactions: 216260 Sorted by model distance: nonbonded pdb=" OG1 THR B 500 " pdb="MG MG B 902 " model vdw 2.082 2.170 nonbonded pdb=" OG1 THR C 500 " pdb="MG MG C 902 " model vdw 2.082 2.170 nonbonded pdb=" OG1 THR D 500 " pdb="MG MG D 902 " model vdw 2.082 2.170 nonbonded pdb=" OG1 THR A 500 " pdb="MG MG A 902 " model vdw 2.082 2.170 nonbonded pdb="MG MG D 902 " pdb=" O1B ACP D 904 " model vdw 2.111 2.170 ... (remaining 216255 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 14.870 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 67.900 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.190 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:14.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 : 0.020 0.211 27540 Z= 1.331 Angle : 1.889 21.199 37460 Z= 1.243 Chirality : 0.119 1.440 4324 Planarity : 0.009 0.039 4872 Dihedral : 12.793 162.032 10400 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.28 % Allowed : 0.84 % Favored : 98.87 % Cbeta Deviations : 1.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.13), residues: 3460 helix: -1.01 (0.13), residues: 1240 sheet: 1.24 (0.22), residues: 564 loop : -0.49 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.004 TRP B 414 HIS 0.022 0.004 HIS C 353 PHE 0.026 0.005 PHE B 58 TYR 0.043 0.008 TYR C 829 ARG 0.007 0.001 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 331 time to evaluate : 3.121 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7150 (tttt) cc_final: 0.6692 (ttpp) REVERT: A 18 ARG cc_start: 0.6582 (mtm-85) cc_final: 0.6212 (mmp80) REVERT: A 168 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7047 (tm-30) REVERT: A 220 LYS cc_start: 0.7129 (mtpp) cc_final: 0.6571 (mmtt) REVERT: A 236 ARG cc_start: 0.7306 (ttt90) cc_final: 0.7005 (ttm-80) REVERT: A 301 ARG cc_start: 0.6778 (ttm170) cc_final: 0.6446 (ttp80) REVERT: A 316 LYS cc_start: 0.8669 (tttt) cc_final: 0.7786 (mtmt) REVERT: A 534 LYS cc_start: 0.7416 (mttt) cc_final: 0.7152 (mtpt) REVERT: A 630 LYS cc_start: 0.7163 (mmtt) cc_final: 0.6663 (mtmm) REVERT: A 641 ASN cc_start: 0.7074 (t0) cc_final: 0.6736 (t0) REVERT: A 689 MET cc_start: 0.7349 (mtm) cc_final: 0.6611 (mmp) REVERT: A 710 ASP cc_start: 0.6671 (t0) cc_final: 0.6443 (m-30) REVERT: B 5 LYS cc_start: 0.7195 (tttt) cc_final: 0.6751 (ttpp) REVERT: B 18 ARG cc_start: 0.6550 (mtm-85) cc_final: 0.6147 (mmp80) REVERT: B 168 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7049 (tm-30) REVERT: B 220 LYS cc_start: 0.7109 (mtpp) cc_final: 0.6557 (mmtt) REVERT: B 236 ARG cc_start: 0.7318 (ttt90) cc_final: 0.7013 (ttm-80) REVERT: B 301 ARG cc_start: 0.6760 (ttm170) cc_final: 0.6454 (ttp80) REVERT: B 316 LYS cc_start: 0.8669 (tttt) cc_final: 0.7792 (mtmt) REVERT: B 416 MET cc_start: 0.8538 (mmp) cc_final: 0.8327 (mmt) REVERT: B 534 LYS cc_start: 0.7380 (mttt) cc_final: 0.7116 (mtpt) REVERT: B 630 LYS cc_start: 0.7164 (mmtt) cc_final: 0.6663 (mtmm) REVERT: B 641 ASN cc_start: 0.7076 (t0) cc_final: 0.6745 (t0) REVERT: B 689 MET cc_start: 0.7367 (mtm) cc_final: 0.6612 (mmp) REVERT: B 710 ASP cc_start: 0.6687 (t0) cc_final: 0.6462 (m-30) REVERT: C 5 LYS cc_start: 0.7175 (tttt) cc_final: 0.6733 (ttpp) REVERT: C 18 ARG cc_start: 0.6487 (mtm-85) cc_final: 0.6082 (mmp80) REVERT: C 168 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7060 (tm-30) REVERT: C 220 LYS cc_start: 0.7106 (mtpp) cc_final: 0.6563 (mmtt) REVERT: C 236 ARG cc_start: 0.7324 (ttt90) cc_final: 0.7019 (ttm-80) REVERT: C 301 ARG cc_start: 0.6764 (ttm170) cc_final: 0.6459 (ttp80) REVERT: C 316 LYS cc_start: 0.8676 (tttt) cc_final: 0.7799 (mtmt) REVERT: C 416 MET cc_start: 0.8538 (mmp) cc_final: 0.8331 (mmt) REVERT: C 534 LYS cc_start: 0.7367 (mttt) cc_final: 0.7112 (mtpt) REVERT: C 630 LYS cc_start: 0.7146 (mmtt) cc_final: 0.6641 (mtmm) REVERT: C 641 ASN cc_start: 0.7093 (t0) cc_final: 0.6762 (t0) REVERT: C 689 MET cc_start: 0.7388 (mtm) cc_final: 0.6628 (mmp) REVERT: C 710 ASP cc_start: 0.6736 (t0) cc_final: 0.6510 (m-30) REVERT: D 5 LYS cc_start: 0.7214 (tttt) cc_final: 0.6743 (ttpp) REVERT: D 18 ARG cc_start: 0.6548 (mtm-85) cc_final: 0.6146 (mmp80) REVERT: D 168 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7072 (tm-30) REVERT: D 220 LYS cc_start: 0.7101 (mtpp) cc_final: 0.6556 (mmtt) REVERT: D 236 ARG cc_start: 0.7332 (ttt90) cc_final: 0.7027 (ttm-80) REVERT: D 301 ARG cc_start: 0.6763 (ttm170) cc_final: 0.6438 (ttp80) REVERT: D 316 LYS cc_start: 0.8666 (tttt) cc_final: 0.7789 (mtmt) REVERT: D 534 LYS cc_start: 0.7371 (mttt) cc_final: 0.7116 (mtpt) REVERT: D 630 LYS cc_start: 0.7167 (mmtt) cc_final: 0.6666 (mtmm) REVERT: D 641 ASN cc_start: 0.7066 (t0) cc_final: 0.6732 (t0) REVERT: D 689 MET cc_start: 0.7383 (mtm) cc_final: 0.6623 (mmp) REVERT: D 710 ASP cc_start: 0.6702 (t0) cc_final: 0.6477 (m-30) outliers start: 8 outliers final: 0 residues processed: 339 average time/residue: 1.6021 time to fit residues: 620.5261 Evaluate side-chains 219 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 175 optimal weight: 10.0000 chunk 139 optimal weight: 0.9980 chunk 269 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 312 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 394 ASN A 696 ASN A 748 HIS B 355 ASN B 394 ASN B 696 ASN B 748 HIS C 355 ASN C 394 ASN C 696 ASN C 748 HIS D 355 ASN D 394 ASN D 696 ASN D 748 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27540 Z= 0.226 Angle : 0.673 9.848 37460 Z= 0.370 Chirality : 0.048 0.206 4324 Planarity : 0.005 0.047 4872 Dihedral : 13.315 175.111 4172 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.51 % Allowed : 4.68 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3460 helix: -0.13 (0.14), residues: 1308 sheet: 0.73 (0.23), residues: 512 loop : -0.74 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 672 HIS 0.008 0.002 HIS A 353 PHE 0.013 0.002 PHE A 638 TYR 0.019 0.002 TYR C 285 ARG 0.004 0.001 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 251 time to evaluate : 2.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7131 (tttt) cc_final: 0.6757 (ttpp) REVERT: A 18 ARG cc_start: 0.6550 (mtm-85) cc_final: 0.6152 (mmp80) REVERT: A 168 GLU cc_start: 0.7498 (mt-10) cc_final: 0.6819 (tm-30) REVERT: A 220 LYS cc_start: 0.6560 (mtpp) cc_final: 0.5987 (mmtt) REVERT: A 316 LYS cc_start: 0.8615 (tttt) cc_final: 0.7866 (mtmt) REVERT: A 534 LYS cc_start: 0.7306 (mttt) cc_final: 0.7022 (mtpt) REVERT: A 630 LYS cc_start: 0.7349 (mmtt) cc_final: 0.6801 (mtmm) REVERT: A 641 ASN cc_start: 0.7270 (t0) cc_final: 0.6792 (t0) REVERT: A 680 LYS cc_start: 0.7457 (pttt) cc_final: 0.6915 (mptp) REVERT: A 689 MET cc_start: 0.7391 (mtm) cc_final: 0.6612 (mmp) REVERT: A 710 ASP cc_start: 0.6682 (t0) cc_final: 0.6402 (m-30) REVERT: B 5 LYS cc_start: 0.7164 (tttt) cc_final: 0.6799 (ttpp) REVERT: B 18 ARG cc_start: 0.6511 (mtm-85) cc_final: 0.6119 (mmp80) REVERT: B 168 GLU cc_start: 0.7498 (mt-10) cc_final: 0.6820 (tm-30) REVERT: B 220 LYS cc_start: 0.6459 (mtpp) cc_final: 0.5880 (mmtt) REVERT: B 316 LYS cc_start: 0.8634 (tttt) cc_final: 0.7884 (mtmt) REVERT: B 534 LYS cc_start: 0.7283 (mttt) cc_final: 0.6998 (mtpt) REVERT: B 630 LYS cc_start: 0.7347 (mmtt) cc_final: 0.6799 (mtmm) REVERT: B 641 ASN cc_start: 0.7253 (t0) cc_final: 0.6780 (t0) REVERT: B 680 LYS cc_start: 0.7477 (pttt) cc_final: 0.6950 (mptp) REVERT: B 689 MET cc_start: 0.7425 (mtm) cc_final: 0.6624 (mmp) REVERT: B 710 ASP cc_start: 0.6693 (t0) cc_final: 0.6421 (m-30) REVERT: C 5 LYS cc_start: 0.7159 (tttt) cc_final: 0.6797 (ttpp) REVERT: C 18 ARG cc_start: 0.6500 (mtm-85) cc_final: 0.6105 (mmp80) REVERT: C 160 ASN cc_start: 0.7155 (OUTLIER) cc_final: 0.6952 (t0) REVERT: C 168 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6806 (tm-30) REVERT: C 220 LYS cc_start: 0.6543 (mtpp) cc_final: 0.5969 (mmtt) REVERT: C 316 LYS cc_start: 0.8603 (tttt) cc_final: 0.7866 (mtmt) REVERT: C 416 MET cc_start: 0.8429 (mmp) cc_final: 0.8177 (mmt) REVERT: C 534 LYS cc_start: 0.7274 (mttt) cc_final: 0.6987 (mtpt) REVERT: C 630 LYS cc_start: 0.7350 (mmtt) cc_final: 0.6801 (mtmm) REVERT: C 641 ASN cc_start: 0.7091 (t0) cc_final: 0.6616 (t0) REVERT: C 680 LYS cc_start: 0.7483 (pttt) cc_final: 0.6954 (mptp) REVERT: C 689 MET cc_start: 0.7417 (mtm) cc_final: 0.6598 (mmp) REVERT: C 710 ASP cc_start: 0.6717 (t0) cc_final: 0.6438 (m-30) REVERT: D 5 LYS cc_start: 0.7164 (tttt) cc_final: 0.6802 (ttpp) REVERT: D 18 ARG cc_start: 0.6508 (mtm-85) cc_final: 0.6118 (mmp80) REVERT: D 160 ASN cc_start: 0.7159 (OUTLIER) cc_final: 0.6949 (t0) REVERT: D 168 GLU cc_start: 0.7495 (mt-10) cc_final: 0.6820 (tm-30) REVERT: D 220 LYS cc_start: 0.6497 (mtpp) cc_final: 0.5921 (mmtt) REVERT: D 316 LYS cc_start: 0.8611 (tttt) cc_final: 0.7856 (mtmt) REVERT: D 534 LYS cc_start: 0.7280 (mttt) cc_final: 0.6993 (mtpt) REVERT: D 630 LYS cc_start: 0.7350 (mmtt) cc_final: 0.6800 (mtmm) REVERT: D 641 ASN cc_start: 0.7100 (t0) cc_final: 0.6624 (t0) REVERT: D 680 LYS cc_start: 0.7467 (pttt) cc_final: 0.6944 (mptp) REVERT: D 689 MET cc_start: 0.7417 (mtm) cc_final: 0.6598 (mmp) REVERT: D 710 ASP cc_start: 0.6707 (t0) cc_final: 0.6436 (m-30) outliers start: 43 outliers final: 10 residues processed: 275 average time/residue: 1.7477 time to fit residues: 544.3375 Evaluate side-chains 209 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 197 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 229 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 173 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 259 optimal weight: 2.9990 chunk 212 optimal weight: 0.4980 chunk 86 optimal weight: 7.9990 chunk 312 optimal weight: 2.9990 chunk 338 optimal weight: 10.0000 chunk 278 optimal weight: 4.9990 chunk 310 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 251 optimal weight: 20.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 707 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27540 Z= 0.281 Angle : 0.643 9.389 37460 Z= 0.346 Chirality : 0.048 0.178 4324 Planarity : 0.005 0.052 4872 Dihedral : 12.688 153.645 4172 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.34 % Allowed : 5.56 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3460 helix: -0.11 (0.14), residues: 1296 sheet: 0.27 (0.21), residues: 532 loop : -1.04 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 181 HIS 0.006 0.001 HIS C 650 PHE 0.012 0.002 PHE B 457 TYR 0.018 0.002 TYR C 519 ARG 0.005 0.001 ARG C 715 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 238 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.6614 (mtm-85) cc_final: 0.6156 (mmp80) REVERT: A 141 ASP cc_start: 0.5589 (t0) cc_final: 0.5220 (p0) REVERT: A 168 GLU cc_start: 0.7535 (mt-10) cc_final: 0.6893 (tm-30) REVERT: A 220 LYS cc_start: 0.6773 (mtpp) cc_final: 0.6173 (mmtt) REVERT: A 301 ARG cc_start: 0.6561 (ttm170) cc_final: 0.6297 (ttp80) REVERT: A 316 LYS cc_start: 0.8671 (tttt) cc_final: 0.7928 (mtmt) REVERT: A 426 ASP cc_start: 0.6665 (p0) cc_final: 0.6351 (m-30) REVERT: A 442 ARG cc_start: 0.8259 (ptt-90) cc_final: 0.7528 (ptm160) REVERT: A 445 ASN cc_start: 0.8059 (t0) cc_final: 0.7851 (t0) REVERT: A 534 LYS cc_start: 0.7334 (mttt) cc_final: 0.7074 (mtpt) REVERT: A 558 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.7909 (pt0) REVERT: A 641 ASN cc_start: 0.7111 (t0) cc_final: 0.6557 (t0) REVERT: A 661 GLU cc_start: 0.7464 (pt0) cc_final: 0.6935 (pp20) REVERT: A 680 LYS cc_start: 0.7701 (pttt) cc_final: 0.7241 (mptp) REVERT: A 689 MET cc_start: 0.7472 (mtm) cc_final: 0.6636 (mmt) REVERT: A 710 ASP cc_start: 0.7003 (t0) cc_final: 0.6605 (m-30) REVERT: B 18 ARG cc_start: 0.6574 (mtm-85) cc_final: 0.6121 (mmp80) REVERT: B 141 ASP cc_start: 0.5617 (t0) cc_final: 0.5247 (p0) REVERT: B 168 GLU cc_start: 0.7522 (mt-10) cc_final: 0.6884 (tm-30) REVERT: B 220 LYS cc_start: 0.6710 (mtpp) cc_final: 0.6097 (mmtt) REVERT: B 301 ARG cc_start: 0.6548 (ttm170) cc_final: 0.6298 (ttp80) REVERT: B 316 LYS cc_start: 0.8640 (tttt) cc_final: 0.7887 (mtmt) REVERT: B 426 ASP cc_start: 0.6625 (p0) cc_final: 0.6319 (m-30) REVERT: B 442 ARG cc_start: 0.8289 (ptt-90) cc_final: 0.7523 (ptm160) REVERT: B 534 LYS cc_start: 0.7335 (mttt) cc_final: 0.7077 (mtpt) REVERT: B 558 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.7913 (pt0) REVERT: B 641 ASN cc_start: 0.7109 (t0) cc_final: 0.6556 (t0) REVERT: B 661 GLU cc_start: 0.7370 (pt0) cc_final: 0.6855 (pp20) REVERT: B 680 LYS cc_start: 0.7705 (pttt) cc_final: 0.7248 (mptp) REVERT: B 689 MET cc_start: 0.7466 (mtm) cc_final: 0.6614 (mmt) REVERT: B 710 ASP cc_start: 0.7008 (t0) cc_final: 0.6614 (m-30) REVERT: C 18 ARG cc_start: 0.6571 (mtm-85) cc_final: 0.6119 (mmp80) REVERT: C 141 ASP cc_start: 0.5702 (t0) cc_final: 0.5329 (p0) REVERT: C 168 GLU cc_start: 0.7535 (mt-10) cc_final: 0.6893 (tm-30) REVERT: C 220 LYS cc_start: 0.6773 (mtpp) cc_final: 0.6170 (mmtt) REVERT: C 301 ARG cc_start: 0.6566 (ttm170) cc_final: 0.6302 (ttp80) REVERT: C 316 LYS cc_start: 0.8629 (tttt) cc_final: 0.7881 (mtmt) REVERT: C 426 ASP cc_start: 0.6657 (p0) cc_final: 0.6341 (m-30) REVERT: C 442 ARG cc_start: 0.8294 (ptt-90) cc_final: 0.7521 (ptm160) REVERT: C 534 LYS cc_start: 0.7344 (mttt) cc_final: 0.7085 (mtpt) REVERT: C 558 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.7894 (pt0) REVERT: C 641 ASN cc_start: 0.7089 (t0) cc_final: 0.6531 (t0) REVERT: C 661 GLU cc_start: 0.7376 (pt0) cc_final: 0.6816 (pp20) REVERT: C 680 LYS cc_start: 0.7698 (pttt) cc_final: 0.7241 (mptp) REVERT: C 689 MET cc_start: 0.7485 (mtm) cc_final: 0.6627 (mmt) REVERT: C 710 ASP cc_start: 0.7000 (t0) cc_final: 0.6613 (m-30) REVERT: D 18 ARG cc_start: 0.6572 (mtm-85) cc_final: 0.6119 (mmp80) REVERT: D 141 ASP cc_start: 0.5705 (t0) cc_final: 0.5326 (p0) REVERT: D 168 GLU cc_start: 0.7522 (mt-10) cc_final: 0.6884 (tm-30) REVERT: D 220 LYS cc_start: 0.6700 (mtpp) cc_final: 0.6094 (mmtt) REVERT: D 301 ARG cc_start: 0.6556 (ttm170) cc_final: 0.6292 (ttp80) REVERT: D 316 LYS cc_start: 0.8643 (tttt) cc_final: 0.7889 (mtmt) REVERT: D 426 ASP cc_start: 0.6626 (p0) cc_final: 0.6324 (m-30) REVERT: D 442 ARG cc_start: 0.8296 (ptt-90) cc_final: 0.7522 (ptm160) REVERT: D 445 ASN cc_start: 0.8057 (t0) cc_final: 0.7852 (t0) REVERT: D 534 LYS cc_start: 0.7333 (mttt) cc_final: 0.7052 (mtpt) REVERT: D 558 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.7902 (pt0) REVERT: D 641 ASN cc_start: 0.7103 (t0) cc_final: 0.6548 (t0) REVERT: D 661 GLU cc_start: 0.7375 (pt0) cc_final: 0.6817 (pp20) REVERT: D 680 LYS cc_start: 0.7700 (pttt) cc_final: 0.7242 (mptp) REVERT: D 689 MET cc_start: 0.7484 (mtm) cc_final: 0.6626 (mmt) REVERT: D 710 ASP cc_start: 0.7017 (t0) cc_final: 0.6626 (m-30) outliers start: 38 outliers final: 17 residues processed: 258 average time/residue: 1.6125 time to fit residues: 475.4381 Evaluate side-chains 229 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 208 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 600 LYS Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 600 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 309 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 314 optimal weight: 0.4980 chunk 332 optimal weight: 0.9990 chunk 164 optimal weight: 0.1980 chunk 297 optimal weight: 0.0870 chunk 89 optimal weight: 0.7980 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 707 ASN B 707 ASN C 707 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 27540 Z= 0.128 Angle : 0.501 5.595 37460 Z= 0.269 Chirality : 0.044 0.159 4324 Planarity : 0.004 0.055 4872 Dihedral : 11.651 115.106 4172 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.74 % Allowed : 7.21 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3460 helix: 0.13 (0.15), residues: 1304 sheet: 0.45 (0.22), residues: 532 loop : -0.98 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 278 HIS 0.003 0.000 HIS A 353 PHE 0.009 0.001 PHE C 638 TYR 0.012 0.001 TYR C 519 ARG 0.005 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 222 time to evaluate : 3.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.6515 (mtm-85) cc_final: 0.6075 (mmp80) REVERT: A 141 ASP cc_start: 0.5490 (t0) cc_final: 0.5110 (p0) REVERT: A 168 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6888 (tm-30) REVERT: A 220 LYS cc_start: 0.6570 (mtpp) cc_final: 0.5969 (mmtt) REVERT: A 316 LYS cc_start: 0.8512 (tttt) cc_final: 0.7839 (mtmt) REVERT: A 534 LYS cc_start: 0.7041 (mttt) cc_final: 0.6794 (mtpt) REVERT: A 641 ASN cc_start: 0.7081 (t0) cc_final: 0.6518 (t0) REVERT: A 661 GLU cc_start: 0.7345 (pt0) cc_final: 0.6776 (pp20) REVERT: A 680 LYS cc_start: 0.7648 (pttt) cc_final: 0.7126 (mptp) REVERT: A 689 MET cc_start: 0.7425 (mtm) cc_final: 0.6651 (mmt) REVERT: A 710 ASP cc_start: 0.6968 (t0) cc_final: 0.6560 (m-30) REVERT: B 18 ARG cc_start: 0.6469 (mtm-85) cc_final: 0.6033 (mmp80) REVERT: B 141 ASP cc_start: 0.5578 (t0) cc_final: 0.5214 (p0) REVERT: B 160 ASN cc_start: 0.7081 (OUTLIER) cc_final: 0.6877 (t0) REVERT: B 168 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6887 (tm-30) REVERT: B 220 LYS cc_start: 0.6686 (mtpp) cc_final: 0.6074 (mmtt) REVERT: B 316 LYS cc_start: 0.8512 (tttt) cc_final: 0.7839 (mtmt) REVERT: B 534 LYS cc_start: 0.7168 (mttt) cc_final: 0.6920 (mtpt) REVERT: B 641 ASN cc_start: 0.7079 (t0) cc_final: 0.6518 (t0) REVERT: B 661 GLU cc_start: 0.7348 (pt0) cc_final: 0.6780 (pp20) REVERT: B 680 LYS cc_start: 0.7661 (pttt) cc_final: 0.7142 (mptp) REVERT: B 689 MET cc_start: 0.7437 (mtm) cc_final: 0.6654 (mmt) REVERT: B 710 ASP cc_start: 0.6971 (t0) cc_final: 0.6568 (m-30) REVERT: C 18 ARG cc_start: 0.6469 (mtm-85) cc_final: 0.6033 (mmp80) REVERT: C 141 ASP cc_start: 0.5609 (t0) cc_final: 0.5210 (p0) REVERT: C 168 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6886 (tm-30) REVERT: C 220 LYS cc_start: 0.6569 (mtpp) cc_final: 0.5967 (mmtt) REVERT: C 316 LYS cc_start: 0.8511 (tttt) cc_final: 0.7838 (mtmt) REVERT: C 534 LYS cc_start: 0.7172 (mttt) cc_final: 0.6921 (mtpt) REVERT: C 641 ASN cc_start: 0.7081 (t0) cc_final: 0.6492 (t0) REVERT: C 661 GLU cc_start: 0.7369 (pt0) cc_final: 0.6792 (pp20) REVERT: C 680 LYS cc_start: 0.7661 (pttt) cc_final: 0.7159 (mptp) REVERT: C 689 MET cc_start: 0.7432 (mtm) cc_final: 0.6649 (mmt) REVERT: C 710 ASP cc_start: 0.6977 (t0) cc_final: 0.6567 (m-30) REVERT: D 18 ARG cc_start: 0.6470 (mtm-85) cc_final: 0.6035 (mmp80) REVERT: D 141 ASP cc_start: 0.5589 (t0) cc_final: 0.5243 (p0) REVERT: D 168 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6889 (tm-30) REVERT: D 220 LYS cc_start: 0.6666 (mtpp) cc_final: 0.6054 (mmtt) REVERT: D 316 LYS cc_start: 0.8511 (tttt) cc_final: 0.7839 (mtmt) REVERT: D 534 LYS cc_start: 0.7173 (mttt) cc_final: 0.6923 (mtpt) REVERT: D 641 ASN cc_start: 0.7073 (t0) cc_final: 0.6509 (t0) REVERT: D 661 GLU cc_start: 0.7368 (pt0) cc_final: 0.6794 (pp20) REVERT: D 680 LYS cc_start: 0.7667 (pttt) cc_final: 0.7161 (mptp) REVERT: D 689 MET cc_start: 0.7433 (mtm) cc_final: 0.6649 (mmt) REVERT: D 710 ASP cc_start: 0.6973 (t0) cc_final: 0.6563 (m-30) outliers start: 21 outliers final: 0 residues processed: 234 average time/residue: 1.4747 time to fit residues: 399.2191 Evaluate side-chains 196 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 276 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 247 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 283 optimal weight: 6.9990 chunk 229 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 169 optimal weight: 0.0370 chunk 298 optimal weight: 3.9990 chunk 83 optimal weight: 0.3980 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 27540 Z= 0.160 Angle : 0.502 5.246 37460 Z= 0.271 Chirality : 0.045 0.166 4324 Planarity : 0.004 0.055 4872 Dihedral : 11.226 102.345 4172 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.34 % Allowed : 7.59 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3460 helix: 0.17 (0.15), residues: 1316 sheet: 0.38 (0.22), residues: 536 loop : -1.02 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 181 HIS 0.004 0.001 HIS C 353 PHE 0.011 0.001 PHE D 638 TYR 0.017 0.001 TYR C 519 ARG 0.003 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 205 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.6568 (mtm-85) cc_final: 0.6113 (mmp80) REVERT: A 141 ASP cc_start: 0.5388 (t0) cc_final: 0.5034 (p0) REVERT: A 168 GLU cc_start: 0.7473 (mt-10) cc_final: 0.6921 (tm-30) REVERT: A 182 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8184 (mtp) REVERT: A 220 LYS cc_start: 0.6664 (mtpp) cc_final: 0.6065 (mmtt) REVERT: A 316 LYS cc_start: 0.8560 (tttt) cc_final: 0.7875 (mtmt) REVERT: A 534 LYS cc_start: 0.7203 (mttt) cc_final: 0.6876 (mmpt) REVERT: A 558 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8022 (pt0) REVERT: A 641 ASN cc_start: 0.7199 (t0) cc_final: 0.6609 (t0) REVERT: A 661 GLU cc_start: 0.7341 (pt0) cc_final: 0.6764 (pp20) REVERT: A 680 LYS cc_start: 0.7665 (pttt) cc_final: 0.7166 (mptp) REVERT: A 710 ASP cc_start: 0.7002 (t0) cc_final: 0.6562 (m-30) REVERT: A 785 LEU cc_start: 0.2176 (OUTLIER) cc_final: 0.1739 (mt) REVERT: B 18 ARG cc_start: 0.6544 (mtm-85) cc_final: 0.6088 (mmp80) REVERT: B 141 ASP cc_start: 0.5512 (t0) cc_final: 0.5159 (p0) REVERT: B 160 ASN cc_start: 0.6964 (OUTLIER) cc_final: 0.6752 (t0) REVERT: B 168 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6921 (tm-30) REVERT: B 182 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8186 (mtp) REVERT: B 220 LYS cc_start: 0.6668 (mtpp) cc_final: 0.6061 (mmtt) REVERT: B 316 LYS cc_start: 0.8559 (tttt) cc_final: 0.7875 (mtmt) REVERT: B 534 LYS cc_start: 0.7239 (mttt) cc_final: 0.6907 (mmpt) REVERT: B 558 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.7991 (pt0) REVERT: B 641 ASN cc_start: 0.7195 (t0) cc_final: 0.6607 (t0) REVERT: B 661 GLU cc_start: 0.7356 (pt0) cc_final: 0.6774 (pp20) REVERT: B 680 LYS cc_start: 0.7686 (pttt) cc_final: 0.7193 (mptp) REVERT: B 689 MET cc_start: 0.7457 (mtm) cc_final: 0.6642 (mmt) REVERT: B 710 ASP cc_start: 0.7004 (t0) cc_final: 0.6567 (m-30) REVERT: B 785 LEU cc_start: 0.2235 (OUTLIER) cc_final: 0.1780 (mt) REVERT: C 18 ARG cc_start: 0.6540 (mtm-85) cc_final: 0.6085 (mmp80) REVERT: C 90 GLU cc_start: 0.6838 (tp30) cc_final: 0.6637 (mm-30) REVERT: C 141 ASP cc_start: 0.5587 (t0) cc_final: 0.5230 (p0) REVERT: C 168 GLU cc_start: 0.7473 (mt-10) cc_final: 0.6921 (tm-30) REVERT: C 182 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8186 (mtp) REVERT: C 220 LYS cc_start: 0.6665 (mtpp) cc_final: 0.6064 (mmtt) REVERT: C 316 LYS cc_start: 0.8558 (tttt) cc_final: 0.7874 (mtmt) REVERT: C 534 LYS cc_start: 0.7236 (mttt) cc_final: 0.6916 (mmpt) REVERT: C 558 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.7988 (pt0) REVERT: C 641 ASN cc_start: 0.7185 (t0) cc_final: 0.6595 (t0) REVERT: C 661 GLU cc_start: 0.7359 (pt0) cc_final: 0.6778 (pp20) REVERT: C 680 LYS cc_start: 0.7674 (pttt) cc_final: 0.7181 (mptp) REVERT: C 689 MET cc_start: 0.7448 (mtm) cc_final: 0.6405 (mmt) REVERT: C 710 ASP cc_start: 0.7009 (t0) cc_final: 0.6571 (m-30) REVERT: C 785 LEU cc_start: 0.2212 (OUTLIER) cc_final: 0.1801 (mt) REVERT: D 18 ARG cc_start: 0.6544 (mtm-85) cc_final: 0.6090 (mmp80) REVERT: D 141 ASP cc_start: 0.5586 (t0) cc_final: 0.5227 (p0) REVERT: D 168 GLU cc_start: 0.7475 (mt-10) cc_final: 0.6923 (tm-30) REVERT: D 182 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8184 (mtp) REVERT: D 220 LYS cc_start: 0.6672 (mtpp) cc_final: 0.6055 (mmtt) REVERT: D 316 LYS cc_start: 0.8558 (tttt) cc_final: 0.7874 (mtmt) REVERT: D 534 LYS cc_start: 0.7239 (mttt) cc_final: 0.6918 (mmpt) REVERT: D 558 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.7988 (pt0) REVERT: D 641 ASN cc_start: 0.7192 (t0) cc_final: 0.6599 (t0) REVERT: D 661 GLU cc_start: 0.7359 (pt0) cc_final: 0.6778 (pp20) REVERT: D 680 LYS cc_start: 0.7678 (pttt) cc_final: 0.7188 (mptp) REVERT: D 710 ASP cc_start: 0.7009 (t0) cc_final: 0.6573 (m-30) REVERT: D 785 LEU cc_start: 0.2247 (OUTLIER) cc_final: 0.1790 (mt) outliers start: 38 outliers final: 1 residues processed: 225 average time/residue: 1.5525 time to fit residues: 402.1864 Evaluate side-chains 215 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 201 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 785 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 111 optimal weight: 6.9990 chunk 299 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 195 optimal weight: 0.0670 chunk 82 optimal weight: 20.0000 chunk 332 optimal weight: 7.9990 chunk 276 optimal weight: 2.9990 chunk 154 optimal weight: 0.0050 chunk 27 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 overall best weight: 1.1536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 27540 Z= 0.172 Angle : 0.508 5.783 37460 Z= 0.273 Chirality : 0.045 0.167 4324 Planarity : 0.004 0.056 4872 Dihedral : 10.840 89.300 4172 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.65 % Allowed : 7.95 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 3460 helix: 0.14 (0.15), residues: 1328 sheet: 0.31 (0.23), residues: 532 loop : -1.12 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 181 HIS 0.004 0.001 HIS A 353 PHE 0.011 0.001 PHE D 638 TYR 0.016 0.001 TYR D 519 ARG 0.004 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 220 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.6650 (mtm-85) cc_final: 0.6182 (mmp80) REVERT: A 141 ASP cc_start: 0.5522 (t0) cc_final: 0.5141 (p0) REVERT: A 160 ASN cc_start: 0.7176 (t0) cc_final: 0.6856 (m110) REVERT: A 168 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6925 (tm-30) REVERT: A 220 LYS cc_start: 0.6681 (mtpp) cc_final: 0.6074 (mmtt) REVERT: A 301 ARG cc_start: 0.6525 (ttm170) cc_final: 0.6178 (ttp80) REVERT: A 316 LYS cc_start: 0.8580 (tttt) cc_final: 0.7894 (mtmt) REVERT: A 534 LYS cc_start: 0.7276 (mttt) cc_final: 0.6913 (mmpt) REVERT: A 558 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.7966 (pt0) REVERT: A 641 ASN cc_start: 0.7159 (t0) cc_final: 0.6559 (t0) REVERT: A 661 GLU cc_start: 0.7495 (pt0) cc_final: 0.6849 (pp20) REVERT: A 680 LYS cc_start: 0.7673 (pttt) cc_final: 0.7273 (mptp) REVERT: A 689 MET cc_start: 0.7282 (mtm) cc_final: 0.6343 (mmm) REVERT: A 710 ASP cc_start: 0.7011 (t0) cc_final: 0.6548 (m-30) REVERT: A 785 LEU cc_start: 0.2107 (OUTLIER) cc_final: 0.1626 (mt) REVERT: B 18 ARG cc_start: 0.6599 (mtm-85) cc_final: 0.6141 (mmp80) REVERT: B 141 ASP cc_start: 0.5560 (t0) cc_final: 0.5163 (p0) REVERT: B 168 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6922 (tm-30) REVERT: B 220 LYS cc_start: 0.6717 (mtpp) cc_final: 0.6099 (mmtt) REVERT: B 301 ARG cc_start: 0.6513 (ttm170) cc_final: 0.6168 (ttp80) REVERT: B 316 LYS cc_start: 0.8621 (tttt) cc_final: 0.7940 (mtmt) REVERT: B 442 ARG cc_start: 0.8237 (ptt-90) cc_final: 0.7551 (ptm160) REVERT: B 534 LYS cc_start: 0.7308 (mttt) cc_final: 0.6951 (mmpt) REVERT: B 558 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.7964 (pt0) REVERT: B 641 ASN cc_start: 0.7146 (t0) cc_final: 0.6542 (t0) REVERT: B 661 GLU cc_start: 0.7522 (pt0) cc_final: 0.6881 (pp20) REVERT: B 680 LYS cc_start: 0.7662 (pttt) cc_final: 0.7265 (mptp) REVERT: B 689 MET cc_start: 0.7503 (mtm) cc_final: 0.6653 (mmt) REVERT: B 710 ASP cc_start: 0.7016 (t0) cc_final: 0.6558 (m-30) REVERT: B 785 LEU cc_start: 0.2153 (OUTLIER) cc_final: 0.1698 (mt) REVERT: C 18 ARG cc_start: 0.6593 (mtm-85) cc_final: 0.6137 (mmp80) REVERT: C 90 GLU cc_start: 0.6908 (tp30) cc_final: 0.6690 (mm-30) REVERT: C 141 ASP cc_start: 0.5572 (t0) cc_final: 0.5170 (p0) REVERT: C 168 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6925 (tm-30) REVERT: C 220 LYS cc_start: 0.6690 (mtpp) cc_final: 0.6084 (mmtt) REVERT: C 301 ARG cc_start: 0.6535 (ttm170) cc_final: 0.6185 (ttp80) REVERT: C 316 LYS cc_start: 0.8621 (tttt) cc_final: 0.7941 (mtmt) REVERT: C 534 LYS cc_start: 0.7293 (mttt) cc_final: 0.6937 (mmpt) REVERT: C 558 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.7968 (pt0) REVERT: C 641 ASN cc_start: 0.7172 (t0) cc_final: 0.6567 (t0) REVERT: C 661 GLU cc_start: 0.7518 (pt0) cc_final: 0.6867 (pp20) REVERT: C 680 LYS cc_start: 0.7670 (pttt) cc_final: 0.7289 (mptp) REVERT: C 710 ASP cc_start: 0.6999 (t0) cc_final: 0.6544 (m-30) REVERT: C 785 LEU cc_start: 0.2168 (OUTLIER) cc_final: 0.1701 (mt) REVERT: D 18 ARG cc_start: 0.6598 (mtm-85) cc_final: 0.6141 (mmp80) REVERT: D 90 GLU cc_start: 0.6909 (tp30) cc_final: 0.6689 (mm-30) REVERT: D 141 ASP cc_start: 0.5574 (t0) cc_final: 0.5167 (p0) REVERT: D 168 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6920 (tm-30) REVERT: D 220 LYS cc_start: 0.6711 (mtpp) cc_final: 0.6095 (mmtt) REVERT: D 301 ARG cc_start: 0.6535 (ttm170) cc_final: 0.6183 (ttp80) REVERT: D 316 LYS cc_start: 0.8580 (tttt) cc_final: 0.7895 (mtmt) REVERT: D 534 LYS cc_start: 0.7307 (mttt) cc_final: 0.6950 (mmpt) REVERT: D 558 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.7903 (pt0) REVERT: D 641 ASN cc_start: 0.7153 (t0) cc_final: 0.6547 (t0) REVERT: D 661 GLU cc_start: 0.7516 (pt0) cc_final: 0.6865 (pp20) REVERT: D 680 LYS cc_start: 0.7668 (pttt) cc_final: 0.7287 (mptp) REVERT: D 710 ASP cc_start: 0.6997 (t0) cc_final: 0.6544 (m-30) REVERT: D 785 LEU cc_start: 0.2139 (OUTLIER) cc_final: 0.1682 (mt) outliers start: 47 outliers final: 4 residues processed: 244 average time/residue: 1.6247 time to fit residues: 454.2907 Evaluate side-chains 224 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 212 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 785 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 320 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 189 optimal weight: 0.9990 chunk 243 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 chunk 280 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 331 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27540 Z= 0.235 Angle : 0.554 5.033 37460 Z= 0.298 Chirality : 0.046 0.230 4324 Planarity : 0.005 0.059 4872 Dihedral : 10.752 89.616 4172 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.13 % Allowed : 8.47 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3460 helix: 0.22 (0.15), residues: 1284 sheet: 0.48 (0.23), residues: 520 loop : -0.96 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 181 HIS 0.005 0.001 HIS C 353 PHE 0.012 0.001 PHE C 638 TYR 0.019 0.002 TYR D 519 ARG 0.005 0.000 ARG A 795 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 226 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.6758 (mtm-85) cc_final: 0.6321 (mmp80) REVERT: A 31 ASP cc_start: 0.6139 (t0) cc_final: 0.5729 (m-30) REVERT: A 124 TYR cc_start: 0.6553 (t80) cc_final: 0.6240 (t80) REVERT: A 141 ASP cc_start: 0.5571 (t0) cc_final: 0.5183 (p0) REVERT: A 168 GLU cc_start: 0.7484 (mt-10) cc_final: 0.6944 (tm-30) REVERT: A 220 LYS cc_start: 0.6746 (mtpp) cc_final: 0.6131 (mmtt) REVERT: A 301 ARG cc_start: 0.6802 (ttm170) cc_final: 0.6446 (ttp80) REVERT: A 316 LYS cc_start: 0.8592 (tttt) cc_final: 0.7887 (mtmt) REVERT: A 442 ARG cc_start: 0.8189 (ptt-90) cc_final: 0.7536 (ptm160) REVERT: A 534 LYS cc_start: 0.7271 (mttt) cc_final: 0.6896 (mmpt) REVERT: A 558 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.7924 (pt0) REVERT: A 641 ASN cc_start: 0.7255 (t0) cc_final: 0.7027 (m-40) REVERT: A 661 GLU cc_start: 0.7633 (pt0) cc_final: 0.6905 (pp20) REVERT: A 680 LYS cc_start: 0.7653 (pttt) cc_final: 0.7275 (mptp) REVERT: A 710 ASP cc_start: 0.7029 (t0) cc_final: 0.6542 (m-30) REVERT: A 785 LEU cc_start: 0.2035 (OUTLIER) cc_final: 0.1570 (mt) REVERT: B 18 ARG cc_start: 0.6704 (mtm-85) cc_final: 0.6270 (mmp80) REVERT: B 31 ASP cc_start: 0.6143 (t0) cc_final: 0.5778 (m-30) REVERT: B 141 ASP cc_start: 0.5605 (t0) cc_final: 0.5205 (p0) REVERT: B 168 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7009 (tm-30) REVERT: B 220 LYS cc_start: 0.6766 (mtpp) cc_final: 0.6150 (mmtt) REVERT: B 301 ARG cc_start: 0.6782 (ttm170) cc_final: 0.6423 (ttp80) REVERT: B 316 LYS cc_start: 0.8590 (tttt) cc_final: 0.7886 (mtmt) REVERT: B 442 ARG cc_start: 0.8180 (ptt-90) cc_final: 0.7533 (ptm160) REVERT: B 534 LYS cc_start: 0.7275 (mttt) cc_final: 0.6897 (mmpt) REVERT: B 558 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.7922 (pt0) REVERT: B 641 ASN cc_start: 0.7250 (t0) cc_final: 0.7017 (m-40) REVERT: B 661 GLU cc_start: 0.7633 (pt0) cc_final: 0.6905 (pp20) REVERT: B 680 LYS cc_start: 0.7649 (pttt) cc_final: 0.7272 (mptp) REVERT: B 689 MET cc_start: 0.7481 (mtm) cc_final: 0.6274 (mmt) REVERT: B 710 ASP cc_start: 0.7033 (t0) cc_final: 0.6551 (m-30) REVERT: B 785 LEU cc_start: 0.1893 (OUTLIER) cc_final: 0.1451 (mt) REVERT: C 18 ARG cc_start: 0.6696 (mtm-85) cc_final: 0.6264 (mmp80) REVERT: C 31 ASP cc_start: 0.6037 (t0) cc_final: 0.5649 (m-30) REVERT: C 90 GLU cc_start: 0.6938 (tp30) cc_final: 0.6726 (mm-30) REVERT: C 141 ASP cc_start: 0.5577 (t0) cc_final: 0.5208 (p0) REVERT: C 168 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7006 (tm-30) REVERT: C 220 LYS cc_start: 0.6752 (mtpp) cc_final: 0.6135 (mmtt) REVERT: C 301 ARG cc_start: 0.6806 (ttm170) cc_final: 0.6448 (ttp80) REVERT: C 316 LYS cc_start: 0.8590 (tttt) cc_final: 0.7886 (mtmt) REVERT: C 534 LYS cc_start: 0.7273 (mttt) cc_final: 0.6896 (mmpt) REVERT: C 558 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.7927 (pt0) REVERT: C 641 ASN cc_start: 0.7264 (t0) cc_final: 0.7030 (m-40) REVERT: C 661 GLU cc_start: 0.7637 (pt0) cc_final: 0.6909 (pp20) REVERT: C 680 LYS cc_start: 0.7646 (pttt) cc_final: 0.7270 (mptp) REVERT: C 710 ASP cc_start: 0.7078 (t0) cc_final: 0.6596 (m-30) REVERT: C 785 LEU cc_start: 0.2122 (OUTLIER) cc_final: 0.1626 (mt) REVERT: D 18 ARG cc_start: 0.6700 (mtm-85) cc_final: 0.6268 (mmp80) REVERT: D 31 ASP cc_start: 0.6012 (t0) cc_final: 0.5689 (m-30) REVERT: D 90 GLU cc_start: 0.6941 (tp30) cc_final: 0.6718 (mm-30) REVERT: D 141 ASP cc_start: 0.5578 (t0) cc_final: 0.5204 (p0) REVERT: D 168 GLU cc_start: 0.7545 (mt-10) cc_final: 0.6999 (tm-30) REVERT: D 220 LYS cc_start: 0.6761 (mtpp) cc_final: 0.6143 (mmtt) REVERT: D 301 ARG cc_start: 0.6774 (ttm170) cc_final: 0.6380 (ttp80) REVERT: D 316 LYS cc_start: 0.8590 (tttt) cc_final: 0.7887 (mtmt) REVERT: D 534 LYS cc_start: 0.7262 (mttt) cc_final: 0.6887 (mmpt) REVERT: D 558 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.7930 (pt0) REVERT: D 641 ASN cc_start: 0.7248 (t0) cc_final: 0.7018 (m-40) REVERT: D 661 GLU cc_start: 0.7632 (pt0) cc_final: 0.6907 (pp20) REVERT: D 680 LYS cc_start: 0.7657 (pttt) cc_final: 0.7281 (mptp) REVERT: D 710 ASP cc_start: 0.7084 (t0) cc_final: 0.6603 (m-30) REVERT: D 785 LEU cc_start: 0.1884 (OUTLIER) cc_final: 0.1437 (mt) outliers start: 32 outliers final: 14 residues processed: 238 average time/residue: 1.5354 time to fit residues: 420.4561 Evaluate side-chains 242 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 220 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 785 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 205 optimal weight: 0.7980 chunk 132 optimal weight: 0.0370 chunk 198 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 210 optimal weight: 6.9990 chunk 225 optimal weight: 0.0970 chunk 163 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 260 optimal weight: 4.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 27540 Z= 0.137 Angle : 0.484 5.169 37460 Z= 0.260 Chirality : 0.044 0.156 4324 Planarity : 0.004 0.057 4872 Dihedral : 10.425 88.897 4172 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.74 % Allowed : 9.11 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3460 helix: 0.14 (0.15), residues: 1356 sheet: 0.41 (0.23), residues: 532 loop : -1.16 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 278 HIS 0.003 0.001 HIS D 353 PHE 0.013 0.001 PHE A 692 TYR 0.013 0.001 TYR C 519 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 239 time to evaluate : 3.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.6757 (mtm-85) cc_final: 0.6319 (mmp80) REVERT: A 31 ASP cc_start: 0.6144 (t0) cc_final: 0.5827 (m-30) REVERT: A 141 ASP cc_start: 0.5663 (t0) cc_final: 0.5280 (p0) REVERT: A 160 ASN cc_start: 0.7161 (t0) cc_final: 0.6789 (m110) REVERT: A 168 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6925 (tm-30) REVERT: A 220 LYS cc_start: 0.6709 (mtpp) cc_final: 0.6097 (mmtt) REVERT: A 301 ARG cc_start: 0.6486 (ttm170) cc_final: 0.6169 (ttp80) REVERT: A 316 LYS cc_start: 0.8584 (tttt) cc_final: 0.7926 (mtmt) REVERT: A 534 LYS cc_start: 0.7281 (mttt) cc_final: 0.6929 (mmpt) REVERT: A 558 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: A 641 ASN cc_start: 0.7225 (t0) cc_final: 0.7005 (m-40) REVERT: A 661 GLU cc_start: 0.7613 (pt0) cc_final: 0.6835 (pp20) REVERT: A 680 LYS cc_start: 0.7662 (pttt) cc_final: 0.7276 (mptp) REVERT: A 710 ASP cc_start: 0.6986 (t0) cc_final: 0.6501 (m-30) REVERT: A 785 LEU cc_start: 0.1801 (OUTLIER) cc_final: 0.1479 (mt) REVERT: B 18 ARG cc_start: 0.6731 (mtm-85) cc_final: 0.6288 (mmp80) REVERT: B 31 ASP cc_start: 0.6086 (t0) cc_final: 0.5784 (m-30) REVERT: B 141 ASP cc_start: 0.5669 (t0) cc_final: 0.5269 (p0) REVERT: B 160 ASN cc_start: 0.6931 (t0) cc_final: 0.6728 (t0) REVERT: B 168 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6928 (tm-30) REVERT: B 220 LYS cc_start: 0.6806 (mtpp) cc_final: 0.6189 (mmtt) REVERT: B 301 ARG cc_start: 0.6472 (ttm170) cc_final: 0.6158 (ttp80) REVERT: B 316 LYS cc_start: 0.8581 (tttt) cc_final: 0.7922 (mtmt) REVERT: B 534 LYS cc_start: 0.7293 (mttt) cc_final: 0.6936 (mmpt) REVERT: B 558 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: B 641 ASN cc_start: 0.7222 (t0) cc_final: 0.6575 (t0) REVERT: B 661 GLU cc_start: 0.7613 (pt0) cc_final: 0.6834 (pp20) REVERT: B 680 LYS cc_start: 0.7646 (pttt) cc_final: 0.7263 (mptp) REVERT: B 689 MET cc_start: 0.7490 (mtm) cc_final: 0.6300 (mmt) REVERT: B 710 ASP cc_start: 0.7005 (t0) cc_final: 0.6530 (m-30) REVERT: B 785 LEU cc_start: 0.2041 (OUTLIER) cc_final: 0.1593 (mt) REVERT: C 18 ARG cc_start: 0.6723 (mtm-85) cc_final: 0.6282 (mmp80) REVERT: C 31 ASP cc_start: 0.6014 (t0) cc_final: 0.5680 (m-30) REVERT: C 90 GLU cc_start: 0.6897 (tp30) cc_final: 0.6676 (mm-30) REVERT: C 141 ASP cc_start: 0.5687 (t0) cc_final: 0.5293 (p0) REVERT: C 160 ASN cc_start: 0.7011 (t0) cc_final: 0.6710 (m110) REVERT: C 168 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6926 (tm-30) REVERT: C 220 LYS cc_start: 0.6717 (mtpp) cc_final: 0.6103 (mmtt) REVERT: C 301 ARG cc_start: 0.6479 (ttm170) cc_final: 0.6169 (ttp80) REVERT: C 304 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7791 (mm-30) REVERT: C 316 LYS cc_start: 0.8583 (tttt) cc_final: 0.7924 (mtmt) REVERT: C 534 LYS cc_start: 0.7292 (mttt) cc_final: 0.6932 (mmpt) REVERT: C 558 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.7824 (pt0) REVERT: C 641 ASN cc_start: 0.7250 (t0) cc_final: 0.7048 (m-40) REVERT: C 661 GLU cc_start: 0.7594 (pt0) cc_final: 0.6889 (pp20) REVERT: C 680 LYS cc_start: 0.7667 (pttt) cc_final: 0.7281 (mptp) REVERT: C 710 ASP cc_start: 0.7013 (t0) cc_final: 0.6540 (m-30) REVERT: C 785 LEU cc_start: 0.2139 (OUTLIER) cc_final: 0.1626 (mt) REVERT: D 18 ARG cc_start: 0.6726 (mtm-85) cc_final: 0.6285 (mmp80) REVERT: D 31 ASP cc_start: 0.6054 (t0) cc_final: 0.5725 (m-30) REVERT: D 90 GLU cc_start: 0.6897 (tp30) cc_final: 0.6677 (mm-30) REVERT: D 141 ASP cc_start: 0.5642 (t0) cc_final: 0.5270 (p0) REVERT: D 160 ASN cc_start: 0.7017 (t0) cc_final: 0.6717 (m110) REVERT: D 168 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6929 (tm-30) REVERT: D 220 LYS cc_start: 0.6801 (mtpp) cc_final: 0.6185 (mmtt) REVERT: D 301 ARG cc_start: 0.6517 (ttm170) cc_final: 0.6199 (ttp80) REVERT: D 316 LYS cc_start: 0.8582 (tttt) cc_final: 0.7924 (mtmt) REVERT: D 534 LYS cc_start: 0.7292 (mttt) cc_final: 0.6933 (mmpt) REVERT: D 558 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.7823 (pt0) REVERT: D 661 GLU cc_start: 0.7592 (pt0) cc_final: 0.6830 (pp20) REVERT: D 680 LYS cc_start: 0.7655 (pttt) cc_final: 0.7274 (mptp) REVERT: D 710 ASP cc_start: 0.7019 (t0) cc_final: 0.6544 (m-30) REVERT: D 785 LEU cc_start: 0.2036 (OUTLIER) cc_final: 0.1578 (mt) outliers start: 21 outliers final: 5 residues processed: 251 average time/residue: 1.5141 time to fit residues: 440.1856 Evaluate side-chains 235 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 222 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 785 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 301 optimal weight: 1.9990 chunk 317 optimal weight: 0.9990 chunk 289 optimal weight: 0.8980 chunk 308 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 242 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 279 optimal weight: 2.9990 chunk 292 optimal weight: 9.9990 chunk 307 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 27540 Z= 0.172 Angle : 0.507 5.199 37460 Z= 0.272 Chirality : 0.044 0.165 4324 Planarity : 0.004 0.060 4872 Dihedral : 10.349 89.079 4172 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.70 % Allowed : 9.25 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3460 helix: 0.27 (0.15), residues: 1312 sheet: 0.40 (0.23), residues: 532 loop : -0.93 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 181 HIS 0.004 0.001 HIS A 79 PHE 0.015 0.001 PHE B 692 TYR 0.017 0.001 TYR B 519 ARG 0.009 0.000 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 231 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.6812 (mtm-85) cc_final: 0.6374 (mmp80) REVERT: A 141 ASP cc_start: 0.5689 (t0) cc_final: 0.5308 (p0) REVERT: A 160 ASN cc_start: 0.7070 (t0) cc_final: 0.6699 (m110) REVERT: A 168 GLU cc_start: 0.7518 (mt-10) cc_final: 0.6993 (tm-30) REVERT: A 182 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8118 (ptp) REVERT: A 220 LYS cc_start: 0.6724 (mtpp) cc_final: 0.6127 (mmtt) REVERT: A 301 ARG cc_start: 0.6718 (ttm170) cc_final: 0.6365 (ttp80) REVERT: A 316 LYS cc_start: 0.8610 (tttt) cc_final: 0.7932 (mtmt) REVERT: A 534 LYS cc_start: 0.7331 (mttt) cc_final: 0.6974 (mmpt) REVERT: A 558 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.7940 (pt0) REVERT: A 641 ASN cc_start: 0.7263 (t0) cc_final: 0.7054 (m-40) REVERT: A 661 GLU cc_start: 0.7633 (pt0) cc_final: 0.6823 (pp20) REVERT: A 680 LYS cc_start: 0.7654 (pttt) cc_final: 0.7281 (mptp) REVERT: A 689 MET cc_start: 0.7732 (mtp) cc_final: 0.7526 (mtt) REVERT: A 710 ASP cc_start: 0.7088 (t0) cc_final: 0.6588 (m-30) REVERT: A 785 LEU cc_start: 0.1844 (OUTLIER) cc_final: 0.1396 (mt) REVERT: B 18 ARG cc_start: 0.6760 (mtm-85) cc_final: 0.6315 (mmp80) REVERT: B 141 ASP cc_start: 0.5602 (t0) cc_final: 0.5277 (p0) REVERT: B 160 ASN cc_start: 0.7075 (t0) cc_final: 0.6869 (t0) REVERT: B 168 GLU cc_start: 0.7519 (mt-10) cc_final: 0.6995 (tm-30) REVERT: B 182 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8113 (ptp) REVERT: B 220 LYS cc_start: 0.6744 (mtpp) cc_final: 0.6120 (mmtt) REVERT: B 301 ARG cc_start: 0.6762 (ttm170) cc_final: 0.6437 (ttp80) REVERT: B 316 LYS cc_start: 0.8606 (tttt) cc_final: 0.7932 (mtmt) REVERT: B 534 LYS cc_start: 0.7333 (mttt) cc_final: 0.6973 (mmpt) REVERT: B 558 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.7985 (pt0) REVERT: B 641 ASN cc_start: 0.7263 (t0) cc_final: 0.7054 (m-40) REVERT: B 661 GLU cc_start: 0.7631 (pt0) cc_final: 0.6824 (pp20) REVERT: B 680 LYS cc_start: 0.7642 (pttt) cc_final: 0.7276 (mptp) REVERT: B 689 MET cc_start: 0.7503 (mtm) cc_final: 0.6300 (mmt) REVERT: B 710 ASP cc_start: 0.7000 (t0) cc_final: 0.6515 (m-30) REVERT: B 785 LEU cc_start: 0.2054 (OUTLIER) cc_final: 0.1582 (mt) REVERT: C 18 ARG cc_start: 0.6753 (mtm-85) cc_final: 0.6309 (mmp80) REVERT: C 141 ASP cc_start: 0.5582 (t0) cc_final: 0.5282 (p0) REVERT: C 168 GLU cc_start: 0.7517 (mt-10) cc_final: 0.6993 (tm-30) REVERT: C 182 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8118 (ptp) REVERT: C 220 LYS cc_start: 0.6733 (mtpp) cc_final: 0.6134 (mmtt) REVERT: C 301 ARG cc_start: 0.6727 (ttm170) cc_final: 0.6377 (ttp80) REVERT: C 316 LYS cc_start: 0.8567 (tttt) cc_final: 0.7885 (mtmt) REVERT: C 534 LYS cc_start: 0.7334 (mttt) cc_final: 0.6976 (mmpt) REVERT: C 558 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.7984 (pt0) REVERT: C 641 ASN cc_start: 0.7254 (t0) cc_final: 0.7053 (m-40) REVERT: C 661 GLU cc_start: 0.7634 (pt0) cc_final: 0.6889 (pp20) REVERT: C 680 LYS cc_start: 0.7650 (pttt) cc_final: 0.7285 (mptp) REVERT: C 710 ASP cc_start: 0.7003 (t0) cc_final: 0.6513 (m-30) REVERT: C 785 LEU cc_start: 0.2132 (OUTLIER) cc_final: 0.1591 (mt) REVERT: D 18 ARG cc_start: 0.6756 (mtm-85) cc_final: 0.6312 (mmp80) REVERT: D 141 ASP cc_start: 0.5496 (t0) cc_final: 0.5254 (p0) REVERT: D 168 GLU cc_start: 0.7526 (mt-10) cc_final: 0.6991 (tm-30) REVERT: D 182 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8116 (ptp) REVERT: D 220 LYS cc_start: 0.6742 (mtpp) cc_final: 0.6119 (mmtt) REVERT: D 301 ARG cc_start: 0.6753 (ttm170) cc_final: 0.6431 (ttp80) REVERT: D 316 LYS cc_start: 0.8609 (tttt) cc_final: 0.7933 (mtmt) REVERT: D 534 LYS cc_start: 0.7332 (mttt) cc_final: 0.6975 (mmpt) REVERT: D 558 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.7985 (pt0) REVERT: D 641 ASN cc_start: 0.7328 (m-40) cc_final: 0.7043 (m-40) REVERT: D 661 GLU cc_start: 0.7632 (pt0) cc_final: 0.6889 (pp20) REVERT: D 680 LYS cc_start: 0.7654 (pttt) cc_final: 0.7291 (mptp) REVERT: D 710 ASP cc_start: 0.7010 (t0) cc_final: 0.6522 (m-30) REVERT: D 785 LEU cc_start: 0.2086 (OUTLIER) cc_final: 0.1575 (mt) outliers start: 20 outliers final: 5 residues processed: 242 average time/residue: 1.5911 time to fit residues: 443.1027 Evaluate side-chains 241 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 224 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 785 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 202 optimal weight: 6.9990 chunk 326 optimal weight: 2.9990 chunk 199 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 342 optimal weight: 6.9990 chunk 315 optimal weight: 0.9980 chunk 272 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 210 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27540 Z= 0.255 Angle : 0.560 5.396 37460 Z= 0.301 Chirality : 0.046 0.176 4324 Planarity : 0.005 0.061 4872 Dihedral : 10.457 87.588 4172 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.81 % Allowed : 9.49 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3460 helix: 0.14 (0.15), residues: 1308 sheet: 0.30 (0.23), residues: 532 loop : -1.01 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 181 HIS 0.005 0.001 HIS C 79 PHE 0.013 0.002 PHE C 692 TYR 0.019 0.002 TYR B 519 ARG 0.006 0.000 ARG D 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 217 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.6919 (mtm-85) cc_final: 0.6484 (mmp80) REVERT: A 141 ASP cc_start: 0.5543 (t0) cc_final: 0.5294 (p0) REVERT: A 168 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7016 (tm-30) REVERT: A 182 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8217 (ptp) REVERT: A 220 LYS cc_start: 0.6776 (mtpp) cc_final: 0.6164 (mmtt) REVERT: A 301 ARG cc_start: 0.6854 (ttm170) cc_final: 0.6491 (ttp80) REVERT: A 316 LYS cc_start: 0.8612 (tttt) cc_final: 0.7888 (mtmt) REVERT: A 534 LYS cc_start: 0.7294 (mttt) cc_final: 0.6916 (mmpt) REVERT: A 558 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.7962 (pt0) REVERT: A 641 ASN cc_start: 0.7289 (t0) cc_final: 0.6888 (m-40) REVERT: A 661 GLU cc_start: 0.7630 (pt0) cc_final: 0.6895 (pp20) REVERT: A 680 LYS cc_start: 0.7640 (pttt) cc_final: 0.7280 (mptp) REVERT: A 689 MET cc_start: 0.7726 (mtp) cc_final: 0.7509 (mtt) REVERT: A 710 ASP cc_start: 0.7129 (t0) cc_final: 0.6618 (m-30) REVERT: A 785 LEU cc_start: 0.2047 (OUTLIER) cc_final: 0.1511 (mt) REVERT: B 18 ARG cc_start: 0.6828 (mtm-85) cc_final: 0.6413 (mmp80) REVERT: B 141 ASP cc_start: 0.5460 (t0) cc_final: 0.5248 (p0) REVERT: B 168 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7016 (tm-30) REVERT: B 182 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8217 (ptp) REVERT: B 220 LYS cc_start: 0.6773 (mtpp) cc_final: 0.6147 (mmtt) REVERT: B 301 ARG cc_start: 0.6858 (ttm170) cc_final: 0.6493 (ttp80) REVERT: B 316 LYS cc_start: 0.8612 (tttt) cc_final: 0.7889 (mtmt) REVERT: B 534 LYS cc_start: 0.7301 (mttt) cc_final: 0.6921 (mmpt) REVERT: B 558 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.7947 (pt0) REVERT: B 641 ASN cc_start: 0.7287 (t0) cc_final: 0.6885 (m-40) REVERT: B 661 GLU cc_start: 0.7635 (pt0) cc_final: 0.6887 (pp20) REVERT: B 680 LYS cc_start: 0.7631 (pttt) cc_final: 0.7268 (mptp) REVERT: B 689 MET cc_start: 0.7515 (mtm) cc_final: 0.6292 (mmt) REVERT: B 710 ASP cc_start: 0.7075 (t0) cc_final: 0.6566 (m-30) REVERT: B 785 LEU cc_start: 0.2085 (OUTLIER) cc_final: 0.1530 (mt) REVERT: C 18 ARG cc_start: 0.6821 (mtm-85) cc_final: 0.6409 (mmp80) REVERT: C 168 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7014 (tm-30) REVERT: C 182 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8219 (ptp) REVERT: C 220 LYS cc_start: 0.6777 (mtpp) cc_final: 0.6162 (mmtt) REVERT: C 301 ARG cc_start: 0.6808 (ttm170) cc_final: 0.6452 (ttp80) REVERT: C 316 LYS cc_start: 0.8611 (tttt) cc_final: 0.7888 (mtmt) REVERT: C 534 LYS cc_start: 0.7296 (mttt) cc_final: 0.6919 (mmpt) REVERT: C 558 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.7943 (pt0) REVERT: C 641 ASN cc_start: 0.7285 (t0) cc_final: 0.6886 (m-40) REVERT: C 661 GLU cc_start: 0.7637 (pt0) cc_final: 0.6889 (pp20) REVERT: C 680 LYS cc_start: 0.7643 (pttt) cc_final: 0.7275 (mptp) REVERT: C 689 MET cc_start: 0.7598 (ptt) cc_final: 0.7330 (ptp) REVERT: C 710 ASP cc_start: 0.7088 (t0) cc_final: 0.6581 (m-30) REVERT: C 785 LEU cc_start: 0.2179 (OUTLIER) cc_final: 0.1603 (mt) REVERT: D 18 ARG cc_start: 0.6823 (mtm-85) cc_final: 0.6411 (mmp80) REVERT: D 141 ASP cc_start: 0.5450 (t0) cc_final: 0.5248 (p0) REVERT: D 168 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7013 (tm-30) REVERT: D 182 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8216 (ptp) REVERT: D 220 LYS cc_start: 0.6779 (mtpp) cc_final: 0.6146 (mmtt) REVERT: D 301 ARG cc_start: 0.6851 (ttm170) cc_final: 0.6489 (ttp80) REVERT: D 316 LYS cc_start: 0.8612 (tttt) cc_final: 0.7889 (mtmt) REVERT: D 534 LYS cc_start: 0.7295 (mttt) cc_final: 0.6917 (mmpt) REVERT: D 558 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.7944 (pt0) REVERT: D 641 ASN cc_start: 0.7371 (m-40) cc_final: 0.7119 (m-40) REVERT: D 661 GLU cc_start: 0.7627 (pt0) cc_final: 0.6894 (pp20) REVERT: D 680 LYS cc_start: 0.7654 (pttt) cc_final: 0.7291 (mptp) REVERT: D 710 ASP cc_start: 0.7062 (t0) cc_final: 0.6563 (m-30) REVERT: D 785 LEU cc_start: 0.2026 (OUTLIER) cc_final: 0.1469 (mt) outliers start: 23 outliers final: 3 residues processed: 230 average time/residue: 1.7063 time to fit residues: 449.9216 Evaluate side-chains 222 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 207 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 785 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 216 optimal weight: 4.9990 chunk 290 optimal weight: 6.9990 chunk 83 optimal weight: 0.0050 chunk 251 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 273 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 280 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.216833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.122906 restraints weight = 26739.275| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.23 r_work: 0.3207 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 27540 Z= 0.187 Angle : 0.514 5.049 37460 Z= 0.276 Chirality : 0.045 0.163 4324 Planarity : 0.004 0.061 4872 Dihedral : 10.345 87.560 4172 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.56 % Allowed : 9.70 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3460 helix: 0.10 (0.15), residues: 1336 sheet: 0.26 (0.23), residues: 536 loop : -0.99 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 181 HIS 0.004 0.001 HIS C 353 PHE 0.016 0.001 PHE A 692 TYR 0.017 0.001 TYR D 519 ARG 0.007 0.000 ARG C 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9326.66 seconds wall clock time: 166 minutes 36.17 seconds (9996.17 seconds total)